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anti-delta  (Developmental Studies Hybridoma Bank)


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    Developmental Studies Hybridoma Bank anti-delta
    Anti Delta, supplied by Developmental Studies Hybridoma Bank, used in various techniques. Bioz Stars score: 96/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/c594%2E9b/anti-Delta/custom%40c594%2E9b%4042502386
    Average 96 stars, based on 54 article reviews
    anti-delta - by Bioz Stars, 2026-09
    96/100 stars

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    Related Articles

    Recombinant:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    CMC:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Virus:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Reverse Transcription:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Protease Inhibitor:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Real-time Polymerase Chain Reaction:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    cDNA Synthesis:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Multiplex Assay:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Microscopy:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Staining:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Incubation:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Blocking Assay:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Biomarker Discovery:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.

    Concentration Assay:

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal anti-Delta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection.
    Article Snippet: For Delta staining, midguts were incubated with mouse monoclonal antiDelta (1:20) (Dl antibody, C594.9B, DSHB, Iowa City, IA, USA) in blocking solution (PBS containing 2% BSA, 0.1% gelatin and 0.1% triton).

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila .
    Article Snippet: Primary antibodies were used at the following concentrations: anti- Zld (1:1000) (gift from M. Harrison) (87), anti- Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti- Ct (1:150) (DSHB, 2b10), anti- CD2 (1:500) (Bio- Rad, catalog no. MCA154R), anti- Dl (1:400) (DSHB, c594.9b), anti- Wg (1:100) (DSHB, 4D4), anti- Frizzled2 (1:50) (DSHB, 1A3G4), anti- Ac (1:10) (DSHB, RRID AB_528066), anti- Ptc (1:50) (DSHB, Apa1), anti- En (1:3) (DSHB, 4D9), anti- Osa (1:1) (DSHB, RRID AB_528420), anti–β- galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A- 11132), anti- Mys (1:50) (DSHB, cf.6 g11), anti- Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06- 570), anti- GFP (1:500) (Abcam, Ab290), anti- GFP (1:1000) (Invitrogen, 3E6), and anti- Arm (1:50) (DSHB, N2 7A1).

    Article Title: Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-DAV GenScript Biotech This study Mouse anti-Delta (1:1000) DSHB Cat# c594.9b; RRID: AB_528194 Mouse anti-Prospero (1:1000) DSHB Cat# Prospero (MR1A); RRID: AB_528440 Rabbit antiAnti-PH3 (1:1000) Merck Millipore Cat# 06-570; RRID: AB_310177 Chicken anti-GFP (1:2000) Invitrogen Cat# A10262; RRID: AB_2534023 Goat anti-rabbit-647 (1:500) Invitrogen Cat# A-21244; RRID: AB_2535812 Goat anti-mouse-488 (1:500) Invitrogen Cat# A-11029; RRID: AB_2534088 Goat anti-chicken-488 (1:500) Invitrogen Cat# A32931; RRID: AB_2762843 Donkey anti-rabbit-HRP (1:2000) Cytiva Cat# NA934; RRID: AB_772206 Bacterial and virus strains Drosophila A virus Nigg et al.36 N/A Drosophila C virus Nigg et al.36 N/A Nora virus Nigg et al.36 N/A Bloomfield virus This isolate is available upon request This study Erwinia carotovora carotovora 15 (Ecc15) B. Lemaitre; Buchon et al.80 N/A Chemicals, peptides, and recombinant proteins TRIzol Invitrogen Cat# 15596026 16% paraformaldehyde Thermo Scientific Cat# 043368.9M Deionized formamide Invitrogen Cat# AM9342 FD&C Blue No.1 Thermo Scientific Cat# 229730250 SuperScript II reverse transcriptase Invitrogen Cat# 18064022 RNaseOUT Recombinant Ribonuclease Inhibitor Invitrogen Cat# 10777019 DNase I recombinant, RNase-free Roche Cat# 04716728001 cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat# 11873580001 Critical commercial assays Luminaris Color HiGreen qPCR Master Mix, low ROX Thermo Scientific Cat# K0374 Maxima H Minus First Strand cDNA Synthesis Kit Thermo Scientific Cat# K1652 Qubit RNA BR Assay Kit Invitrogen Cat# Q10211 1-Step Turbo TMB-ELISA substrate solution Thermo Scientific Cat# 34022 TruSeq Stranded mRNA Library Prep kit Illumina Cat# 20020595 IDT for Illumina TruSeq RNA UD Indexes Illumina Cat# 20022371 NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Cat# E7770L NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E7600S NextSeq 500/550 High Output Kit v2.5 Illumina Cat# 20024907 Deposited data RNAseq data This paper SRA: PRJNA1041289 Microscopy data This paper Zenodo: https://doi.org/10.5281/ zenodo.10079314 (Continued on next page) Current Biology 34, 2785–2800.e1–e7, July 8, 2024 e1

    Article Title: The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
    Article Snippet: Primary antibodies were used at the following concentrations: anti-Zld (1:1000) (gift from M. Harrison) , anti-Nubbin (1:100) [Developmental Studies Hybridoma Band (DSHB), 2D4), anti-Ct (1:150) (DSHB, 2b10), anti-CD2 (1:500) (Bio-Rad, catalog no. MCA154R), anti-Dl (1:400) (DSHB, c594.9b), anti-Wg (1:100) (DSHB, 4D4), anti-Frizzled2 (1:50) (DSHB, 1A3G4), anti-Ac (1:10) (DSHB, RRID AB_528066), anti-Ptc (1:50) (DSHB, Apa1), anti-En (1:3) (DSHB, 4D9), anti-Osa (1:1) (DSHB, RRID AB_528420), anti–β-galactosidase (1:500) (Thermo Fisher Scientific, catalog no. A-11132), anti-Mys (1:50) (DSHB, cf.6 g11), anti-Mew (1:50) (DSHB, DK.1A4), anti–phospho–Histone H3 (1:500) (DSHB, 06-570), anti-GFP (1:500) (Abcam, Ab290), anti-GFP (1:1000) (Invitrogen, 3E6), and anti-Arm (1:50) (DSHB, N2 7A1).

    Article Title: Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken polyclonal anti-GFP Abcam Cat# ab13970; RRID: AB_300798 Mouse anti-Delta DSHB Cat# C594.9B; RRID: AB_528194 Mouse anti-Prospero DSHB Cat# MR1A; RRID: AB_528440 Chicken anti-b-Galactosidase Abcam Cat# ab9361; RRID: AB_307210 anti-Armadillo DSHB Cat# N2 7A1; RRID: AB_528089 Monoclonal anti-mCherry Invitrogen Cat# M11217; RRID: AB_2536611 Rabbit anti-Pdm1 Gifted from XiaoHangYang Zhejiang University School of Medicine Anti-PMP70 Abcam Cat# ab3421; RRID: AB_2219901 Anti-PPARg Proteintech Cat# 16643-1-AP; RRID: AB_10596794 Anti-PEX11b Invitrogen Cat# PA5-37011; RRID: AB_2553864 Anti-alpha-Tubulin Cell Signaling Technology Cat# 2144; RRID: AB_2210548 Anti-SOX9 Abcam Cat# ab185966; RRID: AB_2728660 Anti-ACOX1 Proteintech Cat#10957-1-AP; RRID: AB_2221670 Anti-FATP2 Proteintech Cat# 14048-1-AP; RRID: AB_2239416 Anti-TNKS1/2 Proteintech Cat#18030-1-AP; RRID: AB_2303564 Anti-P62 Cell Signaling Technology Cat# 5114; RRID: AB_10624872 HRP-mouse anti-rabbit Jackson ImmunoResearch Labs Cat# 211-032-171; RRID: AB_2339149 HRP-Goat anti-mouse Jackson ImmunoResearch Labs Cat# 115-035-174; RRID: AB_2338512 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11001; RRID: AB_2534069 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11004; RRID: AB_2534072 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific Cat# A-21235; RRID: AB_2535804 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034; RRID: AB_2576217 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568 Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157 Goat anti-Chicken IgY (H+L) Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11039; RRID: AB_2534096 Chemicals, peptides, and recombinant proteins DAPI (4’,6-Diamidino-2-phenylindole dihydrochloride) Sigma-Aldrich Cat# D8417 Lysotracker Invitrogen Cat# L7528 Bleomycin (BLM) Aladdin Cat# B107423 Dextran sulfate sodium (DSS) Yeasen Cat# 60316EB80 Pioglitazone Aladdin Cat# P129907 Behenic acid (BA) Sigma Cat# 112-85-6) CMC-Na Aladdin Cat# C501052 Arachidic acid (AA) MCE Cat# HY-W004260 Arachidic acid (AA) Sigma Cat# A3631 Eicosapentaenoic acid (EPA) MCE Cat# HY-B0660 Lipofermata MCE Cat# HY-116788 Grassofermata anjiechem Cat# NAV2729 T0070907 Selleck Cat# S2871 (Continued on next page) e1 Developmental Cell 59, 1–17.e1–e8, October 7, 2024

    Article Title: Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
    Article Snippet: Dl antibody (Delta), Cat # C594.9B, DSHB, Iowa City, IA, USA Goat anti-rabbit Alexa 488 cat #A-11008, ThermoFisher Scientific, Waltham, MA, USA Goat anti-rabbit Alexa 594 cat #A-11012, ThermoFisher Scientific, Waltham, MA, USA Goat anti-mouse Alexa 488 cat #A-11001, ThermoFisher Scientific, Waltham, MA, USA oat anti-mouse Alexa 594 cat #A-11005, ThermoFisher Scientific, Waltham, MA, USA Validation All commercial antibodies were validated by their manufacturers and were titrated in the lab to determine optimal concentration for experimentation.

    Article Title: Non-cell autonomous regulation of cell–cell signaling and differentiation by mitochondrial ROS
    Article Snippet: Mouse monoclonal anti-delta (Drosophila) , DSHB , C594.9B.



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