Incubation:Article Title: The DNA methyltransferase DMAP1 is required for tissue maintenance and planarian regeneration.
Article Snippet: .. Tissues in fixed samples were blocked for 4 h and then incubated using primary antibodies overnight: αH3P 1:250 (Millipore Cat# 05–817R); 6G10 1:500 (DSHB Cat# 6G10-2C7); RAD51 1:500 (Abcam Cat# ab109107); and γH2AX antibody 1:1000 (ThermoFisher Cat# LF-PA0025). .. Samples were washed 6 × 10 min in PBSTB and incubated with secondary antibody overnight: 1:500 HRP-conjugated Goat anti-rabbit antibody (Millipore Cat# 12–348) followed by washes 6 x 10 with PBSTB and mounted in VECTASHIELD mounting media.
Article Title: The DNA Methyltransferase DMAP1 is Required for Tissue Maintenance and Planarian Regeneration
Article Snippet: .. Tissues in fixed samples were blocked for 4 hours and then incubated using primary antibodies overnight: αH3P 1:250 (Millipore Cat# 05-817R); 6G10 1:500 (DSHB Cat# 6G10-2C7); RAD51 1:500 (Abcam Cat# ab109107); and ψH2AX antibody 1:1000 (ThermoFisher Cat# LF-PA0025). .. Samples were washed 6 x 10 mins in PBSTB and incubated with secondary antibody overnight: 1:500 HRP-conjugated Goat anti-rabbit antibody (Millipore Cat# 12-348) followed by washes 6 x 10 with PBSTB and mounted in VECTASHIELD mounting media.
Control:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Recombinant:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Protease Inhibitor:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Western Blot:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Real-time Polymerase Chain Reaction:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Software:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
Microscopy:Article Title: Redox-modulated ERK dynamics support wound-dependent tissue formation during early planarian regeneration
Article Snippet: .. 824 STAR★METHODS 825 KEY RESOURCES TABLE 826 REAGENT or RESOURCE SOURCE IDENTIFIER Jo urn al Pr e-p roo f 16 Antibodies Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb Cell Signaling Technology Cat#4370S; RRID: AB_2315112 Anti-beta Actin antibody - Loading Control Abcam Cat# ab8227, RRID: AB_2305186 m-IgGκ BP-HRP Antibody Santa Cruz Biotechnology Cat# sc-516102; RRID: AB_2687626 Goat Anti-IgG (H&L) Polyclonal HRP Antibody AgriSera Cat# AS09 602; RRID: AB_1966902 Mouse Anti-Synapsin Monoclonal Antibody (antiSYNORF1), Unconjugated Developmental studies hybridoma Bank Cat# 3C11; RRID: AB_528479 Mouse Anti-Muscle Fibers Antibody (6G10-2C7), Unconjugated Developmental studies hybridoma Bank Cat# 6G10-2C7; RRID: AB_2619613 Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 568 Conjugated Molecular Probes Cat# A-11004; RRID: AB_2534072 Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa FluorTM 488 Conjugated Molecular Probes Cat# A-11008; RRID: AB_143165 Chemicals, peptides, and recombinant proteins Diphenyleneiodonium chloride Enzo Life Sciences Cat#BML-CN2400010 PD0325901 Sigma-Aldrich (Roche) Cat#PZ0162 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich (Roche) Cat#1187358000 PhosSTOPTM Sigma-Aldrich (Roche) Cat#4906845001 Peroxy Orange 1 (PO1) Sigma-Aldrich Cat#SML0688 Critical commercial assays ROS-ID® Superoxide detection kit Enzo Life Sciences Cat#ENZ-51012 Western Lightning Plus, Chemiluminescent Substrate pErkinElmer Cat#NEL103E001E A Experimental models: Organisms/strains Schmidtea mediterranea This paper N/A Oligonucleotides Primers for RNAi probes, see Table S1 This paper N/A Primers for qPCR, see Table S2 This paper N/A Software and algorithms Fiji (ImageJ) Fiji RRID:SCR_002285 R Project for Statistical Computing R Development Core Team RRID:SCR_001905 RSudio Team RStudio RRID:SCR_000432 Nikon NIS Elements software Nikon RRID:SCR_014329 ZEISS ZEN Microscopy Software ZEISS RRID:SCR_013672 827 EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS 828 For all experiments, an asexual strain of the freshwater planarian Schmidtea mediterranea was used. ..
Virus:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
Single Cell:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
Sequencing:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
DNA Library Preparation:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
In Situ:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
Fluorescence In Situ Hybridization:Article Title: Molecular and cellular characterization of planarian stem cell microenvironments.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 (phospho S10T11) Abcam Cat# ab32107; RRID: AB_732930 Anti-muscle G610 Developmental Studies Hybridoma Bank (DSHB) Cat# 6G10-2C7; RRID: AB_2619613 Goat Anti-rabbit Alexa Fluor 555 Abcam Cat# ab150086; RRID: AB_2890032 Goat Anti-rabbit Alexa Fluor 647 Abcam Cat# ab150083; RRID: AB_2714032 Anti-Digoxigenin-POD, Fab fragments Roche Cat# 11207733910; RRID: AB_514500 Anti-Digoxigenin-AP, Fab fragments Roche Cat# 11093274910; RRID: AB_514497 Peroxidase-conjugated IgG Fraction Mouse Anti-Fluorescein Jackson ImmunoResearch Cat# 200-032-037; RRID: AB_2314402 Bacterial and virus strains E. coli strain HT115 Caenorhabditis Genetics Center HT115(DE3) Critical commercial assays Chromium GEM-X Single Cell 3 ′ Reagent Kits v4 10× Genomics PN-1000691 AMPure XP beads Beckman Coulter A63881 SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Takara 634890 Nextera XT DNA Library Preparation Kit Illumina FC-131-1096 IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A Illumina 20027213 Deposited data Raw Sequencing Data This paper GEO: GSE199348 dd_v6 transcriptome Liu et al. 75 http://planmine.mpi-cbg.de/planmine/begin.do schMedS3 Genome Grohme et al. 76 http://planmine.mpi-cbg.de/planmine/begin.do Schmidtea mediterranea unigene transcriptome Robb et al. 77 http://planmine.mpi-cbg.de/planmine/begin.do Experimental models: Organisms/strains Schmidtea mediterranea, asexual clonal strain CIW4 Sá nchez Alvarado Laboratory, Stowers Institute CIW4 Oligonucleotides Sequences for in situ probes and RNAi vectors are provided in Table S7 This Paper Table S7 Sequences for HCR v3 RNA FISH probes were provided by Molecular Instruments to detect the list of transcripts in Table S7 Molecular Instruments N/A Software and algorithms ImageJ (FIJI) Schindelin et al. 38 RRID:SCR_002285; https://fiji.sc Jupyter Notebook Granger and Perez 78 RRID:SCR_018315; https://jupyter.org/ Custom segmentation code This paper https://github.com/jouyun/Mann_2023 Python Programming Language Python Software Foundation RRID:SCR_008394; http//www.python.org Blender Blender Foundation RRID:SCR_008606; http://www.blender.org R Project for Statistical Computing The R Foundation RRID: SCR_001905; https://www.r-project.org/ Syrah Brewster et al. 79 https://github.com/0x644BE25/Syrah (Continued on next page) 18 Cell Reports ▪▪, 116401, ▪▪, 2025 OPEN ACCESS ..
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