Membrane:Article Title: Biotransformation of the Fluoroquinolone, Levofloxacin, by the White-Rot Fungus Coriolopsis gallica
Article Snippet: .. For each culture condition (with or without levofloxacin), supernatants of C. gallica cultures (Day 7) were prepared in triplicate, filtered on a Miracloth membrane (EMD Millipore Corp, Billerica, MA, USA), and centrifuged at 8000× g for 10 min at 4 °C. .. The resulting supernatants were successively filtered via 2.7, 1.6, and 0.7 μm glass microfiber filters (GD, A, and F, respectively) (GE Healthcare Life Sciences, Whatman TM , ThermoFisher Scientific, Madison, WI, USA) and 0.4 μm and 0.2 μm PES membranes (Acrodisc ® , Pall Corporation, Saint-Germain-en-Laye, France).
Article Title: Characterization of the Nuclear Proteome of Chlamydomonas in Response to Salt Stress
Article Snippet: To avoid proteolytic degradation, Plant protease inhibitor (Sigma, USA) was added, and all steps performed at 4° C. Pellet of 250 mL cell culture was re-suspended in 600 μL of NIB solution, harvested, macerated in liquid nitrogen using a mortar and pestle. .. The powdered material was suspended in 10 mL of NIB solution, filtered through a miracloth membrane (22–25 μm; Calbiochem, Bad Soden, Germany) and centrifuged at 1,260 g for 10 minutes. ..
Article Title: Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid.
Article Snippet: .. Residual biomass was filtered through the Miracloth membrane (EMD Millipore Corp., Burlington, MA, USA) and incubated at 60 °C overnight. .. The dry weight was measured using an analytical balance (Ohaus, Pioner, Darmstadt, Germany), and the residual biomass weight was expressed as percentage of the untreated biomass (incubated under the same conditions without enzymes and/or MA-13 cells) used as reference (100%).
Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
Article Title: Mis-splicing of a neuronal microexon promotes CPEB4 aggregation in ASD.
Article Snippet: .. To further clarify the combined supernatants, they were filtered through a Miracloth membrane (Millipore) to remove lipids and then passed through a 0.45 μm filter. .. Exploiting the histidine-rich regions present in the sequence of nCPEB4 (23RFHPHLQP PHHHQN36 and 229LSQHHPHHPHFQHHHSQHQQ248), a 2-elution step Ni2+-affinity chromatography was carried out using a Histrap HP 5 ml (GE Healthcare) on a FPLC apparatus (ÄKTA Pure, GE Healthcare).
Article Title: Plasma Membrane-Associated Proteins Identified in Arabidopsis Wild Type, lbr2-2 and bak1-4 Mutants Treated with LPSs from Pseudomonas syringae and Xanthomonas campestris
Article Snippet: The ground tissue was transferred into a beaker containing ice-cold 50 mL homogenising buffer (250 mM sucrose (Sigma-Aldrich, St. Louis, MO, USA), 3 mM EDTA (Saarchem, Gauteng, South Africa), 10% ( v / v ) glycerol, 250 mM potassium iodide (KI; Saarchem, Gauteng, South Africa), 2 mM phenylmethylsulfonyl fluoride (PMSF; Boehringer, Mannheim, Germany), 0.5% poly(vinylpolypyrrolidone) (PVPP; Sigma-Aldrich, St. Louis, MO, USA), 15 mM β-mercaptoethanol, 70 mM Tris-HCl pH 7.5, 4 mM dithiothreitol (DTT, ThermoFisher Scientific, Vilnius, Lithuania) and 1% bovine serum albumin (BSA, Boehringer, Mannheim, Germany)), and homogenised further with an Ultraturrax homogeniser (IKA, Staufen, Germany) for 2 min. .. The homogenate (HM) was filtered through a two-layered miracloth membrane (EMD Millipore, Burlington, MA, USA). .. The HM fraction was centrifuged at 6000× g , 4 °C for 3 min, in a fixed angle Beckman Avanti™ J-30 centrifuge.
Article Title: Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid
Article Snippet: .. Residual biomass was filtered through the Miracloth membrane (EMD Millipore Corp., Burlington, MA, USA) and incubated at 60 °C overnight. .. The dry weight was measured using an analytical balance (Ohaus, Pioner, Darmstadt, Germany), and the residual biomass weight was expressed as percentage of the untreated biomass (incubated under the same conditions without enzymes and/or MA-13 cells) used as reference (100%).
Incubation:Article Title: Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid.
Article Snippet: .. Residual biomass was filtered through the Miracloth membrane (EMD Millipore Corp., Burlington, MA, USA) and incubated at 60 °C overnight. .. The dry weight was measured using an analytical balance (Ohaus, Pioner, Darmstadt, Germany), and the residual biomass weight was expressed as percentage of the untreated biomass (incubated under the same conditions without enzymes and/or MA-13 cells) used as reference (100%).
Article Title: Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid
Article Snippet: .. Residual biomass was filtered through the Miracloth membrane (EMD Millipore Corp., Burlington, MA, USA) and incubated at 60 °C overnight. .. The dry weight was measured using an analytical balance (Ohaus, Pioner, Darmstadt, Germany), and the residual biomass weight was expressed as percentage of the untreated biomass (incubated under the same conditions without enzymes and/or MA-13 cells) used as reference (100%).
Recombinant:Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
Protease Inhibitor:Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
Isolation:Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
SYBR Green Assay:Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
Polymerase Chain Reaction:Article Title: piRNA-independent transposon silencing by the Drosophila THO complex.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-Hpr1 Rehwinkel et al., 2004 N/A Rabbit anti Piwi Li et al., 2009a N/A Rabbit anti Ago3 Li et al., 2009a N/A Rabbit anti Aub Li et al., 2009a N/A Rat IgM anti-Vasa DSHB RRID: AB_760351 Mouse anti-Engrailed (4D9) DSHB RRID: AB_528224 Rabbit anti H3K9me3 Abcam Cat# ab8898; RRID: AB_306848 Rabbit anti H3K4me2 EMDMillipore Cat# 07–030; RRID: AB_310342 Mouse Anti-a-Tubulin Sigma Aldrich Cat# T5168; RRID: AB_477579 Rabbit anti-GFP ThermoFisher Scientific Cat# A11122; RRID: AB_221569 Chemicals, peptides, and recombinant proteins 4-Thiouridine MilliporeSigma Cat# T4509 Iodoacetamide MilliporeSigma Cat# I1149 Superscript III ThermoFisher Scientific Cat# 18080-085 RNase OUT ThermoFisher Scientific Cat# 10777-019 TURBO DNase ThermoFisher Scientific Cat# AM2238 RNaseH ThermoFisher Scientific Cat# 18021-071 T4 RNA Ligase ThermoFisher Scientific Cat# AM2141 AccuPrime Pfx DNA Polymerase ThermoFisher Scientific Cat# 12344024 TRIzol Reagent ThermoFisher Scientific Cat# 15596026 UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) ThermoFisher Scientific Cat# 15593031 dNTP Set (100 mM) ThermoFisher Scientific Cat# 10297018 dUTP Solution (100 mM) ThermoFisher Scientific Cat# R0133 Grace’s Insect Medium, unsupplemented ThermoFisher Scientific Cat# 11595030 Hybridase Lucigen Cat# H39500 dNTP mix NEB Cat# N0447L DNA polymerase I NEB Cat# M0209S T4 DNA polymerase NEB Cat# M0203L Klenow DNA polymerase NEB Cat# M0210S T4 PNK NEB Cat# M0201L Klenow 3’ to 5’ exo NEB Cat# M0212L UDG NEB Cat# M0280S Phusion Polymerase NEB Cat# M0530S T4 RNA Ligase 2, truncated NEB Cat# M0242L 50% PEG8000 NEB Cat# B1004S T4 DNA ligase Enzymatics Inc. Cat# L6030-HC-L EDTA-free Protease Inhibitor Cocktail (Roche) Sigma Cat# 11873580001 16% formaldehyde Ted Pella Inc Cat# 18505 Miracloth membrane (Calbiochem) EMDMillipore Cat# 475855 Critical commercial assays mirVANA miRNA isolation kit ThermoFisher Scientific Cat# AM1560 RNeasy Mini Kit Qiagen Cat# 74104 QuantiTect SYBR Green PCR Kits Qiagen Cat# 204145 (Continued on next page) e1 Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Protein G ThermoFisher Scientific Cat# 10004D Dynabeads Protein A ThermoFisher Scientific Cat# 10001D RNA Clean & Concentrator-5 Zymo Research Cat# R1015 In-Fusion HD Cloning Plus Takara Cat# 638909 Agencourt AMPure XP Beckman Coulter Cat# A63880 Deposited data High throughput Sequencing This study BioProject: RJNA590287 small RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7686976 small RNAseq for thoc5[e00906]/thoc5[1]_rep2 Zhang et al., 2018 SRA: SRR7686977 small RNAseq for w[1]_rep1 Zhang et al., 2018 SRA: SRR7408119 small RNAseq for thoc7[d05792]/Df(3L)BSC128 Zhang et al., 2018 SRA: SRR7408136 Small RNAseq of rhi mut ovary Parhad et al., 2017 SRA: SRR5803097 RNAseq for thoc5[e00906]/thoc5[1]_rep1 Zhang et al., 2018 SRA: SRR7408102 RNAseq for thoc7[d05792]/Df(3L)BSC128_rep2 Zhang et al., 2018 SRA: SRR7408139 input RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408152 input RNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408157 Hpr1IP RNAseq from w[1]_rep1 Zhang et al., 2018 SRA: SRR7408151 Hpr1IPRNAseq from w[1]_rep2 Zhang et al., 2018 SRA: SRR7408156 Experimental models: Organisms/strains D. melanogaster/thoc7d05792 Harvard Exelixis stock collection Stock # d05792 D. melanogaster/Df(3L)BSC128 Bloomington Drosophila Stock Center Stock# 9293 D. melanogaster/thoc5e00906 Harvard Exelixis stock collection Stock# e00906 D. melanogaster/thoc51 Moon et al., 2011 N/A D. melanogaster/rhino2 Klattenhoff et al., 2009 N/A D. melanogaster/rhinoKG Klattenhoff et al., 2009 N/A D. melanogaster/piwi2 Bloomington Drosophila Stock Center Stock# 43319 D. melanogaster/piwiNLS Klenov et al., 2011 N/A D. melanogaster/panoramixM4 Yu et al., 2015 N/A D. melanogaster/Df(2R)BSC821 Yu et al., 2015 Stock# 27582 D. melanogaster/ pUASp>lambdaN-HACG9754 [attP40]/CyO; tub>EGFP_5xBoxB_ SV40 [attP2]/TM3, Ser; VDRC Stock Center Stock# 313393 D. melanogaster/w1 William Theurkauf lab N/A Oligonucleotides Random primers ThermoFisher Scientific Cat# 48190011 Primers for qPCR, see Table S1 Brennecke et al., 2007; Czech et al., 2013; Zhang et al., 2014, 2011 N/A Software and algorithms Prism 7 GraphPad Prism https://www.graphpad.com/ Image Studio Lite LI-COR https://www.licor.com/bio/products/ software/image_studio_lite/ R RStudio https://www.rstudio.com/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ UCSC Genome Browser Kent et al., 2002 https://genome.ucsc.edu/ cgi-bin/hgGateway Developmental Cell 56, 2623–2635.e1–e5, September 27, 2021 e2
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