{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and tissue_curation = \"Head\"", "rows": [[41908, "SRR5338229", "SRX2635543", "SRS2044322", "SRP101781", "PRJNA378947", "Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes", "GSE96534", "Transcriptome Analysis", "A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour  cancer cells have escaped the initial immune response mechanisms. To date  no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q  HRasG12V  KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma  revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1  fgf6  cathepsin H  cathepsin L  galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.", null, "pubmed:29666124", null, "mpo RNAseqnuclear +mifNRas+ 2", "GSM2535110", null, "tissue:mpo RNAseqnuclear +mif head 2|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:1 \u03bcM mifeprist1 added to embryo water from 24 hpf|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "mpo RNAseqnuclear +mifNRas+ 2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts", "mpo RNAseqnuclear +mif head 2", "Incrossed larvae were treated with 1 \u03bcM from 24 hpf", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:1 \u03bcM mifeprist1 added to embryo water from 24 hpf|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "GSM2535110", "GSM2535110: mpo RNAseqnuclear +mifNRas+ 2; Danio rerio; RNA Seq", "GSM2535110", null, "1", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #'s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2535110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP101781", null, null, "shead_mif2Aligned.out.sort.bam", "bam", 7581928543.0, 47699195.0, "GSM2535110 r1", "0:79.48 1:79.48", "A:2083595704;C:1751859031;G:1833743542;T:1912626493;N:103773", 79, 79, null, null, 2083595704, 1751859031, 1833743542, 1912626493, 103773, "SRX2635543", "SRS2044322", "SRA544939", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.93437, 0.93246, 0.08098, 0.08538, 0.78589, 0.79125, 0.39046, 0.38599, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-03-13", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [41909, "SRR5338228", "SRX2635542", "SRS2044321", "SRP101781", "PRJNA378947", "Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes", "GSE96534", "Transcriptome Analysis", "A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour  cancer cells have escaped the initial immune response mechanisms. To date  no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q  HRasG12V  KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma  revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1  fgf6  cathepsin H  cathepsin L  galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.", null, "pubmed:29666124", null, "mpo RNAseqnuclear  +mifNRas+ 1", "GSM2535109", null, "tissue:mpo RNAseqnuclear +mif head 1|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:1 \u03bcM mifeprist1 added to embryo water from 24 hpf|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "mpo RNAseqnuclear  +mifNRas+ 1", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts", "mpo RNAseqnuclear +mif head 1", "Incrossed larvae were treated with 1 \u03bcM from 24 hpf", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:1 \u03bcM mifeprist1 added to embryo water from 24 hpf|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "GSM2535109", "GSM2535109: mpo RNAseqnuclear  +mifNRas+ 1; Danio rerio; RNA Seq", "GSM2535109", null, "1", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #'s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2535109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP101781", null, null, "shead_mif1Aligned.out.sort.bam", "bam", 7904423201.0, 49746704.0, "GSM2535109 r1", "0:79.45 1:79.45", "A:2153404550;C:1843316968;G:1926669197;T:1980935189;N:97297", 79, 79, null, null, 2153404550, 1843316968, 1926669197, 1980935189, 97297, "SRX2635542", "SRS2044321", "SRA544939", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.9341, 0.931, 0.07739, 0.07981, 0.79971, 0.80568, 0.38474, 0.38892, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-03-13", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [41910, "SRR5338227", "SRX2635541", "SRS2044320", "SRP101781", "PRJNA378947", "Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes", "GSE96534", "Transcriptome Analysis", "A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour  cancer cells have escaped the initial immune response mechanisms. To date  no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q  HRasG12V  KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma  revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1  fgf6  cathepsin H  cathepsin L  galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.", null, "pubmed:29666124", null, "mpo RNAseqnuclear  mifcntrl 2", "GSM2535108", null, "tissue:mpo RNAseqnuclear  mif head 2|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:n1|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "mpo RNAseqnuclear  mifcntrl 2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts", "mpo RNAseqnuclear  mif head 2", "Incrossed larvae were treated with 1 \u03bcM from 24 hpf", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:n1|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "GSM2535108", "GSM2535108: mpo RNAseqnuclear  mifcntrl 2; Danio rerio; RNA Seq", "GSM2535108", null, "1", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #'s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2535108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP101781", null, null, "shead2Aligned.out.sort.bam", "bam", 8216508851.0, 51890331.0, "GSM2535108 r1", "0:79.18 1:79.17", "A:2297720467;C:1839611761;G:1894426911;T:2184654439;N:95273", 79, 79, null, null, 2297720467, 1839611761, 1894426911, 2184654439, 95273, "SRX2635541", "SRS2044320", "SRA544939", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.91404, 0.91129, 0.16863, 0.17306, 0.76108, 0.76347, 0.47228, 0.47663, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-03-13", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [41911, "SRR5338226", "SRX2635540", "SRS2044319", "SRP101781", "PRJNA378947", "Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes", "GSE96534", "Transcriptome Analysis", "A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour  cancer cells have escaped the initial immune response mechanisms. To date  no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q  HRasG12V  KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma  revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1  fgf6  cathepsin H  cathepsin L  galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.", null, "pubmed:29666124", null, "mpo RNAseqnuclear  mifcntrl 1", "GSM2535107", null, "tissue:mpo RNAseqnuclear  mif head 1|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:n1|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "mpo RNAseqnuclear  mifcntrl 1", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts", "mpo RNAseqnuclear  mif head 1", "Incrossed larvae were treated with 1 \u03bcM from 24 hpf", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130|development:5 dpf method:In Vivo Biotinylated Nuclei|treatment:n1|amplification:SMART seqTMv4|strand:reverse|assay:RNA seq", "GSM2535107", "GSM2535107: mpo RNAseqnuclear  mifcntrl 1; Danio rerio; RNA Seq", "GSM2535107", null, "1", "For nuclei isolation  zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 \u00b0C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 \u00b0C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous\u00ae Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #'s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2535107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP101781", null, null, "shead1Aligned.out.sort.bam", "bam", 6223616133.0, 39173742.0, "GSM2535107 r1", "0:79.44 1:79.43", "A:1628842481;C:1512759691;G:1559820323;T:1522127590;N:66048", 79, 79, null, null, 1628842481, 1512759691, 1559820323, 1522127590, 66048, "SRX2635540", "SRS2044319", "SRA544939", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.91702, 0.91416, 0.08978, 0.09081, 0.80825, 0.81225, 0.47575, 0.46407, 78, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-03-13", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [50953, "SRR8383314", "SRX5193232", "SRS4199232", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e6", "GSM3536476", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536476", "GSM3536476: 3 primemRNAseq zPCF11deltaPAS1 hom e6; Danio rerio; RNA Seq", "GSM3536476", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCTCGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 170117572.0, 1936836.0, "GSM3536476 r1", "0:87.83", "A:57043415;C:29867475;G:33401453;T:49804679;N:550", 87, null, null, null, 57043415, 29867475, 33401453, 49804679, 550, "SRX5193232", "SRS4199232", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82781, null, 0.11752, null, 0.7791, null, 0.51275, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50954, "SRR8383315", "SRX5193232", "SRS4199232", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e6", "GSM3536476", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536476", "GSM3536476: 3 primemRNAseq zPCF11deltaPAS1 hom e6; Danio rerio; RNA Seq", "GSM3536476", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536476", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GCTCGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 175173536.0, 1995191.0, "GSM3536476 r2", "0:87.80", "A:58844991;C:30708254;G:34327735;T:51292146;N:410", 87, null, null, null, 58844991, 30708254, 34327735, 51292146, 410, "SRX5193232", "SRS4199232", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82604, null, 0.11764, null, 0.78029, null, 0.51756, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50955, "SRR8383312", "SRX5193231", "SRS4199231", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e5", "GSM3536475", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536475", "GSM3536475: 3 primemRNAseq zPCF11deltaPAS1 hom e5; Danio rerio; RNA Seq", "GSM3536475", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536475", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CAAGCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 606360323.0, 6905543.0, "GSM3536475 r1", "0:87.81", "A:198106425;C:109559199;G:122893662;T:175799225;N:1812", 87, null, null, null, 198106425, 109559199, 122893662, 175799225, 1812, "SRX5193231", "SRS4199231", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8427, null, 0.1325, null, 0.78879, null, 0.51921, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50956, "SRR8383313", "SRX5193231", "SRS4199231", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e5", "GSM3536475", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536475", "GSM3536475: 3 primemRNAseq zPCF11deltaPAS1 hom e5; Danio rerio; RNA Seq", "GSM3536475", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536475", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CAAGCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 624201360.0, 7110625.0, "GSM3536475 r2", "0:87.78", "A:204175038;C:112645351;G:126392625;T:180986966;N:1380", 87, null, null, null, 204175038, 112645351, 126392625, 180986966, 1380, "SRX5193231", "SRS4199231", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84211, null, 0.13385, null, 0.7895, null, 0.52023, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50957, "SRR8383310", "SRX5193230", "SRS4199230", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e4", "GSM3536474", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536474", "GSM3536474: 3 primemRNAseq zPCF11deltaPAS1 hom e4; Danio rerio; RNA Seq", "GSM3536474", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AACGCCATC.bam.fastq_trimmed.fastq.gz", "fastq", 892780335.0, 10219904.0, "GSM3536474 r1", "0:87.36", "A:300258267;C:163189097;G:178114941;T:251215317;N:2713", 87, null, null, null, 300258267, 163189097, 178114941, 251215317, 2713, "SRX5193230", "SRS4199230", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83419, null, 0.14585, null, 0.80255, null, 0.50109, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50958, "SRR8383311", "SRX5193230", "SRS4199230", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e4", "GSM3536474", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536474", "GSM3536474: 3 primemRNAseq zPCF11deltaPAS1 hom e4; Danio rerio; RNA Seq", "GSM3536474", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536474", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AACGCCATC.bam.fastq_trimmed.fastq.gz", "fastq", 921074852.0, 10547533.0, "GSM3536474 r2", "0:87.33", "A:310174374;C:168106596;G:183538421;T:259253357;N:2104", 87, null, null, null, 310174374, 168106596, 183538421, 259253357, 2104, "SRX5193230", "SRS4199230", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83245, null, 0.14487, null, 0.80359, null, 0.50415, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50959, "SRR8383308", "SRX5193229", "SRS4199229", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e3", "GSM3536473", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536473", "GSM3536473: 3 primemRNAseq zPCF11deltaPAS1 hom e3; Danio rerio; RNA Seq", "GSM3536473", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TTTATGATC.bam.fastq_trimmed.fastq.gz", "fastq", 1018559174.0, 11616470.0, "GSM3536473 r1", "0:87.68", "A:347433965;C:179438057;G:202582370;T:289101606;N:3176", 87, null, null, null, 347433965, 179438057, 202582370, 289101606, 3176, "SRX5193229", "SRS4199229", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81678, null, 0.16376, null, 0.79295, null, 0.52685, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50960, "SRR8383309", "SRX5193229", "SRS4199229", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e3", "GSM3536473", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536473", "GSM3536473: 3 primemRNAseq zPCF11deltaPAS1 hom e3; Danio rerio; RNA Seq", "GSM3536473", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536473", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TTTATGATC.bam.fastq_trimmed.fastq.gz", "fastq", 1049029756.0, 11967431.0, "GSM3536473 r2", "0:87.66", "A:358315722;C:184586479;G:208348099;T:297777016;N:2440", 87, null, null, null, 358315722, 184586479, 208348099, 297777016, 2440, "SRX5193229", "SRS4199229", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81613, null, 0.16396, null, 0.7931, null, 0.51637, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50961, "SRR8383306", "SRX5193228", "SRS4199228", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e2", "GSM3536472", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536472", "GSM3536472: 3 primemRNAseq zPCF11deltaPAS1 hom e2; Danio rerio; RNA Seq", "GSM3536472", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CCGCAAATC.bam.fastq_trimmed.fastq.gz", "fastq", 95347510.0, 1083083.0, "GSM3536472 r1", "0:88.03", "A:31277905;C:16917301;G:19217962;T:27934061;N:281", 88, null, null, null, 31277905, 16917301, 19217962, 27934061, 281, "SRX5193228", "SRS4199228", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84359, null, 0.1281, null, 0.77849, null, 0.50658, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50962, "SRR8383307", "SRX5193228", "SRS4199228", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e2", "GSM3536472", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536472", "GSM3536472: 3 primemRNAseq zPCF11deltaPAS1 hom e2; Danio rerio; RNA Seq", "GSM3536472", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536472", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CCGCAAATC.bam.fastq_trimmed.fastq.gz", "fastq", 98289209.0, 1116653.0, "GSM3536472 r2", "0:88.02", "A:32271861;C:17428261;G:19780092;T:28808779;N:216", 88, null, null, null, 32271861, 17428261, 19780092, 28808779, 216, "SRX5193228", "SRS4199228", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84257, null, 0.12826, null, 0.77881, null, 0.51159, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50963, "SRR8383304", "SRX5193227", "SRS4199227", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e1", "GSM3536471", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536471", "GSM3536471: 3 primemRNAseq zPCF11deltaPAS1 hom e1; Danio rerio; RNA Seq", "GSM3536471", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536471", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CACACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 151964150.0, 1729761.0, "GSM3536471 r1", "0:87.85", "A:51182251;C:27047472;G:29597244;T:44136727;N:456", 87, null, null, null, 51182251, 27047472, 29597244, 44136727, 456, "SRX5193227", "SRS4199227", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83286, null, 0.13372, null, 0.78023, null, 0.44685, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50964, "SRR8383305", "SRX5193227", "SRS4199227", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 hom e1", "GSM3536471", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "3 primemRNAseq zPCF11deltaPAS1 hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1  / ", "GSM3536471", "GSM3536471: 3 primemRNAseq zPCF11deltaPAS1 hom e1; Danio rerio; RNA Seq", "GSM3536471", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536471", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CACACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 156746824.0, 1784420.0, "GSM3536471 r2", "0:87.84", "A:52870952;C:27860644;G:30505998;T:45508859;N:371", 87, null, null, null, 52870952, 27860644, 30505998, 45508859, 371, "SRX5193227", "SRS4199227", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83111, null, 0.13281, null, 0.78001, null, 0.44609, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50965, "SRR8383302", "SRX5193226", "SRS4199226", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e5", "GSM3536470", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536470", "GSM3536470: 3 primemRNAseq zPCF11deltaPAS1 het e5; Danio rerio; RNA Seq", "GSM3536470", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TACCTTATC.bam.fastq_trimmed.fastq.gz", "fastq", 132241407.0, 1505632.0, "GSM3536470 r1", "0:87.83", "A:44701797;C:23272762;G:25927608;T:38338866;N:374", 87, null, null, null, 44701797, 23272762, 25927608, 38338866, 374, "SRX5193226", "SRS4199226", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82845, null, 0.13469, null, 0.7767, null, 0.52442, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50966, "SRR8383303", "SRX5193226", "SRS4199226", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e5", "GSM3536470", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536470", "GSM3536470: 3 primemRNAseq zPCF11deltaPAS1 het e5; Danio rerio; RNA Seq", "GSM3536470", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536470", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TACCTTATC.bam.fastq_trimmed.fastq.gz", "fastq", 136234092.0, 1551581.0, "GSM3536470 r2", "0:87.80", "A:46139985;C:23944780;G:26663569;T:39485404;N:354", 87, null, null, null, 46139985, 23944780, 26663569, 39485404, 354, "SRX5193226", "SRS4199226", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82629, null, 0.13474, null, 0.7794, null, 0.51749, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50967, "SRR8383300", "SRX5193225", "SRS4199225", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e4", "GSM3536469", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536469", "GSM3536469: 3 primemRNAseq zPCF11deltaPAS1 het e4; Danio rerio; RNA Seq", "GSM3536469", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_ATGAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 219395486.0, 2496420.0, "GSM3536469 r1", "0:87.88", "A:74049072;C:38996524;G:43402255;T:62946930;N:705", 87, null, null, null, 74049072, 38996524, 43402255, 62946930, 705, "SRX5193225", "SRS4199225", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83282, null, 0.14125, null, 0.78474, null, 0.5102, null, 42, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50968, "SRR8383301", "SRX5193225", "SRS4199225", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e4", "GSM3536469", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536469", "GSM3536469: 3 primemRNAseq zPCF11deltaPAS1 het e4; Danio rerio; RNA Seq", "GSM3536469", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_ATGAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 225177913.0, 2562839.0, "GSM3536469 r2", "0:87.86", "A:76113440;C:39951108;G:44487323;T:64625459;N:583", 87, null, null, null, 76113440, 39951108, 44487323, 64625459, 583, "SRX5193225", "SRS4199225", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82913, null, 0.13953, null, 0.78681, null, 0.50967, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50969, "SRR8383298", "SRX5193224", "SRS4199224", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e3", "GSM3536468", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536468", "GSM3536468: 3 primemRNAseq zPCF11deltaPAS1 het e3; Danio rerio; RNA Seq", "GSM3536468", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536468", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TTAACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 499775526.0, 5688628.0, "GSM3536468 r1", "0:87.86", "A:163216421;C:88556243;G:100895279;T:147106087;N:1496", 87, null, null, null, 163216421, 88556243, 100895279, 147106087, 1496, "SRX5193224", "SRS4199224", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84129, null, 0.13912, null, 0.78194, null, 0.5187, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50970, "SRR8383299", "SRX5193224", "SRS4199224", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e3", "GSM3536468", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536468", "GSM3536468: 3 primemRNAseq zPCF11deltaPAS1 het e3; Danio rerio; RNA Seq", "GSM3536468", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536468", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TTAACTATC.bam.fastq_trimmed.fastq.gz", "fastq", 514657493.0, 5859797.0, "GSM3536468 r2", "0:87.83", "A:168321204;C:91084703;G:103742599;T:151507844;N:1143", 87, null, null, null, 168321204, 91084703, 103742599, 151507844, 1143, "SRX5193224", "SRS4199224", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83984, null, 0.1389, null, 0.78291, null, 0.51811, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50971, "SRR8383296", "SRX5193223", "SRS4199223", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e2", "GSM3536467", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536467", "GSM3536467: 3 primemRNAseq zPCF11deltaPAS1 het e2; Danio rerio; RNA Seq", "GSM3536467", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536467", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CGGTTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 628544705.0, 7145719.0, "GSM3536467 r1", "0:87.96", "A:208540640;C:110628846;G:124026622;T:185346588;N:2009", 87, null, null, null, 208540640, 110628846, 124026622, 185346588, 2009, "SRX5193223", "SRS4199223", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83647, null, 0.11358, null, 0.7821, null, 0.50973, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50972, "SRR8383297", "SRX5193223", "SRS4199223", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e2", "GSM3536467", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536467", "GSM3536467: 3 primemRNAseq zPCF11deltaPAS1 het e2; Danio rerio; RNA Seq", "GSM3536467", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536467", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CGGTTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 647232214.0, 7359619.0, "GSM3536467 r2", "0:87.94", "A:215025740;C:113794072;G:127525437;T:190885451;N:1514", 87, null, null, null, 215025740, 113794072, 127525437, 190885451, 1514, "SRX5193223", "SRS4199223", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83376, null, 0.11387, null, 0.78305, null, 0.51943, null, 79, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50973, "SRR8383294", "SRX5193222", "SRS4199222", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e1", "GSM3536466", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536466", "GSM3536466: 3 primemRNAseq zPCF11deltaPAS1 het e1; Danio rerio; RNA Seq", "GSM3536466", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536466", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TCAGGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 789817010.0, 8990777.0, "GSM3536466 r1", "0:87.85", "A:255721217;C:143531700;G:162243420;T:228318196;N:2477", 87, null, null, null, 255721217, 143531700, 162243420, 228318196, 2477, "SRX5193222", "SRS4199222", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85167, null, 0.14197, null, 0.78813, null, 0.51648, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50974, "SRR8383295", "SRX5193222", "SRS4199222", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 het e1", "GSM3536466", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "3 primemRNAseq zPCF11deltaPAS1 het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/ ", "GSM3536466", "GSM3536466: 3 primemRNAseq zPCF11deltaPAS1 het e1; Danio rerio; RNA Seq", "GSM3536466", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536466", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TCAGGAATC.bam.fastq_trimmed.fastq.gz", "fastq", 812333266.0, 9249708.0, "GSM3536466 r2", "0:87.82", "A:263342967;C:147474874;G:166670966;T:234842610;N:1849", 87, null, null, null, 263342967, 147474874, 166670966, 234842610, 1849, "SRX5193222", "SRS4199222", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85028, null, 0.14374, null, 0.78754, null, 0.51112, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50975, "SRR8383292", "SRX5193221", "SRS4199221", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e3", "GSM3536465", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536465", "GSM3536465: 3 primemRNAseq zPCF11deltaPAS1 wt e3; Danio rerio; RNA Seq", "GSM3536465", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536465", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GGCTGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 164145508.0, 1870416.0, "GSM3536465 r1", "0:87.76", "A:53096508;C:29983980;G:33483503;T:47581048;N:469", 87, null, null, null, 53096508, 29983980, 33483503, 47581048, 469, "SRX5193221", "SRS4199221", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85271, null, 0.13713, null, 0.78626, null, 0.42953, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50976, "SRR8383293", "SRX5193221", "SRS4199221", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e3", "GSM3536465", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536465", "GSM3536465: 3 primemRNAseq zPCF11deltaPAS1 wt e3; Danio rerio; RNA Seq", "GSM3536465", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536465", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GGCTGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 168774555.0, 1923679.0, "GSM3536465 r2", "0:87.74", "A:54636127;C:30795817;G:34408599;T:48933579;N:433", 87, null, null, null, 54636127, 30795817, 34408599, 48933579, 433, "SRX5193221", "SRS4199221", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.85284, null, 0.136, null, 0.78595, null, 0.51852, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50977, "SRR8383290", "SRX5193220", "SRS4199220", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e2", "GSM3536464", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536464", "GSM3536464: 3 primemRNAseq zPCF11deltaPAS1 wt e2; Danio rerio; RNA Seq", "GSM3536464", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536464", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AATCCGATC.bam.fastq_trimmed.fastq.gz", "fastq", 237761677.0, 2716138.0, "GSM3536464 r1", "0:87.54", "A:77086804;C:43323233;G:48823094;T:68527734;N:812", 87, null, null, null, 77086804, 43323233, 48823094, 68527734, 812, "SRX5193220", "SRS4199220", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84891, null, 0.16038, null, 0.78839, null, 0.53051, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50978, "SRR8383291", "SRX5193220", "SRS4199220", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e2", "GSM3536464", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536464", "GSM3536464: 3 primemRNAseq zPCF11deltaPAS1 wt e2; Danio rerio; RNA Seq", "GSM3536464", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536464", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AATCCGATC.bam.fastq_trimmed.fastq.gz", "fastq", 244669202.0, 2795847.0, "GSM3536464 r2", "0:87.51", "A:79391766;C:44532003;G:50184304;T:70560584;N:545", 87, null, null, null, 79391766, 44532003, 50184304, 70560584, 545, "SRX5193220", "SRS4199220", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84722, null, 0.16156, null, 0.79011, null, 0.53158, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50979, "SRR8383288", "SRX5193219", "SRS4199219", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e1", "GSM3536463", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536463", "GSM3536463: 3 primemRNAseq zPCF11deltaPAS1 wt e1; Danio rerio; RNA Seq", "GSM3536463", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536463", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CCTAAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 129332543.0, 1472338.0, "GSM3536463 r1", "0:87.84", "A:43564845;C:22890586;G:25561204;T:37315459;N:449", 87, null, null, null, 43564845, 22890586, 25561204, 37315459, 449, "SRX5193219", "SRS4199219", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83187, null, 0.13547, null, 0.78234, null, 0.52271, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50980, "SRR8383289", "SRX5193219", "SRS4199219", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11deltaPAS1 wt e1", "GSM3536463", null, "tissue:single embryo head 32hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "3 primemRNAseq zPCF11deltaPAS1 wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 32hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11deltaPAS1 +/+", "GSM3536463", "GSM3536463: 3 primemRNAseq zPCF11deltaPAS1 wt e1; Danio rerio; RNA Seq", "GSM3536463", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536463", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CCTAAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 133356093.0, 1518522.0, "GSM3536463 r2", "0:87.82", "A:44962657;C:23585729;G:26335793;T:38471613;N:301", 87, null, null, null, 44962657, 23585729, 26335793, 38471613, 301, "SRX5193219", "SRS4199219", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83065, null, 0.13598, null, 0.78378, null, 0.53247, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50981, "SRR8383286", "SRX5193218", "SRS4199218", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e6", "GSM3536462", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536462", "GSM3536462: 3 primemRNAseq zPCF11null hom e6; Danio rerio; RNA Seq", "GSM3536462", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TCGAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 685570157.0, 7880276.0, "GSM3536462 r1", "0:87.00", "A:220749091;C:129576519;G:144120777;T:191121622;N:2148", 87, null, null, null, 220749091, 129576519, 144120777, 191121622, 2148, "SRX5193218", "SRS4199218", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82107, null, 0.23078, null, 0.81941, null, 0.59068, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50982, "SRR8383287", "SRX5193218", "SRS4199218", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e6", "GSM3536462", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e6", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536462", "GSM3536462: 3 primemRNAseq zPCF11null hom e6; Danio rerio; RNA Seq", "GSM3536462", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TCGAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 704276360.0, 8098980.0, "GSM3536462 r2", "0:86.96", "A:227042988;C:132957237;G:147852510;T:196421958;N:1667", 86, null, null, null, 227042988, 132957237, 147852510, 196421958, 1667, "SRX5193218", "SRS4199218", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81976, null, 0.23195, null, 0.82014, null, 0.58764, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50983, "SRR8383284", "SRX5193217", "SRS4199217", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e5", "GSM3536461", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536461", "GSM3536461: 3 primemRNAseq zPCF11null hom e5; Danio rerio; RNA Seq", "GSM3536461", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GTGCCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 770954082.0, 8859450.0, "GSM3536461 r1", "0:87.02", "A:257152925;C:141557495;G:158071178;T:214170140;N:2344", 87, null, null, null, 257152925, 141557495, 158071178, 214170140, 2344, "SRX5193217", "SRS4199217", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80635, null, 0.19837, null, 0.81355, null, 0.40061, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50984, "SRR8383285", "SRX5193217", "SRS4199217", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e5", "GSM3536461", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e5", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536461", "GSM3536461: 3 primemRNAseq zPCF11null hom e5; Danio rerio; RNA Seq", "GSM3536461", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GTGCCAATC.bam.fastq_trimmed.fastq.gz", "fastq", 792682872.0, 9113148.0, "GSM3536461 r2", "0:86.98", "A:264818153;C:145303306;G:162291530;T:220268109;N:1774", 86, null, null, null, 264818153, 145303306, 162291530, 220268109, 1774, "SRX5193217", "SRS4199217", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80446, null, 0.1978, null, 0.81397, null, 0.57793, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50985, "SRR8383282", "SRX5193216", "SRS4199216", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e4", "GSM3536460", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536460", "GSM3536460: 3 primemRNAseq zPCF11null hom e4; Danio rerio; RNA Seq", "GSM3536460", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AATAGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 128394352.0, 1469184.0, "GSM3536460 r1", "0:87.39", "A:41878409;C:23656471;G:26363280;T:36495822;N:370", 87, null, null, null, 41878409, 23656471, 26363280, 36495822, 370, "SRX5193216", "SRS4199216", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8404, null, 0.20794, null, 0.81635, null, 0.57453, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50986, "SRR8383283", "SRX5193216", "SRS4199216", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e4", "GSM3536460", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536460", "GSM3536460: 3 primemRNAseq zPCF11null hom e4; Danio rerio; RNA Seq", "GSM3536460", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AATAGCATC.bam.fastq_trimmed.fastq.gz", "fastq", 131964907.0, 1510456.0, "GSM3536460 r2", "0:87.37", "A:43071448;C:24301835;G:27045591;T:37545716;N:317", 87, null, null, null, 43071448, 24301835, 27045591, 37545716, 317, "SRX5193216", "SRS4199216", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.84091, null, 0.21002, null, 0.8168, null, 0.57732, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50987, "SRR8383280", "SRX5193215", "SRS4199215", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e3", "GSM3536459", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536459", "GSM3536459: 3 primemRNAseq zPCF11null hom e3; Danio rerio; RNA Seq", "GSM3536459", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCATGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 198921603.0, 2281764.0, "GSM3536459 r1", "0:87.18", "A:67933819;C:36044297;G:40047977;T:54894929;N:581", 87, null, null, null, 67933819, 36044297, 40047977, 54894929, 581, "SRX5193215", "SRS4199215", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80512, null, 0.21831, null, 0.81856, null, 0.58328, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50988, "SRR8383281", "SRX5193215", "SRS4199215", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e3", "GSM3536459", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536459", "GSM3536459: 3 primemRNAseq zPCF11null hom e3; Danio rerio; RNA Seq", "GSM3536459", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GCATGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 204339172.0, 2344861.0, "GSM3536459 r2", "0:87.14", "A:69852605;C:36969411;G:41077998;T:56438756;N:402", 87, null, null, null, 69852605, 36969411, 41077998, 56438756, 402, "SRX5193215", "SRS4199215", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80367, null, 0.21762, null, 0.81858, null, 0.58312, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50989, "SRR8383278", "SRX5193214", "SRS4199214", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e2", "GSM3536458", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536458", "GSM3536458: 3 primemRNAseq zPCF11null hom e2; Danio rerio; RNA Seq", "GSM3536458", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CTCCATATC.bam.fastq_trimmed.fastq.gz", "fastq", 243678478.0, 2785241.0, "GSM3536458 r1", "0:87.49", "A:80921391;C:44962028;G:49483835;T:68310471;N:753", 87, null, null, null, 80921391, 44962028, 49483835, 68310471, 753, "SRX5193214", "SRS4199214", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.8288, null, 0.19506, null, 0.82674, null, 0.5695, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50990, "SRR8383279", "SRX5193214", "SRS4199214", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e2", "GSM3536458", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536458", "GSM3536458: 3 primemRNAseq zPCF11null hom e2; Danio rerio; RNA Seq", "GSM3536458", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CTCCATATC.bam.fastq_trimmed.fastq.gz", "fastq", 251121623.0, 2871387.0, "GSM3536458 r2", "0:87.46", "A:83477676;C:46277942;G:50927013;T:70438422;N:570", 87, null, null, null, 83477676, 46277942, 50927013, 70438422, 570, "SRX5193214", "SRS4199214", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82553, null, 0.19377, null, 0.82674, null, 0.56696, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50991, "SRR8383276", "SRX5193213", "SRS4199213", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e1", "GSM3536457", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536457", "GSM3536457: 3 primemRNAseq zPCF11null hom e1; Danio rerio; RNA Seq", "GSM3536457", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TAGGCTATC.bam.fastq_trimmed.fastq.gz", "fastq", 125156975.0, 1440450.0, "GSM3536457 r1", "0:86.89", "A:41125276;C:23385340;G:26101084;T:34544902;N:373", 86, null, null, null, 41125276, 23385340, 26101084, 34544902, 373, "SRX5193213", "SRS4199213", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82681, null, 0.23851, null, 0.82162, null, 0.59477, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50992, "SRR8383277", "SRX5193213", "SRS4199213", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null hom e1", "GSM3536457", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "3 primemRNAseq zPCF11null hom e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null  / ", "GSM3536457", "GSM3536457: 3 primemRNAseq zPCF11null hom e1; Danio rerio; RNA Seq", "GSM3536457", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TAGGCTATC.bam.fastq_trimmed.fastq.gz", "fastq", 128831164.0, 1483314.0, "GSM3536457 r2", "0:86.85", "A:42399550;C:24025044;G:26817005;T:35589296;N:269", 86, null, null, null, 42399550, 24025044, 26817005, 35589296, 269, "SRX5193213", "SRS4199213", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82598, null, 0.23646, null, 0.82207, null, 0.59052, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50993, "SRR8383274", "SRX5193212", "SRS4199212", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e4", "GSM3536456", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536456", "GSM3536456: 3 primemRNAseq zPCF11null het e4; Danio rerio; RNA Seq", "GSM3536456", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CGAAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 118253929.0, 1353894.0, "GSM3536456 r1", "0:87.34", "A:41106016;C:21057430;G:23427525;T:32662627;N:331", 87, null, null, null, 41106016, 21057430, 23427525, 32662627, 331, "SRX5193212", "SRS4199212", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81195, null, 0.18309, null, 0.82191, null, 0.55215, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50994, "SRR8383275", "SRX5193212", "SRS4199212", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e4", "GSM3536456", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536456", "GSM3536456: 3 primemRNAseq zPCF11null het e4; Danio rerio; RNA Seq", "GSM3536456", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CGAAGGATC.bam.fastq_trimmed.fastq.gz", "fastq", 121725680.0, 1394241.0, "GSM3536456 r2", null, null, null, null, null, null, null, null, null, null, null, "SRX5193212", "SRS4199212", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.76785, null, 0.17246, null, 0.81962, null, 0.55625, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50995, "SRR8383272", "SRX5193211", "SRS4199211", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e3", "GSM3536455", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536455", "GSM3536455: 3 primemRNAseq zPCF11null het e3; Danio rerio; RNA Seq", "GSM3536455", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_ACCTACATC.bam.fastq_trimmed.fastq.gz", "fastq", 186888249.0, 2140393.0, "GSM3536455 r1", "0:87.31", "A:65786002;C:32923065;G:36796601;T:51382007;N:574", 87, null, null, null, 65786002, 32923065, 36796601, 51382007, 574, "SRX5193211", "SRS4199211", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80995, null, 0.19928, null, 0.8033, null, 0.5594, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50996, "SRR8383273", "SRX5193211", "SRS4199211", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e3", "GSM3536455", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536455", "GSM3536455: 3 primemRNAseq zPCF11null het e3; Danio rerio; RNA Seq", "GSM3536455", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_ACCTACATC.bam.fastq_trimmed.fastq.gz", "fastq", 192642130.0, 2206994.0, "GSM3536455 r2", "0:87.29", "A:67912529;C:33877053;G:37899068;T:52953002;N:478", 87, null, null, null, 67912529, 33877053, 37899068, 52953002, 478, "SRX5193211", "SRS4199211", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.80759, null, 0.19797, null, 0.80348, null, 0.55867, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50997, "SRR8383270", "SRX5193210", "SRS4199210", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e2", "GSM3536454", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536454", "GSM3536454: 3 primemRNAseq zPCF11null het e2; Danio rerio; RNA Seq", "GSM3536454", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TGGATTATC.bam.fastq_trimmed.fastq.gz", "fastq", 198506304.0, 2271548.0, "GSM3536454 r1", "0:87.39", "A:65363370;C:36248554;G:40646664;T:56247077;N:639", 87, null, null, null, 65363370, 36248554, 40646664, 56247077, 639, "SRX5193210", "SRS4199210", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81892, null, 0.1808, null, 0.81558, null, 0.55265, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50998, "SRR8383271", "SRX5193210", "SRS4199210", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e2", "GSM3536454", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536454", "GSM3536454: 3 primemRNAseq zPCF11null het e2; Danio rerio; RNA Seq", "GSM3536454", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TGGATTATC.bam.fastq_trimmed.fastq.gz", "fastq", 204546039.0, 2341528.0, "GSM3536454 r2", "0:87.36", "A:67442570;C:37300418;G:41843482;T:57959051;N:518", 87, null, null, null, 67442570, 37300418, 41843482, 57959051, 518, "SRX5193210", "SRS4199210", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81597, null, 0.18014, null, 0.81714, null, 0.55071, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [50999, "SRR8383268", "SRX5193209", "SRS4199209", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e1", "GSM3536453", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536453", "GSM3536453: 3 primemRNAseq zPCF11null het e1; Danio rerio; RNA Seq", "GSM3536453", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536453", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GCGAATATC.bam.fastq_trimmed.fastq.gz", "fastq", 166454199.0, 1896918.0, "GSM3536453 r1", "0:87.75", "A:54362704;C:30210406;G:33769933;T:48110651;N:505", 87, null, null, null, 54362704, 30210406, 33769933, 48110651, 505, "SRX5193209", "SRS4199209", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83471, null, 0.17434, null, 0.80231, null, 0.55417, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51000, "SRR8383269", "SRX5193209", "SRS4199209", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null het e1", "GSM3536453", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "3 primemRNAseq zPCF11null het e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/ ", "GSM3536453", "GSM3536453: 3 primemRNAseq zPCF11null het e1; Danio rerio; RNA Seq", "GSM3536453", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536453", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GCGAATATC.bam.fastq_trimmed.fastq.gz", "fastq", 171370619.0, 1953554.0, "GSM3536453 r2", "0:87.72", "A:56037972;C:31055338;G:34710723;T:49566184;N:402", 87, null, null, null, 56037972, 31055338, 34710723, 49566184, 402, "SRX5193209", "SRS4199209", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83503, null, 0.17275, null, 0.80389, null, 0.54802, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51001, "SRR8383266", "SRX5193208", "SRS4199208", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e4", "GSM3536452", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536452", "GSM3536452: 3 primemRNAseq zPCF11null wt e4; Danio rerio; RNA Seq", "GSM3536452", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536452", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_CGCAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 174611360.0, 2002483.0, "GSM3536452 r1", "0:87.20", "A:56929522;C:32074265;G:35774482;T:49832562;N:529", 87, null, null, null, 56929522, 32074265, 35774482, 49832562, 529, "SRX5193208", "SRS4199208", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83372, null, 0.18461, null, 0.80811, null, 0.54823, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51002, "SRR8383267", "SRX5193208", "SRS4199208", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e4", "GSM3536452", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e4", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536452", "GSM3536452: 3 primemRNAseq zPCF11null wt e4; Danio rerio; RNA Seq", "GSM3536452", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536452", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_CGCAACATC.bam.fastq_trimmed.fastq.gz", "fastq", 179927114.0, 2064019.0, "GSM3536452 r2", "0:87.17", "A:58698795;C:32998345;G:36824253;T:51405334;N:387", 87, null, null, null, 58698795, 32998345, 36824253, 51405334, 387, "SRX5193208", "SRS4199208", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83291, null, 0.18273, null, 0.80898, null, 0.54951, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51003, "SRR8383264", "SRX5193207", "SRS4199207", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e3", "GSM3536451", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536451", "GSM3536451: 3 primemRNAseq zPCF11null wt e3; Danio rerio; RNA Seq", "GSM3536451", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536451", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_GTTACCATC.bam.fastq_trimmed.fastq.gz", "fastq", 423907322.0, 4857964.0, "GSM3536451 r1", "0:87.26", "A:142119526;C:76370356;G:86122715;T:119293410;N:1315", 87, null, null, null, 142119526, 76370356, 86122715, 119293410, 1315, "SRX5193207", "SRS4199207", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82515, null, 0.17866, null, 0.80598, null, 0.5424, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51004, "SRR8383265", "SRX5193207", "SRS4199207", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e3", "GSM3536451", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e3", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536451", "GSM3536451: 3 primemRNAseq zPCF11null wt e3; Danio rerio; RNA Seq", "GSM3536451", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536451", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_GTTACCATC.bam.fastq_trimmed.fastq.gz", "fastq", 436230914.0, 5000909.0, "GSM3536451 r2", "0:87.23", "A:146479519;C:78476816;G:88511770;T:122761779;N:1030", 87, null, null, null, 146479519, 78476816, 88511770, 122761779, 1030, "SRX5193207", "SRS4199207", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.82369, null, 0.17724, null, 0.80799, null, 0.53506, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51005, "SRR8383262", "SRX5193206", "SRS4199206", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e2", "GSM3536450", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536450", "GSM3536450: 3 primemRNAseq zPCF11null wt e2; Danio rerio; RNA Seq", "GSM3536450", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536450", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_TTGGTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 496496816.0, 5671581.0, "GSM3536450 r1", "0:87.54", "A:167742127;C:88470896;G:98690606;T:141591736;N:1451", 87, null, null, null, 167742127, 88470896, 98690606, 141591736, 1451, "SRX5193206", "SRS4199206", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81921, null, 0.15966, null, 0.8071, null, 0.53472, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51006, "SRR8383263", "SRX5193206", "SRS4199206", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e2", "GSM3536450", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e2", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536450", "GSM3536450: 3 primemRNAseq zPCF11null wt e2; Danio rerio; RNA Seq", "GSM3536450", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536450", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_TTGGTAATC.bam.fastq_trimmed.fastq.gz", "fastq", 510651572.0, 5835386.0, "GSM3536450 r2", "0:87.51", "A:172754168;C:90870653;G:101360243;T:145665418;N:1090", 87, null, null, null, 172754168, 90870653, 101360243, 145665418, 1090, "SRX5193206", "SRS4199206", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.81817, null, 0.15907, null, 0.8071, null, 0.54188, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51007, "SRR8383260", "SRX5193205", "SRS4199205", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e1", "GSM3536449", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536449", "GSM3536449: 3 primemRNAseq zPCF11null wt e1; Danio rerio; RNA Seq", "GSM3536449", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536449", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam4__sel_AGATAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 765801085.0, 8788307.0, "GSM3536449 r1", "0:87.14", "A:248760821;C:142857406;G:160149415;T:214031144;N:2299", 87, null, null, null, 248760821, 142857406, 160149415, 214031144, 2299, "SRX5193205", "SRS4199205", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83838, null, 0.2174, null, 0.81341, null, 0.56038, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [51008, "SRR8383261", "SRX5193205", "SRS4199205", "SRP175015", "PRJNA512489", "Selective roles of vertebrate PCF11 in premature and full length transcript termination zebrafish three prime mRNA seq", "GSE124555", "Other", "The pervasive nature of RNA polymerase II Pol II transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation CPA factor PCF11  which directly binds to the Pol II C terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11 mediated termination is essential for vertebrate development. A range of genomic analyses  including: mNET seq  three prime mRNA seq  chromatin RNA seq and ChIP seq  reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome wide. PCF11 binds preferentially between closely spaced genes  where it prevents transcriptional interference and downstream gene silencing. Notably  PCF11 is sub stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto regulatory mechanism involving premature termination of its own transcript  and are important for normal development. Both in human cell culture and during zebrafish development  PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Overall design: three prime mRNA seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild type wt  +/+  heterozygous het  +/  and homozygous mutant hom   /  embryos were analyzed. Wild type and heterozygous animals were phenotypically indistinguishable.", "parent bioproject:PRJNA507553", "pubmed:30819644", null, "3 primemRNAseq zPCF11null wt e1", "GSM3536449", null, "tissue:single embryo head 19hpf|molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "3 primemRNAseq zPCF11null wt e1", "3\u2019 mRNA seq data were mapped according to the guidelines of QuantSeq library kit manufacturer Lexogen. Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx TopHat 2 component Kim et al.  2013. post overview with FastQC reads were trimmed with BBtools sourceforge.net/projects/bbmap/ script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 . post trimming control with FastQC curated reads were mapped with STAR2.5b Dobin et al.  2013 aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation. Aligned 3\u2019 mRNA seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome encoded polyA stretches. To do this  first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand  an analogous T rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T rich regions by strand specifically unmasking 20 nucleotide intervals centred at annotated 3\u2019 gene ends. 3\u2019 mRNA seq reads falling into those refined strand specific masks were then removed  and the filtered reads reduced to the most distal nucleotide 3\u2019 end nucleotide. Genome build: GRCz10/danRer10 Supplementary files format and content: bigWig files: genome coverage files  mean from replicates", "single embryo head 19hpf", null, "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq 3\u2019mRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature  14/10 hr light/dark cycle. TLAB fish  generated by crossing zebrafish AB and the natural variant TL Tupfel Long fin stocks  served as wild type zebrafish for all experiments. zPCF11 null and zPCF11 \u2206PAS1 mutant zebrafish were generated by Cas9 mediated mutagenesis Gagnon et al.  2014", "molecule subtype:3 prime end of mRNA|genotype/treatment:zPCF11null +/+", "GSM3536449", "GSM3536449: 3 primemRNAseq zPCF11null wt e1; Danio rerio; RNA Seq", "GSM3536449", null, "1", "Dechorionated embryos of heterozygous Pcf11 mutant incrosses were cut in half with a razor blade at 19 hpf zPCF11null or 32 hpf zPCF11deltaPAS1 and  and each head and tail was  collected individually in PCR tubes. The anterior halves heads were lysed in 10 \u00b5l of TCL buffer with 1% beta mercaptoethanol and flash frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves tails were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Libraries were prepared according to the protocols of QuantSeq three primemRNA Seq library prep kit FW for Illumina LEXOGEN Cat# SKU 015.96 3 4 wild type  4 5 heterozygous  and six homozygous samples of both zPCF11 null and zPCF11 delta PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads A63987  Beckman Coulter. Strand specific libraries were generated using the QuantSeq three prime mRNA Library Prep Kit FW Lexogen and used for 100 bp single end sequencing on the Illumina HiSeq 2500.", "GEO Accession:GSM3536449", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP175015", null, null, "bam5__sel_AGATAGATC.bam.fastq_trimmed.fastq.gz", "fastq", 786372640.0, 9027751.0, "GSM3536449 r2", "0:87.11", "A:255738065;C:146505167;G:164268319;T:219859234;N:1855", 87, null, null, null, 255738065, 146505167, 164268319, 219859234, 1855, "SRX5193205", "SRS4199205", "SRA828489", "GEO", "Sir William Dunn School of Pathology, University of Oxford", 1, 0.83666, null, 0.21536, null, 0.81428, null, 0.5556, null, 89, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-01-02", "Multi-stage", "Embryo", "Head", "Nervous System"], [55541, "SRR10550579", "SRX7232580", "SRS5733210", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 6", "GSM4196113", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 6", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196113", "GSM4196113: Lrv FLX Str whole 6; Danio rerio; RNA Seq", "GSM4196113", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_6_S55_R1_001.trimmed.fastq.gz", "fastq", 1667637008.0, 22201140.0, "GSM4196113 r1", "0:75.11 1:0", "A:438989346;C:397147842;G:367576938;T:463905385;N:17497", 75, 0, null, null, 438989346, 397147842, 367576938, 463905385, 17497, "SRX7232580", "SRS5733210", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94774, null, 0.13955, null, 0.69842, null, 0.47883, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55542, "SRR10550578", "SRX7232579", "SRS5733211", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 5", "GSM4196112", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 5", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196112", "GSM4196112: Lrv FLX Str whole 5; Danio rerio; RNA Seq", "GSM4196112", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_5_S59_R1_001.trimmed.fastq.gz", "fastq", 1682694124.0, 22385497.0, "GSM4196112 r1", "0:75.17 1:0", "A:404424623;C:427018922;G:386032112;T:465200972;N:17495", 75, 0, null, null, 404424623, 427018922, 386032112, 465200972, 17495, "SRX7232579", "SRS5733211", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95782, null, 0.11464, null, 0.69404, null, 0.47678, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55543, "SRR10550577", "SRX7232578", "SRS5733209", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 4", "GSM4196111", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 4", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196111", "GSM4196111: Lrv FLX Str whole 4; Danio rerio; RNA Seq", "GSM4196111", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_4_S50_R1_001.trimmed.fastq.gz", "fastq", 1087107196.0, 14458795.0, "GSM4196111 r1", "0:75.19 1:0", "A:267171751;C:268993662;G:244811629;T:306118431;N:11723", 75, 0, null, null, 267171751, 268993662, 244811629, 306118431, 11723, "SRX7232578", "SRS5733209", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95236, null, 0.12138, null, 0.69725, null, 0.46512, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55544, "SRR10550576", "SRX7232577", "SRS5733208", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 3", "GSM4196110", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 3", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196110", "GSM4196110: Lrv FLX Str whole 3; Danio rerio; RNA Seq", "GSM4196110", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_3_S62_R1_001.trimmed.fastq.gz", "fastq", 1652611529.0, 21987509.0, "GSM4196110 r1", "0:75.16 1:0", "A:442049125;C:388222499;G:359554341;T:462768582;N:16982", 75, 0, null, null, 442049125, 388222499, 359554341, 462768582, 16982, "SRX7232577", "SRS5733208", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94763, null, 0.15049, null, 0.69875, null, 0.49665, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55545, "SRR10550575", "SRX7232576", "SRS5733207", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 2", "GSM4196109", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 2", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196109", "GSM4196109: Lrv FLX Str whole 2; Danio rerio; RNA Seq", "GSM4196109", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_2_S70_R1_001.trimmed.fastq.gz", "fastq", 1525352669.0, 20291623.0, "GSM4196109 r1", "0:75.17 1:0", "A:415549321;C:352941285;G:326282134;T:430564543;N:15386", 75, 0, null, null, 415549321, 352941285, 326282134, 430564543, 15386, "SRX7232576", "SRS5733207", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94391, null, 0.16406, null, 0.69613, null, 0.48758, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55546, "SRR10550574", "SRX7232575", "SRS5733206", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Str whole 1", "GSM4196108", null, "source name:Lrv FLX Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "Lrv FLX Str whole 1", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:FLX|tissue:larvae head", "GSM4196108", "GSM4196108: Lrv FLX Str whole 1; Danio rerio; RNA Seq", "GSM4196108", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Str_1_S57_R1_001.trimmed.fastq.gz", "fastq", 1572443197.0, 20910507.0, "GSM4196108 r1", "0:75.20 1:0", "A:391749194;C:388029990;G:350196422;T:442451463;N:16128", 75, 0, null, null, 391749194, 388029990, 350196422, 442451463, 16128, "SRX7232575", "SRS5733206", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95111, null, 0.1268, null, 0.69587, null, 0.47885, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55547, "SRR10550573", "SRX7232574", "SRS5733205", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 6", "GSM4196107", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 6", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196107", "GSM4196107: Lrv FLX Bsal whole 6; Danio rerio; RNA Seq", "GSM4196107", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal_6_S64_R1_001.trimmed.fastq.gz", "fastq", 1819465903.0, 24220618.0, "GSM4196107 r1", "0:75.12 1:0", "A:454377540;C:446747596;G:411720425;T:506601808;N:18534", 75, 0, null, null, 454377540, 446747596, 411720425, 506601808, 18534, "SRX7232574", "SRS5733205", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95274, null, 0.12081, null, 0.67389, null, 0.47068, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55548, "SRR10550572", "SRX7232573", "SRS5733204", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 4", "GSM4196106", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 4", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196106", "GSM4196106: Lrv FLX Bsal whole 4; Danio rerio; RNA Seq", "GSM4196106", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal_4_S69_R1_001.trimmed.fastq.gz", "fastq", 1802344612.0, 23981363.0, "GSM4196106 r1", "0:75.16 1:0", "A:455847939;C:444174899;G:406307504;T:495995239;N:19031", 75, 0, null, null, 455847939, 444174899, 406307504, 495995239, 19031, "SRX7232573", "SRS5733204", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.9537, null, 0.13958, null, 0.6929, null, 0.4996, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55549, "SRR10550571", "SRX7232572", "SRS5733203", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 3", "GSM4196105", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 3", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196105", "GSM4196105: Lrv FLX Bsal whole 3; Danio rerio; RNA Seq", "GSM4196105", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal_3_S53_R1_001.trimmed.fastq.gz", "fastq", 1536979688.0, 20489086.0, "GSM4196105 r1", "0:75.01 1:0", "A:379743513;C:383792979;G:353602367;T:419825271;N:15558", 75, 0, null, null, 379743513, 383792979, 353602367, 419825271, 15558, "SRX7232572", "SRS5733203", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95655, null, 0.12079, null, 0.69666, null, 0.48202, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55550, "SRR10550570", "SRX7232571", "SRS5733202", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 2", "GSM4196104", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 2", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196104", "GSM4196104: Lrv FLX Bsal whole 2; Danio rerio; RNA Seq", "GSM4196104", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal_2_S51_R1_001.trimmed.fastq.gz", "fastq", 1461206417.0, 19438024.0, "GSM4196104 r1", "0:75.17 1:0", "A:356069261;C:366658372;G:336019907;T:402443848;N:15029", 75, 0, null, null, 356069261, 366658372, 336019907, 402443848, 15029, "SRX7232571", "SRS5733202", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95627, null, 0.11745, null, 0.697, null, 0.47178, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55551, "SRR10550569", "SRX7232570", "SRS5733201", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 1", "GSM4196103", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 1", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196103", "GSM4196103: Lrv FLX Bsal whole 1; Danio rerio; RNA Seq", "GSM4196103", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal_1_S58_R1_001.trimmed.fastq.gz", "fastq", 1274881809.0, 16955491.0, "GSM4196103 r1", "0:75.19 1:0", "A:313269199;C:315319719;G:289025501;T:357254917;N:12473", 75, 0, null, null, 313269199, 315319719, 289025501, 357254917, 12473, "SRX7232570", "SRS5733201", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95224, null, 0.12115, null, 0.69749, null, 0.45972, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55552, "SRR10550568", "SRX7232569", "SRS5733200", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv FLX Bsal whole 5", "GSM4196102", null, "source name:Lrv FLX Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "Lrv FLX Bsal whole 5", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv FLX Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:FLX|tissue:larvae head", "GSM4196102", "GSM4196102: Lrv FLX Bsal whole 5; Danio rerio; RNA Seq", "GSM4196102", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_FLX_Bsal__5_S65_R1_001.trimmed.fastq.gz", "fastq", 1857265782.0, 24701079.0, "GSM4196102 r1", "0:75.19 1:0", "A:462562803;C:458171000;G:416821299;T:519691519;N:19161", 75, 0, null, null, 462562803, 458171000, 416821299, 519691519, 19161, "SRX7232569", "SRS5733200", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95278, null, 0.11954, null, 0.6871, null, 0.46728, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55553, "SRR10550567", "SRX7232568", "SRS5733199", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 6", "GSM4196101", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 6", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196101", "GSM4196101: Lrv Ctl Str whole 6; Danio rerio; RNA Seq", "GSM4196101", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_6_S71_R1_001.trimmed.fastq.gz", "fastq", 1957288376.0, 26046412.0, "GSM4196101 r1", "0:75.15 1:0", "A:514272402;C:461987308;G:431480575;T:549528052;N:20039", 75, 0, null, null, 514272402, 461987308, 431480575, 549528052, 20039, "SRX7232568", "SRS5733199", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94563, null, 0.13089, null, 0.68682, null, 0.47639, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55554, "SRR10550566", "SRX7232567", "SRS5733198", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 5", "GSM4196100", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 5", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196100", "GSM4196100: Lrv Ctl Str whole 5; Danio rerio; RNA Seq", "GSM4196100", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_5_S68_R1_001.trimmed.fastq.gz", "fastq", 1939162181.0, 25790355.0, "GSM4196100 r1", "0:75.19 1:0", "A:478145766;C:489708772;G:441830545;T:529458428;N:18670", 75, 0, null, null, 478145766, 489708772, 441830545, 529458428, 18670, "SRX7232567", "SRS5733198", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95788, null, 0.13698, null, 0.69564, null, 0.50856, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55555, "SRR10550565", "SRX7232566", "SRS5733197", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 4", "GSM4196099", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 4", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196099", "GSM4196099: Lrv Ctl Str whole 4; Danio rerio; RNA Seq", "GSM4196099", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_4_S63_R1_001.trimmed.fastq.gz", "fastq", 1661252715.0, 22112240.0, "GSM4196099 r1", "0:75.13 1:0", "A:426247799;C:401717650;G:370519308;T:462751124;N:16834", 75, 0, null, null, 426247799, 401717650, 370519308, 462751124, 16834, "SRX7232566", "SRS5733197", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95211, null, 0.11993, null, 0.68905, null, 0.47345, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55556, "SRR10550564", "SRX7232565", "SRS5733196", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 3", "GSM4196098", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 3", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196098", "GSM4196098: Lrv Ctl Str whole 3; Danio rerio; RNA Seq", "GSM4196098", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196098", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_3_S61_R1_001.trimmed.fastq.gz", "fastq", 2128433399.0, 28315796.0, "GSM4196098 r1", "0:75.17 1:0", "A:527968641;C:529216046;G:482537279;T:588689313;N:22120", 75, 0, null, null, 527968641, 529216046, 482537279, 588689313, 22120, "SRX7232565", "SRS5733196", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95484, null, 0.12615, null, 0.69899, null, 0.48613, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55557, "SRR10550563", "SRX7232564", "SRS5733195", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 2", "GSM4196097", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 2", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196097", "GSM4196097: Lrv Ctl Str whole 2; Danio rerio; RNA Seq", "GSM4196097", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196097", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_2_S49_R1_001.trimmed.fastq.gz", "fastq", 1308174499.0, 17399094.0, "GSM4196097 r1", "0:75.19 1:0", "A:324097251;C:321883043;G:297347816;T:364832719;N:13670", 75, 0, null, null, 324097251, 321883043, 297347816, 364832719, 13670, "SRX7232564", "SRS5733195", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95352, null, 0.12304, null, 0.70305, null, 0.47639, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55558, "SRR10550562", "SRX7232563", "SRS5733194", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Str whole 1", "GSM4196096", null, "source name:Lrv Ctl Str whole|genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "Lrv Ctl Str whole 1", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Str whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Str|drug status:Ctl|tissue:larvae head", "GSM4196096", "GSM4196096: Lrv Ctl Str whole 1; Danio rerio; RNA Seq", "GSM4196096", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196096", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Str_1_S56_R1_001.trimmed.fastq.gz", "fastq", 1578778770.0, 21026926.0, "GSM4196096 r1", "0:75.08 1:0", "A:402927986;C:380655464;G:355045267;T:440133814;N:16239", 75, 0, null, null, 402927986, 380655464, 355045267, 440133814, 16239, "SRX7232563", "SRS5733194", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95088, null, 0.13051, null, 0.69686, null, 0.48234, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55559, "SRR10550561", "SRX7232562", "SRS5733193", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 6", "GSM4196095", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 6", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196095", "GSM4196095: Lrv Ctl Bsal whole 6; Danio rerio; RNA Seq", "GSM4196095", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196095", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal_6_S67_R1_001.trimmed.fastq.gz", "fastq", 1996483532.0, 26552956.0, "GSM4196095 r1", "0:75.19 1:0", "A:486227608;C:499380161;G:458068110;T:552786593;N:21060", 75, 0, null, null, 486227608, 499380161, 458068110, 552786593, 21060, "SRX7232562", "SRS5733193", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95673, null, 0.10298, null, 0.68511, null, 0.46098, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55560, "SRR10550560", "SRX7232561", "SRS5733192", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 4", "GSM4196094", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 4", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196094", "GSM4196094: Lrv Ctl Bsal whole 4; Danio rerio; RNA Seq", "GSM4196094", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196094", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal_4_S54_R1_001.trimmed.fastq.gz", "fastq", 1827456990.0, 24323614.0, "GSM4196094 r1", "0:75.13 1:0", "A:482938455;C:430636548;G:401296463;T:512566219;N:19305", 75, 0, null, null, 482938455, 430636548, 401296463, 512566219, 19305, "SRX7232561", "SRS5733192", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.94602, null, 0.14275, null, 0.69777, null, 0.46678, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55561, "SRR10550559", "SRX7232560", "SRS5733191", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 3", "GSM4196093", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 3", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196093", "GSM4196093: Lrv Ctl Bsal whole 3; Danio rerio; RNA Seq", "GSM4196093", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196093", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal_3_S72_R1_001.trimmed.fastq.gz", "fastq", 1920853986.0, 25551216.0, "GSM4196093 r1", "0:75.18 1:0", "A:488636639;C:465699839;G:429574280;T:536923951;N:19277", 75, 0, null, null, 488636639, 465699839, 429574280, 536923951, 19277, "SRX7232560", "SRS5733191", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95469, null, 0.09186, null, 0.66373, null, 0.47662, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55562, "SRR10550558", "SRX7232559", "SRS5733190", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 2", "GSM4196092", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 2", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196092", "GSM4196092: Lrv Ctl Bsal whole 2; Danio rerio; RNA Seq", "GSM4196092", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196092", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal_2_S66_R1_001.trimmed.fastq.gz", "fastq", 1715077991.0, 22808137.0, "GSM4196092 r1", "0:75.20 1:0", "A:412795011;C:426393295;G:392381205;T:483491023;N:17457", 75, 0, null, null, 412795011, 426393295, 392381205, 483491023, 17457, "SRX7232559", "SRS5733190", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95866, null, 0.07909, null, 0.66352, null, 0.47768, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55563, "SRR10550557", "SRX7232558", "SRS5733189", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 1", "GSM4196091", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 1", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196091", "GSM4196091: Lrv Ctl Bsal whole 1; Danio rerio; RNA Seq", "GSM4196091", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196091", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal_1_S52_R1_001.trimmed.fastq.gz", "fastq", 1771075713.0, 23584154.0, "GSM4196091 r1", "0:75.10 1:0", "A:431209517;C:441715839;G:407237232;T:490894491;N:18634", 75, 0, null, null, 431209517, 441715839, 407237232, 490894491, 18634, "SRX7232558", "SRS5733189", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95568, null, 0.10232, null, 0.65904, null, 0.49156, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [55564, "SRR10550556", "SRX7232557", "SRS5733188", "SRP233586", "PRJNA592212", "Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults", "GSE141144", "Transcriptome Analysis", "Our previous study suggested persistent transgenerational effects of fluoxetine FLX exposure  in both environmental and therapeutic concentrations  on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects  we studied the effect of FLX on stress response in brain tissues telencephalon and hypothalamus of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response  we used a transgenic zebrafish line SR4G which are expressing green fluorescence protein GFP in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control  provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control Unstressed Cnt U  Control Stressed Cnt S  Fluoxetine Unstressed FLX U  and Fluoxetine Stressed FLX S using pools of larvae heads  telencephalon  and hypothalamus. post total RNA extraction  using Illumina technology all samples were sequence and the list of differentially expressed genes DEGs were produced using DSEQ pipeline in R. Overall design: Three different target tissue  two from 6 mpf adults Telencephalon and Hypothalamus and one from 6 dpf larvae dissected heads. One treatment  Fluoxetine  One control ethanol as vehicle  two condition Stressed  Unstressed", null, null, null, "Lrv Ctl Bsal whole 5", "GSM4196090", null, "source name:Lrv Ctl Bsal whole|genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "Lrv Ctl Bsal whole 5", "Illumina bcl2fastq v2.17.1.14 software used for basecalling. Sequenced reads were trimmed for adaptor sequence with CutAdapt  then aligned with STAR v 2.5 with parameter   clip5pNbases 10 and   quantMode TranscriptomeSAM GeneCounts. Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups. Genome build: GRCz11v92 Supplementary files format and content: tab delimited text files include raw count values for each sample.", "Lrv Ctl Bsal whole", "Exposing to Fluoxetine 54ug/L as treatment or Ethanol 0.0053% as vehicle from 0 dpf to 6 dpf in larvae", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer\u2019s protocol using 250ng of starting material.", null, "genotype/variation:SR4G transgenic|stress status:Bsal|drug status:Ctl|tissue:larvae head", "GSM4196090", "GSM4196090: Lrv Ctl Bsal whole 5; Danio rerio; RNA Seq", "GSM4196090", null, "1", "Qiagene miliamp total RNA extraction  column based Illumina TruSeq Stranded mRNA libraries were built following the manufacturer's protocol using 250ng of starting material.", "GEO Accession:GSM4196090", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233586", null, null, "Lrv_Ctl_Bsal__5_S60_R1_001.trimmed.fastq.gz", "fastq", 2072397830.0, 27567241.0, "GSM4196090 r1", "0:75.18 1:0", "A:499993390;C:522808790;G:477072306;T:572501982;N:21362", 75, 0, null, null, 499993390, 522808790, 477072306, 572501982, 21362, "SRX7232557", "SRS5733188", "SRA1003923", "GEO", "Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada", 1, 0.95652, null, 0.11456, null, 0.69384, null, 0.4738, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2019-11-27", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76963, "SRR25396266", "SRX21134300", "SRS18399045", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "ABwt rep3", "GSM7658116", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf|geo loc name:missing|collection date:missing", "ABwt rep3", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf", "GSM7658116", "GSM7658116: ABwt rep3; Danio rerio; RNA Seq", "GSM7658116 r1", "GSM7658116", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-WT_iii_NGS22-Y626_AH5MKYDSX5_S648_L002_R1_001.fastq.gz fbln1-WT_iii_NGS22-Y626_AH5MKYDSX5_S648_L002_R2_001.fastq.gz", "fastq fastq", 6634706556.0, 24788052.0, "GSM7658116 r1", "0:133.79 1:133.87", "A:1794257291;C:1506457485;G:1526166840;T:1807502501;N:322439", 133, 133, null, null, 1794257291, 1506457485, 1526166840, 1807502501, 322439, "SRX21134300", "SRS18399045", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.88742, 0.88401, 0.12393, 0.12124, 0.68306, 0.6832, 0.47859, 0.46588, 128, 128, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76964, "SRR25396267", "SRX21134299", "SRS18399044", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "ABwt rep2", "GSM7658115", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf|geo loc name:missing|collection date:missing", "ABwt rep2", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf", "GSM7658115", "GSM7658115: ABwt rep2; Danio rerio; RNA Seq", "GSM7658115 r1", "GSM7658115", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-WT-ii_NGS22-Y627_AH5MKYDSX5_S649_L002_R1_001.fastq.gz fbln1-WT-ii_NGS22-Y627_AH5MKYDSX5_S649_L002_R2_001.fastq.gz", "fastq fastq", 7071028989.0, 26154663.0, "GSM7658115 r1", "0:135.14 1:135.21", "A:1917429043;C:1600107106;G:1615290315;T:1937914414;N:288111", 135, 135, null, null, 1917429043, 1600107106, 1615290315, 1937914414, 288111, "SRX21134299", "SRS18399044", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.90352, 0.90003, 0.12911, 0.12614, 0.67929, 0.68016, 0.48562, 0.48784, 103, 103, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76965, "SRR25396268", "SRX21134298", "SRS18399042", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "ABwt rep1", "GSM7658114", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf|geo loc name:missing|collection date:missing", "ABwt rep1", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ABwt|time point:10 dpf", "GSM7658114", "GSM7658114: ABwt rep1; Danio rerio; RNA Seq", "GSM7658114 r1", "GSM7658114", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-WT-i_NGS22-Y625_AH5MKYDSX5_S647_L002_R1_001.fastq.gz fbln1-WT-i_NGS22-Y625_AH5MKYDSX5_S647_L002_R2_001.fastq.gz", "fastq fastq", 6970434611.0, 26052125.0, "GSM7658114 r1", "0:133.74 1:133.81", "A:1884921652;C:1582428412;G:1601771780;T:1900977711;N:335056", 133, 133, null, null, 1884921652, 1582428412, 1601771780, 1900977711, 335056, "SRX21134298", "SRS18399042", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.89264, 0.89039, 0.12573, 0.12308, 0.68734, 0.68834, 0.48102, 0.48212, 135, 135, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76966, "SRR25396269", "SRX21134297", "SRS18399043", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "fbln rep3", "GSM7658113", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf|geo loc name:missing|collection date:missing", "fbln rep3", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf", "GSM7658113", "GSM7658113: fbln rep3; Danio rerio; RNA Seq", "GSM7658113 r1", "GSM7658113", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-mu-iii_NGS22-Y630_AH5MKYDSX5_S652_L002_R1_001.fastq.gz fbln1-mu-iii_NGS22-Y630_AH5MKYDSX5_S652_L002_R2_001.fastq.gz", "fastq fastq", 7897839439.0, 29176341.0, "GSM7658113 r1", "0:135.32 1:135.37", "A:2124108601;C:1805125896;G:1825004607;T:2143248362;N:351973", 135, 135, null, null, 2124108601, 1805125896, 1825004607, 2143248362, 351973, "SRX21134297", "SRS18399043", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.90473, 0.90217, 0.11614, 0.1131, 0.66959, 0.66996, 0.48247, 0.48066, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76967, "SRR25396270", "SRX21134296", "SRS18399041", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "fbln rep2", "GSM7658112", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf|geo loc name:missing|collection date:missing", "fbln rep2", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf", "GSM7658112", "GSM7658112: fbln rep2; Danio rerio; RNA Seq", "GSM7658112 r1", "GSM7658112", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-mu-ii_NGS22-Y628_AH5MKYDSX5_S650_L002_R1_001.fastq.gz fbln1-mu-ii_NGS22-Y628_AH5MKYDSX5_S650_L002_R2_001.fastq.gz", "fastq fastq", 6620926405.0, 24273768.0, "GSM7658112 r1", "0:136.35 1:136.41", "A:1779196105;C:1513133139;G:1531673859;T:1796617651;N:305651", 136, 136, null, null, 1779196105, 1513133139, 1531673859, 1796617651, 305651, "SRX21134296", "SRS18399041", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.90799, 0.90607, 0.10967, 0.10744, 0.66553, 0.66561, 0.48504, 0.48733, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"], [76968, "SRR25396271", "SRX21134295", "SRS18399040", "SRP451003", "PRJNA997901", "Zebrafish fbln1 mutant ulg075 larvae at 10dpf versus AB wt", "GSE238059", "Transcriptome Analysis", "We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae. Overall design: fbln1+/  parents were crossed  wt and fbln1 /  homozygous mutants were selected in three independant batches about 20 individuals/sample for extracting RNA and performing RNA Seq. Each mutant batch was compared to its wt siblings.", null, null, null, "fbln rep1", "GSM7658111", null, "source name:larvae heads|tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf|geo loc name:missing|collection date:missing", "fbln rep1", "Approximatively 20\u201325 M reads were sequenced per sample. The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels  Peltzer et al. 2020 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org; accessed 1 May 2020 Differential gene expression analysis was performed using the DESeq2 pipeline Love  Huber et al. 2014. Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Table counts fbln1/wt.csv containing individual counts: Ensembl gene Id  gene name fbln1 WT i R1 fbln1 WT ii R1 fbln1 WT iii R1 fbln1 mu i R1 fbln1 mu ii R1 fbln1 mu iii R1 Supplementary files format and content: Table fbln1/wt.csv containing:  Ensembl gene ID gene name log2FoldChange lfcSE stat pvalue padj Mu baseMean WT baseMean baseMean", "larvae heads", "Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS 222 Ethyl 3 aminobenzoate methane sulfonate; Merck  Overijse  Belgium  10dpf larvae were stored in RNA later Fisher Scientific  Merelbeek  Belgium. Individual fish were decapitated  the heads anterior of each individual were stored in a 96 well plate for later RNA extraction  whereas the body posterior was used for DNA extraction and genotyping using q PCR. Once the genotypes were known  the heads were recovered and pooled to constitute wt and fbln1 /  batches of 21 individuals.", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer\u2019s instructions.", "Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute  Liege  Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28\u00b0C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28  29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding  adult male and female zebrafish were set up in several breeding tanks  separated by a clear plastic wall. post the light was turned on the next morning  walls are removed  and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting  fertilized clean eggs are moved to Petri dishes and incubated at 28\u00b0C in E3 medium 5 mM Na Cl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4  0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf", "tissue:larvae heads|strain background:AB|genotype:ulg075|time point:10 dpf", "GSM7658111", "GSM7658111: fbln rep1; Danio rerio; RNA Seq", "GSM7658111 r1", "GSM7658111", "1", "Three independent batches of wt and fbln1 /  pooled heads n= 21controls & 21 mutants were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit Qiagen  Hilden  Germany. Samples were lysed in RLT+ buffer with \u03b2 mercaptoethanol Sigma Aldrich  St. Louis  MO  USA and homogenized at least 10 times with a 26 gauge needle in a 1 mL syringe. An amount of 22 \u03bcL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI Qiagen  Hilden  Germany to avoid DNA contamination. Quantity ng/\u03bcL and quality 260/280 and 260/230 ratios of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation  followed by 2 times pellet washing with 70% ethanol  and resuspended in 51 \u00b5L of RNAse free water and stored at \u221280 \u00b0C. The integrity of total RNA extracts was assessed using the BioAnalyzer Agilent  Santa Clara  CA  USA. RIN RNA integrity number scores were > 9 for each sample. From the mRNAs extracted from wt and fbln1 mutants  the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit Illumina  San Diego  CA  USA according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP451003", null, "loader:fastq load.py", "fbln1-mu_i_NGS22-Y629_AH5MKYDSX5_S651_L002_R1_001.fastq.gz fbln1-mu_i_NGS22-Y629_AH5MKYDSX5_S651_L002_R2_001.fastq.gz", "fastq fastq", 6961206835.0, 25675483.0, "GSM7658111 r1", "0:135.53 1:135.59", "A:1873338006;C:1589509564;G:1608298056;T:1889789695;N:271514", 135, 135, null, null, 1873338006, 1589509564, 1608298056, 1889789695, 271514, "SRX21134295", "SRS18399040", "SRA1678716", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", "Organogenesis and Regeneration, Life Sciences, Universit\u00e9 de Li\u00e8ge", 2, 0.9041, 0.90203, 0.11033, 0.10785, 0.66776, 0.66906, 0.4888, 0.47976, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-07-24", "Multi-stage", "Multi-stage", "Head", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 90, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Multi-stage", "p1": "Head"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "cDNA", "label": "cDNA", "count": 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"toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "Embryo", "label": "Embryo", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&devstage_curation_coarse=Multi-stage", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Head", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "Nervous System", "label": "Nervous System", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&tissue_curation_coarse=Nervous+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "Head", "label": "Head", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head", "results": [{"value": "unknown", "label": "unknown", "count": 86, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&technology=unknown", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&tissue_curation=Head&technology=smartseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 111.2363090069266}