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 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.,,pubmed:29666124,,mpo RNAseqnuclear +mifNRas+ 2,GSM2535110,,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 μM 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 μM 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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002.,,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 μM 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,,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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for 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,,SRP101781,,,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,,,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,,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.,,pubmed:29666124,,mpo RNAseqnuclear +mifNRas+ 1,GSM2535109,,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 μM 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 μM 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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002.,,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 μM 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,,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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for 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,,SRP101781,,,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,,,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,,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.,,pubmed:29666124,,mpo RNAseqnuclear mifcntrl 2,GSM2535108,,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 μM 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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002.,,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,,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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for 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,,SRP101781,,,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,,,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,,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.,,pubmed:29666124,,mpo RNAseqnuclear mifcntrl 1,GSM2535107,,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 μM 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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002.,,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,,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 MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL 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 °C 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 °C. 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® 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 – 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™ 500 High Output Kit for 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,,SRP101781,,,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,,,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,,United Kingdom,2017-03-13,Multi-stage,Multi-stage,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,,,,Lrv FLX Str whole 6,GSM4196113,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,438989346,397147842,367576938,463905385,17497,SRX7232580,SRS5733210,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.94774,,0.13955,,0.69842,,0.47883,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Str whole 5,GSM4196112,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,404424623,427018922,386032112,465200972,17495,SRX7232579,SRS5733211,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95782,,0.11464,,0.69404,,0.47678,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Str whole 4,GSM4196111,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,267171751,268993662,244811629,306118431,11723,SRX7232578,SRS5733209,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95236,,0.12138,,0.69725,,0.46512,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Str whole 3,GSM4196110,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,442049125,388222499,359554341,462768582,16982,SRX7232577,SRS5733208,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.94763,,0.15049,,0.69875,,0.49665,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Str whole 2,GSM4196109,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,415549321,352941285,326282134,430564543,15386,SRX7232576,SRS5733207,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.94391,,0.16406,,0.69613,,0.48758,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Str whole 1,GSM4196108,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,391749194,388029990,350196422,442451463,16128,SRX7232575,SRS5733206,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95111,,0.1268,,0.69587,,0.47885,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 6,GSM4196107,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,454377540,446747596,411720425,506601808,18534,SRX7232574,SRS5733205,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95274,,0.12081,,0.67389,,0.47068,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 4,GSM4196106,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,455847939,444174899,406307504,495995239,19031,SRX7232573,SRS5733204,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.9537,,0.13958,,0.6929,,0.4996,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 3,GSM4196105,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,379743513,383792979,353602367,419825271,15558,SRX7232572,SRS5733203,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95655,,0.12079,,0.69666,,0.48202,,72,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 2,GSM4196104,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,356069261,366658372,336019907,402443848,15029,SRX7232571,SRS5733202,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95627,,0.11745,,0.697,,0.47178,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 1,GSM4196103,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,313269199,315319719,289025501,357254917,12473,SRX7232570,SRS5733201,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95224,,0.12115,,0.69749,,0.45972,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv FLX Bsal whole 5,GSM4196102,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,462562803,458171000,416821299,519691519,19161,SRX7232569,SRS5733200,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95278,,0.11954,,0.6871,,0.46728,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 6,GSM4196101,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,514272402,461987308,431480575,549528052,20039,SRX7232568,SRS5733199,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.94563,,0.13089,,0.68682,,0.47639,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 5,GSM4196100,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,478145766,489708772,441830545,529458428,18670,SRX7232567,SRS5733198,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95788,,0.13698,,0.69564,,0.50856,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 4,GSM4196099,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,426247799,401717650,370519308,462751124,16834,SRX7232566,SRS5733197,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95211,,0.11993,,0.68905,,0.47345,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 3,GSM4196098,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,527968641,529216046,482537279,588689313,22120,SRX7232565,SRS5733196,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95484,,0.12615,,0.69899,,0.48613,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 2,GSM4196097,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,324097251,321883043,297347816,364832719,13670,SRX7232564,SRS5733195,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95352,,0.12304,,0.70305,,0.47639,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Str whole 1,GSM4196096,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,402927986,380655464,355045267,440133814,16239,SRX7232563,SRS5733194,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95088,,0.13051,,0.69686,,0.48234,,71,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 6,GSM4196095,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,486227608,499380161,458068110,552786593,21060,SRX7232562,SRS5733193,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95673,,0.10298,,0.68511,,0.46098,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 4,GSM4196094,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,482938455,430636548,401296463,512566219,19305,SRX7232561,SRS5733192,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.94602,,0.14275,,0.69777,,0.46678,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 3,GSM4196093,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,488636639,465699839,429574280,536923951,19277,SRX7232560,SRS5733191,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95469,,0.09186,,0.66373,,0.47662,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 2,GSM4196092,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,412795011,426393295,392381205,483491023,17457,SRX7232559,SRS5733190,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95866,,0.07909,,0.66352,,0.47768,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 1,GSM4196091,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,431209517,441715839,407237232,490894491,18634,SRX7232558,SRS5733189,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95568,,0.10232,,0.65904,,0.49156,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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,,,,Lrv Ctl Bsal whole 5,GSM4196090,,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’s protocol using 250ng of starting material.,,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,,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,,SRP233586,,,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,,,499993390,522808790,477072306,572501982,21362,SRX7232557,SRS5733188,SRA1003923,GEO,"Mechanistic Studies Division Genomics Laboratory, Health Canada, Government of Canada",1,0.95652,,0.11456,,0.69384,,0.4738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,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.,,,,ABwt rep3,GSM7658116,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,1794257291,1506457485,1526166840,1807502501,322439,SRX21134300,SRS18399045,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,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.,,,,ABwt rep2,GSM7658115,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,1917429043,1600107106,1615290315,1937914414,288111,SRX21134299,SRS18399044,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,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.,,,,ABwt rep1,GSM7658114,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,1884921652,1582428412,1601771780,1900977711,335056,SRX21134298,SRS18399042,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,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.,,,,fbln rep3,GSM7658113,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,2124108601,1805125896,1825004607,2143248362,351973,SRX21134297,SRS18399043,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,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.,,,,fbln rep2,GSM7658112,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,1779196105,1513133139,1531673859,1796617651,305651,SRX21134296,SRS18399041,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,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.,,,,fbln rep1,GSM7658111,,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 20–25 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,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°C. 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°C 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 β 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 μL 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/μL 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 µL of RNAse free water and stored at −80 °C. 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP451003,,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,,,1873338006,1589509564,1608298056,1889789695,271514,SRX21134295,SRS18399040,SRA1678716,"Organogenesis and Regeneration, Life Sciences, Université de Liège","Organogenesis and Regeneration, Life Sciences, Université de Liège",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,,Belgium,2023-07-24,Multi-stage,Multi-stage,Head,Nervous System