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
60257,SRR12194979,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L001_R1_001.fastq.gz P6-1_S19_L001_R2_001.fastq.gz,fastq fastq,626505630.0,2077251.0,GSM4666897 r1,0:150.88 1:150.72,A:231784841;C:80425574;G:110085227;T:204102624;N:107364,150,150,,,231784841,80425574,110085227,204102624,107364,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00014,0.00014,0.00013,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60258,SRR12194980,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L002_R1_001.fastq.gz P6-1_S19_L002_R2_001.fastq.gz,fastq fastq,646447345.0,2143304.0,GSM4666897 r2,0:150.88 1:150.73,A:237189853;C:82748065;G:118625007;T:207787390;N:97030,150,150,,,237189853,82748065,118625007,207787390,97030,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00023,0.0002,0.00022,0.00019,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60259,SRR12194981,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L003_R1_001.fastq.gz P6-1_S19_L003_R2_001.fastq.gz,fastq fastq,603701501.0,2001537.0,GSM4666897 r3,0:150.88 1:150.74,A:223744015;C:77591778;G:105364702;T:196924362;N:76644,150,150,,,223744015,77591778,105364702,196924362,76644,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00018,0.00016,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60260,SRR12194982,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L004_R1_001.fastq.gz P6-1_S19_L004_R2_001.fastq.gz,fastq fastq,626999718.0,2078709.0,GSM4666897 r4,0:150.89 1:150.74,A:230679756;C:80184689;G:114353798;T:201714990;N:66485,150,150,,,230679756,80184689,114353798,201714990,66485,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00023,0.00014,0.00022,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60261,SRR12194975,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L001_R1_001.fastq.gz P5-6_S18_L001_R2_001.fastq.gz,fastq fastq,362632647.0,1202487.0,GSM4666896 r1,0:150.85 1:150.72,A:134187427;C:47593733;G:60920059;T:119870940;N:60488,150,150,,,134187427,47593733,60920059,119870940,60488,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00018,0.0001,0.00015,0.99997,0.99997,0.0,0.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60262,SRR12194976,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L002_R2_001.fastq.gz P5-6_S18_L002_R1_001.fastq.gz,fastq fastq,371328815.0,1231316.0,GSM4666896 r2,0:150.85 1:150.72,A:136045457;C:48493148;G:65714953;T:121017397;N:57860,150,150,,,136045457,48493148,65714953,121017397,57860,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00017,0.00014,0.00015,1.0,0.99997,,1.0,149,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60263,SRR12194977,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L003_R1_001.fastq.gz P5-6_S18_L003_R2_001.fastq.gz,fastq fastq,349651276.0,1159376.0,GSM4666896 r3,0:150.85 1:150.74,A:129571477;C:45879693;G:58514844;T:115645628;N:39634,150,150,,,129571477,45879693,58514844,115645628,39634,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,0.00018,0.0001,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60264,SRR12194978,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L004_R1_001.fastq.gz P5-6_S18_L004_R2_001.fastq.gz,fastq fastq,359741298.0,1192811.0,GSM4666896 r4,0:150.85 1:150.74,A:132192036;C:47006274;G:63129910;T:117375509;N:37569,150,150,,,132192036,47006274,63129910,117375509,37569,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00015,0.00014,0.00014,0.99995,1.0,0.0,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60265,SRR12194971,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L001_R1_001.fastq.gz P6-2_S20_L001_R2_001.fastq.gz,fastq fastq,767379925.0,2544544.0,GSM4666895 r1,0:150.86 1:150.72,A:285185142;C:99053157;G:127959880;T:255052821;N:128925,150,150,,,285185142,99053157,127959880,255052821,128925,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.0002,0.00014,0.00019,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60266,SRR12194972,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L002_R1_001.fastq.gz P6-2_S20_L002_R2_001.fastq.gz,fastq fastq,801048716.0,2656168.0,GSM4666895 r2,0:150.86 1:150.72,A:294948276;C:103019861;G:140485071;T:262473164;N:122344,150,150,,,294948276,103019861,140485071,262473164,122344,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00021,0.00014,0.0002,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60267,SRR12194973,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L003_R1_001.fastq.gz P6-2_S20_L003_R2_001.fastq.gz,fastq fastq,740955391.0,2456791.0,GSM4666895 r3,0:150.86 1:150.73,A:275837928;C:95675216;G:123037692;T:246311396;N:93159,150,150,,,275837928,95675216,123037692,246311396,93159,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,0.0003,0.00013,0.00029,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60268,SRR12194974,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L004_R1_001.fastq.gz P6-2_S20_L004_R2_001.fastq.gz,fastq fastq,776243814.0,2573716.0,GSM4666895 r4,0:150.86 1:150.74,A:286702347;C:99810593;G:135079256;T:254574374;N:77244,150,150,,,286702347,99810593,135079256,254574374,77244,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00029,0.00021,0.00026,0.0002,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60269,SRR12194967,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L001_R2_001.fastq.gz P5-5_S17_L001_R1_001.fastq.gz,fastq fastq,818338842.0,2713477.0,GSM4666894 r1,0:150.86 1:150.72,A:301830002;C:107389155;G:139489598;T:269496153;N:133934,150,150,,,301830002,107389155,139489598,269496153,133934,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00019,0.00014,0.00018,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60270,SRR12194968,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L002_R1_001.fastq.gz P5-5_S17_L002_R2_001.fastq.gz,fastq fastq,846228975.0,2805930.0,GSM4666894 r2,0:150.86 1:150.72,A:308870822;C:110466773;G:152421867;T:274347549;N:121964,150,150,,,308870822,110466773,152421867,274347549,121964,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0002,0.00015,0.00018,0.00011,0.99997,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60271,SRR12194969,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L003_R2_001.fastq.gz P5-5_S17_L003_R1_001.fastq.gz,fastq fastq,790658387.0,2621591.0,GSM4666894 r3,0:150.86 1:150.73,A:292027450;C:103748394;G:134258887;T:260520383;N:103273,150,150,,,292027450,103748394,134258887,260520383,103273,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00016,0.00014,0.00013,0.00013,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60272,SRR12194970,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L004_R1_001.fastq.gz P5-5_S17_L004_R2_001.fastq.gz,fastq fastq,815907660.0,2705210.0,GSM4666894 r4,0:150.86 1:150.74,A:298609755;C:106483104;G:145958694;T:264775944;N:80163,150,150,,,298609755,106483104,145958694,264775944,80163,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00029,0.00012,0.00028,0.99997,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60273,SRR12194963,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L001_R1_001.fastq.gz P5-4_S16_L001_R2_001.fastq.gz,fastq fastq,700559459.0,2322745.0,GSM4666893 r1,0:150.89 1:150.72,A:258008915;C:91134331;G:124267705;T:227032496;N:116012,150,150,,,258008915,91134331,124267705,227032496,116012,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00017,0.00012,0.00016,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60274,SRR12194964,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L002_R2_001.fastq.gz P5-4_S16_L002_R1_001.fastq.gz,fastq fastq,728622859.0,2415726.0,GSM4666893 r2,0:150.89 1:150.73,A:265918573;C:94480694;G:135330434;T:232783961;N:109197,150,150,,,265918573,94480694,135330434,232783961,109197,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00022,0.00014,0.00021,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60275,SRR12194965,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L003_R1_001.fastq.gz P5-4_S16_L003_R2_001.fastq.gz,fastq fastq,676046027.0,2241356.0,GSM4666893 r3,0:150.89 1:150.74,A:249345303;C:88016423;G:119300461;T:219299203;N:84637,150,150,,,249345303,88016423,119300461,219299203,84637,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00022,0.00024,0.00021,0.00023,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60276,SRR12194966,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L004_R1_001.fastq.gz P5-4_S16_L004_R2_001.fastq.gz,fastq fastq,703809171.0,2333304.0,GSM4666893 r4,0:150.89 1:150.75,A:257462138;C:91215734;G:129931298;T:225132059;N:67942,150,150,,,257462138,91215734,129931298,225132059,67942,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00022,0.00014,0.00021,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60277,SRR12194959,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L001_R1_001.fastq.gz P5-3_S15_L001_R2_001.fastq.gz,fastq fastq,875916606.0,2904546.0,GSM4666892 r1,0:150.85 1:150.72,A:323769382;C:115778670;G:148157089;T:288058377;N:153088,150,150,,,323769382,115778670,148157089,288058377,153088,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,9e-05,0.00014,6e-05,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60278,SRR12194960,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L002_R1_001.fastq.gz P5-3_S15_L002_R2_001.fastq.gz,fastq fastq,906266878.0,3005123.0,GSM4666892 r2,0:150.85 1:150.73,A:331841540;C:119200098;G:161492735;T:293597000;N:135505,150,150,,,331841540,119200098,161492735,293597000,135505,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00015,0.00013,0.00012,0.99997,0.99997,0.0,1.0,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60279,SRR12194961,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L003_R1_001.fastq.gz P5-3_S15_L003_R2_001.fastq.gz,fastq fastq,845425773.0,2803262.0,GSM4666892 r3,0:150.85 1:150.74,A:312923215;C:111769611;G:142528786;T:278100796;N:103365,150,150,,,312923215,111769611,142528786,278100796,103365,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00017,0.00018,0.00015,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60280,SRR12194962,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L004_R1_001.fastq.gz P5-3_S15_L004_R2_001.fastq.gz,fastq fastq,879089154.0,2914795.0,GSM4666892 r4,0:150.85 1:150.74,A:322802592;C:115646186;G:155527621;T:285023759;N:88996,150,150,,,322802592,115646186,155527621,285023759,88996,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00016,0.00014,0.00013,0.00013,0.99993,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60281,SRR12194955,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L001_R1_001.fastq.gz P5-2_S14_L001_R2_001.fastq.gz,fastq fastq,612289518.0,2030276.0,GSM4666891 r1,0:150.86 1:150.72,A:225461166;C:80840857;G:104624118;T:201255710;N:107667,150,150,,,225461166,80840857,104624118,201255710,107667,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00021,0.00014,0.00019,0.99995,0.99997,0.5,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60282,SRR12194956,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L002_R1_001.fastq.gz P5-2_S14_L002_R2_001.fastq.gz,fastq fastq,634607694.0,2104258.0,GSM4666891 r2,0:150.86 1:150.73,A:231299105;C:83482957;G:114131270;T:205602870;N:91492,150,150,,,231299105,83482957,114131270,205602870,91492,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00028,0.00014,0.00027,0.00013,1.0,1.0,,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60283,SRR12194957,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L003_R1_001.fastq.gz P5-2_S14_L003_R2_001.fastq.gz,fastq fastq,590348631.0,1957422.0,GSM4666891 r3,0:150.86 1:150.74,A:217666345;C:77986590;G:100434245;T:194187946;N:73505,150,150,,,217666345,77986590,100434245,194187946,73505,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00017,0.00014,0.00016,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60284,SRR12194958,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L004_R1_001.fastq.gz P5-2_S14_L004_R2_001.fastq.gz,fastq fastq,613280111.0,2033405.0,GSM4666891 r4,0:150.86 1:150.74,A:224142863;C:80650974;G:109510542;T:198916747;N:58985,150,150,,,224142863,80650974,109510542,198916747,58985,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00015,0.00016,0.00014,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60285,SRR12194951,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L001_R1_001.fastq.gz P5-1_S13_L001_R2_001.fastq.gz,fastq fastq,871269001.0,2888776.0,GSM4666890 r1,0:150.89 1:150.72,A:314795365;C:112414599;G:160314482;T:283594068;N:150487,150,150,,,314795365,112414599,160314482,283594068,150487,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00015,0.00012,0.00014,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60286,SRR12194952,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L002_R1_001.fastq.gz P5-1_S13_L002_R2_001.fastq.gz,fastq fastq,902501754.0,2992248.0,GSM4666890 r2,0:150.89 1:150.72,A:322645331;C:115934758;G:174818254;T:288967241;N:136170,150,150,,,322645331,115934758,174818254,288967241,136170,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00026,0.0001,0.00025,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60287,SRR12194953,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L003_R1_001.fastq.gz P5-1_S13_L003_R2_001.fastq.gz,fastq fastq,839686349.0,2783900.0,GSM4666890 r3,0:150.89 1:150.73,A:303601399;C:108395743;G:153892840;T:273690404;N:105963,150,150,,,303601399,108395743,153892840,273690404,105963,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00018,0.00011,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60288,SRR12194954,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L004_R1_001.fastq.gz P5-1_S13_L004_R2_001.fastq.gz,fastq fastq,872412889.0,2892296.0,GSM4666890 r4,0:150.89 1:150.74,A:312195512;C:111967601;G:168316892;T:279843866;N:89018,150,150,,,312195512,111967601,168316892,279843866,89018,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00021,0.00034,0.00018,0.00033,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60369,SRR12194867,SRX8707723,SRS6984310,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C4,GSM4666869,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666869,GSM4666869: adult whole brain C4; Danio rerio; Bisulfite Seq,GSM4666869,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666869,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-6_S24_L001_R1_001.fastq.gz P6-6_S24_L001_R2_001.fastq.gz,fastq fastq,304787189.0,1010584.0,GSM4666869 r1,0:150.87 1:150.73,A:111934026;C:39797760;G:53187383;T:99815969;N:52051,150,150,,,111934026,39797760,53187383,99815969,52051,SRX8707723,SRS6984310,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,0.00012,0.00013,9e-05,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60370,SRR12194868,SRX8707723,SRS6984310,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C4,GSM4666869,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666869,GSM4666869: adult whole brain C4; Danio rerio; Bisulfite Seq,GSM4666869,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666869,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-6_S24_L002_R1_001.fastq.gz P6-6_S24_L002_R2_001.fastq.gz,fastq fastq,314920656.0,1044164.0,GSM4666869 r2,0:150.87 1:150.73,A:114476348;C:40979530;G:57739426;T:101679643;N:45709,150,150,,,114476348,40979530,57739426,101679643,45709,SRX8707723,SRS6984310,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00021,0.0001,0.00018,0.99997,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60371,SRR12194869,SRX8707723,SRS6984310,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C4,GSM4666869,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666869,GSM4666869: adult whole brain C4; Danio rerio; Bisulfite Seq,GSM4666869,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666869,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-6_S24_L003_R1_001.fastq.gz P6-6_S24_L003_R2_001.fastq.gz,fastq fastq,292903128.0,971143.0,GSM4666869 r3,0:150.87 1:150.74,A:107673316;C:38265783;G:50933669;T:95993806;N:36554,150,150,,,107673316,38265783,50933669,95993806,36554,SRX8707723,SRS6984310,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,0.00014,8e-05,0.00013,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60372,SRR12194870,SRX8707723,SRS6984310,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C4,GSM4666869,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666869,GSM4666869: adult whole brain C4; Danio rerio; Bisulfite Seq,GSM4666869,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666869,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-6_S24_L004_R1_001.fastq.gz P6-6_S24_L004_R2_001.fastq.gz,fastq fastq,305220950.0,1011949.0,GSM4666869 r4,0:150.87 1:150.74,A:111184499;C:39677014;G:55707179;T:98622813;N:29445,150,150,,,111184499,39677014,55707179,98622813,29445,SRX8707723,SRS6984310,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00023,0.00017,0.0002,0.99997,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60373,SRR12194863,SRX8707722,SRS6984309,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C3,GSM4666868,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666868,GSM4666868: adult whole brain C3; Danio rerio; Bisulfite Seq,GSM4666868,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666868,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-5_S23_L001_R1_001.fastq.gz P6-5_S23_L001_R2_001.fastq.gz,fastq fastq,384086423.0,1273533.0,GSM4666868 r1,0:150.86 1:150.73,A:142127808;C:50033069;G:65777344;T:126084004;N:64198,150,150,,,142127808,50033069,65777344,126084004,64198,SRX8707722,SRS6984309,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00018,0.00018,0.00017,0.00016,1.0,0.99997,,1.0,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60374,SRR12194864,SRX8707722,SRS6984309,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C3,GSM4666868,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666868,GSM4666868: adult whole brain C3; Danio rerio; Bisulfite Seq,GSM4666868,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666868,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-5_S23_L002_R1_001.fastq.gz P6-5_S23_L002_R2_001.fastq.gz,fastq fastq,398629251.0,1321737.0,GSM4666868 r2,0:150.86 1:150.73,A:146113114;C:51731026;G:71688416;T:129043136;N:53559,150,150,,,146113114,51731026,71688416,129043136,53559,SRX8707722,SRS6984309,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00028,0.00016,0.00027,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60375,SRR12194865,SRX8707722,SRS6984309,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C3,GSM4666868,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666868,GSM4666868: adult whole brain C3; Danio rerio; Bisulfite Seq,GSM4666868,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666868,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-5_S23_L003_R1_001.fastq.gz P6-5_S23_L003_R2_001.fastq.gz,fastq fastq,371101497.0,1230425.0,GSM4666868 r3,0:150.86 1:150.74,A:137555478;C:48346781;G:63328538;T:121826568;N:44132,150,150,,,137555478,48346781,63328538,121826568,44132,SRX8707722,SRS6984309,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00028,0.00014,0.00023,1.0,0.99995,,0.5,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60376,SRR12194866,SRX8707722,SRS6984309,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C3,GSM4666868,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666868,GSM4666868: adult whole brain C3; Danio rerio; Bisulfite Seq,GSM4666868,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666868,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-5_S23_L004_R1_001.fastq.gz P6-5_S23_L004_R2_001.fastq.gz,fastq fastq,386042646.0,1279936.0,GSM4666868 r4,0:150.87 1:150.74,A:141836188;C:50092775;G:69024122;T:125051137;N:38424,150,150,,,141836188,50092775,69024122,125051137,38424,SRX8707722,SRS6984309,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00021,0.00034,0.00019,0.0003,0.99997,0.99995,1.0,0.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60377,SRR12194859,SRX8707721,SRS6984308,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C2,GSM4666867,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666867,GSM4666867: adult whole brain C2; Danio rerio; Bisulfite Seq,GSM4666867,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666867,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-4_S22_L001_R1_001.fastq.gz P6-4_S22_L001_R2_001.fastq.gz,fastq fastq,399102512.0,1323245.0,GSM4666867 r1,0:150.88 1:150.73,A:146809857;C:52048650;G:70826675;T:129350753;N:66577,150,150,,,146809857,52048650,70826675,129350753,66577,SRX8707721,SRS6984308,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,0.00023,0.00011,0.0002,0.99995,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60378,SRR12194860,SRX8707721,SRS6984308,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C2,GSM4666867,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666867,GSM4666867: adult whole brain C2; Danio rerio; Bisulfite Seq,GSM4666867,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666867,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-4_S22_L002_R1_001.fastq.gz P6-4_S22_L002_R2_001.fastq.gz,fastq fastq,417305040.0,1383581.0,GSM4666867 r2,0:150.88 1:150.73,A:152110329;C:54210434;G:77487609;T:133438411;N:58257,150,150,,,152110329,54210434,77487609,133438411,58257,SRX8707721,SRS6984308,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00024,0.00012,0.00021,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60379,SRR12194861,SRX8707721,SRS6984308,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C2,GSM4666867,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666867,GSM4666867: adult whole brain C2; Danio rerio; Bisulfite Seq,GSM4666867,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666867,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-4_S22_L003_R1_001.fastq.gz P6-4_S22_L003_R2_001.fastq.gz,fastq fastq,383950902.0,1272973.0,GSM4666867 r3,0:150.88 1:150.74,A:141466983;C:50127160;G:67790136;T:124523049;N:43574,150,150,,,141466983,50127160,67790136,124523049,43574,SRX8707721,SRS6984308,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00024,0.00028,0.00022,0.00027,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60380,SRR12194862,SRX8707721,SRS6984308,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C2,GSM4666867,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666867,GSM4666867: adult whole brain C2; Danio rerio; Bisulfite Seq,GSM4666867,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666867,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-4_S22_L004_R1_001.fastq.gz P6-4_S22_L004_R2_001.fastq.gz,fastq fastq,403741509.0,1338545.0,GSM4666867 r4,0:150.88 1:150.75,A:147522710;C:52413958;G:74494222;T:129270040;N:40579,150,150,,,147522710,52413958,74494222,129270040,40579,SRX8707721,SRS6984308,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00019,0.00012,0.00016,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60381,SRR12194855,SRX8707720,SRS6984307,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C1,GSM4666866,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666866,GSM4666866: adult whole brain C1; Danio rerio; Bisulfite Seq,GSM4666866,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666866,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-3_S21_L001_R1_001.fastq.gz P6-3_S21_L001_R2_001.fastq.gz,fastq fastq,472811076.0,1567808.0,GSM4666866 r1,0:150.85 1:150.72,A:174884663;C:61769393;G:78501350;T:157575062;N:80608,150,150,,,174884663,61769393,78501350,157575062,80608,SRX8707720,SRS6984307,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00016,0.00017,0.00015,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60382,SRR12194856,SRX8707720,SRS6984307,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C1,GSM4666866,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666866,GSM4666866: adult whole brain C1; Danio rerio; Bisulfite Seq,GSM4666866,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666866,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-3_S21_L002_R1_001.fastq.gz P6-3_S21_L002_R2_001.fastq.gz,fastq fastq,478337329.0,1586116.0,GSM4666866 r2,0:150.86 1:150.72,A:175366374;C:62311224;G:83072522;T:157517983;N:69226,150,150,,,175366374,62311224,83072522,157517983,69226,SRX8707720,SRS6984307,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00029,0.00033,0.00027,0.00031,0.99995,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60383,SRR12194857,SRX8707720,SRS6984307,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C1,GSM4666866,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666866,GSM4666866: adult whole brain C1; Danio rerio; Bisulfite Seq,GSM4666866,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666866,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-3_S21_L003_R1_001.fastq.gz P6-3_S21_L003_R2_001.fastq.gz,fastq fastq,456942158.0,1515111.0,GSM4666866 r3,0:150.86 1:150.73,A:169258998;C:59691317;G:75612919;T:152320341;N:58583,150,150,,,169258998,59691317,75612919,152320341,58583,SRX8707720,SRS6984307,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00026,0.00014,0.00021,0.99995,0.99995,0.0,1.0,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60384,SRR12194858,SRX8707720,SRS6984307,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain C1,GSM4666866,,tissue:adult whole brain|strain:AB line|generation:F2|Sex:female,adult whole brain C1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F2|Sex:F,GSM4666866,GSM4666866: adult whole brain C1; Danio rerio; Bisulfite Seq,GSM4666866,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666866,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-3_S21_L004_R1_001.fastq.gz P6-3_S21_L004_R2_001.fastq.gz,fastq fastq,463724824.0,1537541.0,GSM4666866 r4,0:150.86 1:150.74,A:170447296;C:60379582;G:80038557;T:152813727;N:45662,150,150,,,170447296,60379582,80038557,152813727,45662,SRX8707720,SRS6984307,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00022,0.00021,0.00021,0.0002,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60401,SRR12194835,SRX8707715,SRS6984302,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A12,GSM4666861,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666861,GSM4666861: adult whole brain A12; Danio rerio; Bisulfite Seq,GSM4666861,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666861,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-6_S12_L001_R1_001.fastq.gz P2-6_S12_L001_R2_001.fastq.gz,fastq fastq,640746216.0,2124831.0,GSM4666861 r1,0:150.82 1:150.73,A:232841363;C:90121064;G:115697548;T:201973307;N:112934,150,150,,,232841363,90121064,115697548,201973307,112934,SRX8707715,SRS6984302,SRA1097340,GEO,"UMR MARBEC, INRAE",2,8e-05,4e-05,7e-05,3e-05,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60402,SRR12194836,SRX8707715,SRS6984302,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A12,GSM4666861,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666861,GSM4666861: adult whole brain A12; Danio rerio; Bisulfite Seq,GSM4666861,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666861,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-6_S12_L002_R1_001.fastq.gz P2-6_S12_L002_R2_001.fastq.gz,fastq fastq,664662445.0,2204129.0,GSM4666861 r2,0:150.82 1:150.74,A:239827950;C:93145490;G:124837703;T:206752076;N:99226,150,150,,,239827950,93145490,124837703,206752076,99226,SRX8707715,SRS6984302,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,0.0001,8e-05,7e-05,0.99995,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60403,SRR12194837,SRX8707715,SRS6984302,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A12,GSM4666861,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666861,GSM4666861: adult whole brain A12; Danio rerio; Bisulfite Seq,GSM4666861,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666861,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-6_S12_L003_R1_001.fastq.gz P2-6_S12_L003_R2_001.fastq.gz,fastq fastq,617578973.0,2047884.0,GSM4666861 r3,0:150.82 1:150.75,A:224775230;C:86902706;G:111110211;T:194714512;N:76314,150,150,,,224775230,86902706,111110211,194714512,76314,SRX8707715,SRS6984302,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,4e-05,5e-05,3e-05,0.99997,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60404,SRR12194838,SRX8707715,SRS6984302,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A12,GSM4666861,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666861,GSM4666861: adult whole brain A12; Danio rerio; Bisulfite Seq,GSM4666861,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666861,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-6_S12_L004_R1_001.fastq.gz P2-6_S12_L004_R2_001.fastq.gz,fastq fastq,645401612.0,2140091.0,GSM4666861 r4,0:150.82 1:150.75,A:233571892;C:90350008;G:120516939;T:200896054;N:66719,150,150,,,233571892,90350008,120516939,200896054,66719,SRX8707715,SRS6984302,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,6e-05,0.00012,5e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60405,SRR12194831,SRX8707714,SRS6984301,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A11,GSM4666860,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666860,GSM4666860: adult whole brain A11; Danio rerio; Bisulfite Seq,GSM4666860,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666860,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-5_S11_L001_R1_001.fastq.gz P2-5_S11_L001_R2_001.fastq.gz,fastq fastq,436988378.0,1448917.0,GSM4666860 r1,0:150.86 1:150.74,A:157045714;C:60391982;G:80917455;T:138560122;N:73105,150,150,,,157045714,60391982,80917455,138560122,73105,SRX8707714,SRS6984301,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00016,0.00018,0.00015,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60406,SRR12194832,SRX8707714,SRS6984301,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A11,GSM4666860,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666860,GSM4666860: adult whole brain A11; Danio rerio; Bisulfite Seq,GSM4666860,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666860,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-5_S11_L002_R1_001.fastq.gz P2-5_S11_L002_R2_001.fastq.gz,fastq fastq,452799003.0,1501358.0,GSM4666860 r2,0:150.86 1:150.73,A:161245863;C:62451886;G:87267556;T:141761550;N:72148,150,150,,,161245863,62451886,87267556,141761550,72148,SRX8707714,SRS6984301,SRA1097340,GEO,"UMR MARBEC, INRAE",2,8e-05,7e-05,6e-05,6e-05,0.99997,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60407,SRR12194833,SRX8707714,SRS6984301,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A11,GSM4666860,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666860,GSM4666860: adult whole brain A11; Danio rerio; Bisulfite Seq,GSM4666860,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666860,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-5_S11_L003_R1_001.fastq.gz P2-5_S11_L003_R2_001.fastq.gz,fastq fastq,419431829.0,1390658.0,GSM4666860 r3,0:150.86 1:150.75,A:150986487;C:57981423;G:77253124;T:133159517;N:51278,150,150,,,150986487,57981423,77253124,133159517,51278,SRX8707714,SRS6984301,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,8e-05,0.00013,7e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60408,SRR12194834,SRX8707714,SRS6984301,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A11,GSM4666860,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666860,GSM4666860: adult whole brain A11; Danio rerio; Bisulfite Seq,GSM4666860,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666860,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-5_S11_L004_R1_001.fastq.gz P2-5_S11_L004_R2_001.fastq.gz,fastq fastq,439416765.0,1456871.0,GSM4666860 r4,0:150.86 1:150.75,A:157009035;C:60508877;G:84112587;T:137742173;N:44093,150,150,,,157009035,60508877,84112587,137742173,44093,SRX8707714,SRS6984301,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,8e-05,8e-05,7e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60409,SRR12194827,SRX8707713,SRS6984300,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A10,GSM4666859,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666859,GSM4666859: adult whole brain A10; Danio rerio; Bisulfite Seq,GSM4666859,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666859,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-4_S10_L001_R1_001.fastq.gz P2-4_S10_L001_R2_001.fastq.gz,fastq fastq,472327626.0,1566063.0,GSM4666859 r1,0:150.87 1:150.74,A:169093682;C:64056756;G:91936515;T:147158507;N:82166,150,150,,,169093682,64056756,91936515,147158507,82166,SRX8707713,SRS6984300,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,0.0001,0.00012,7e-05,0.99997,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60410,SRR12194828,SRX8707713,SRS6984300,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A10,GSM4666859,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666859,GSM4666859: adult whole brain A10; Danio rerio; Bisulfite Seq,GSM4666859,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666859,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-4_S10_L002_R1_001.fastq.gz P2-4_S10_L002_R2_001.fastq.gz,fastq fastq,484221591.0,1605467.0,GSM4666859 r2,0:150.87 1:150.74,A:171832392;C:65423954;G:98160401;T:148728893;N:75951,150,150,,,171832392,65423954,98160401,148728893,75951,SRX8707713,SRS6984300,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,8e-05,0.00011,7e-05,1.0,1.0,,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60411,SRR12194829,SRX8707713,SRS6984300,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A10,GSM4666859,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666859,GSM4666859: adult whole brain A10; Danio rerio; Bisulfite Seq,GSM4666859,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666859,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-4_S10_L003_R1_001.fastq.gz P2-4_S10_L003_R2_001.fastq.gz,fastq fastq,449533778.0,1490399.0,GSM4666859 r3,0:150.87 1:150.75,A:161225475;C:61017137;G:86970920;T:140264952;N:55294,150,150,,,161225475,61017137,86970920,140264952,55294,SRX8707713,SRS6984300,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,5e-05,0.00011,4e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60412,SRR12194830,SRX8707713,SRS6984300,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A10,GSM4666859,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666859,GSM4666859: adult whole brain A10; Danio rerio; Bisulfite Seq,GSM4666859,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666859,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-4_S10_L004_R1_001.fastq.gz P2-4_S10_L004_R2_001.fastq.gz,fastq fastq,467863400.0,1551114.0,GSM4666859 r4,0:150.87 1:150.76,A:166475662;C:63183052;G:94209111;T:143951772;N:43803,150,150,,,166475662,63183052,94209111,143951772,43803,SRX8707713,SRS6984300,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,3e-05,0.00014,2e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60413,SRR12194823,SRX8707712,SRS6984299,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A9,GSM4666858,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666858,GSM4666858: adult whole brain A9; Danio rerio; Bisulfite Seq,GSM4666858,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666858,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-3_S9_L001_R2_001.fastq.gz P2-3_S9_L001_R1_001.fastq.gz,fastq fastq,426627155.0,1414674.0,GSM4666858 r1,0:150.84 1:150.73,A:153172353;C:59496116;G:80358537;T:133527930;N:72219,150,150,,,153172353,59496116,80358537,133527930,72219,SRX8707712,SRS6984299,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,9e-05,9e-05,8e-05,0.99995,1.0,0.5,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60414,SRR12194824,SRX8707712,SRS6984299,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A9,GSM4666858,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666858,GSM4666858: adult whole brain A9; Danio rerio; Bisulfite Seq,GSM4666858,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666858,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-3_S9_L002_R1_001.fastq.gz P2-3_S9_L002_R2_001.fastq.gz,fastq fastq,439419220.0,1457078.0,GSM4666858 r2,0:150.84 1:150.74,A:156019225;C:61040122;G:86757381;T:135536016;N:66476,150,150,,,156019225,61040122,86757381,135536016,66476,SRX8707712,SRS6984299,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,7e-05,9e-05,6e-05,1.0,1.0,,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60415,SRR12194825,SRX8707712,SRS6984299,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A9,GSM4666858,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666858,GSM4666858: adult whole brain A9; Danio rerio; Bisulfite Seq,GSM4666858,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666858,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-3_S9_L003_R1_001.fastq.gz P2-3_S9_L003_R2_001.fastq.gz,fastq fastq,410972632.0,1362670.0,GSM4666858 r3,0:150.84 1:150.75,A:147790443;C:57336660;G:76947855;T:128851133;N:46541,150,150,,,147790443,57336660,76947855,128851133,46541,SRX8707712,SRS6984299,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,8e-05,0.00018,7e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60416,SRR12194826,SRX8707712,SRS6984299,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A9,GSM4666858,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666858,GSM4666858: adult whole brain A9; Danio rerio; Bisulfite Seq,GSM4666858,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666858,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-3_S9_L004_R1_001.fastq.gz P2-3_S9_L004_R2_001.fastq.gz,fastq fastq,424633765.0,1407946.0,GSM4666858 r4,0:150.85 1:150.75,A:151303507;C:58922267;G:83095120;T:131270666;N:42205,150,150,,,151303507,58922267,83095120,131270666,42205,SRX8707712,SRS6984299,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,6e-05,0.0001,5e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60417,SRR12194819,SRX8707711,SRS6984297,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A7,GSM4666857,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A7,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666857,GSM4666857: adult whole brain A7; Danio rerio; Bisulfite Seq,GSM4666857,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666857,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-1_S7_L001_R1_001.fastq.gz P2-1_S7_L001_R2_001.fastq.gz,fastq fastq,562178616.0,1864206.0,GSM4666857 r1,0:150.83 1:150.73,A:201731345;C:78993282;G:104786180;T:176566787;N:101022,150,150,,,201731345,78993282,104786180,176566787,101022,SRX8707711,SRS6984297,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,0.00012,7e-05,9e-05,0.99995,0.99997,0.5,1.0,151,149,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60418,SRR12194820,SRX8707711,SRS6984297,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A7,GSM4666857,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A7,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666857,GSM4666857: adult whole brain A7; Danio rerio; Bisulfite Seq,GSM4666857,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666857,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-1_S7_L002_R1_001.fastq.gz P2-1_S7_L002_R2_001.fastq.gz,fastq fastq,583782947.0,1935839.0,GSM4666857 r2,0:150.83 1:150.73,A:207850069;C:81713244;G:113177983;T:180953566;N:88085,150,150,,,207850069,81713244,113177983,180953566,88085,SRX8707711,SRS6984297,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,6e-05,0.00018,5e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60419,SRR12194821,SRX8707711,SRS6984297,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A7,GSM4666857,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A7,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666857,GSM4666857: adult whole brain A7; Danio rerio; Bisulfite Seq,GSM4666857,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666857,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-1_S7_L003_R1_001.fastq.gz P2-1_S7_L003_R2_001.fastq.gz,fastq fastq,540880454.0,1793475.0,GSM4666857 r3,0:150.83 1:150.75,A:194456709;C:75999836;G:100275578;T:170081362;N:66969,150,150,,,194456709,75999836,100275578,170081362,66969,SRX8707711,SRS6984297,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,9e-05,5e-05,8e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60420,SRR12194822,SRX8707711,SRS6984297,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A7,GSM4666857,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A7,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666857,GSM4666857: adult whole brain A7; Danio rerio; Bisulfite Seq,GSM4666857,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666857,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P2-1_S7_L004_R1_001.fastq.gz P2-1_S7_L004_R2_001.fastq.gz,fastq fastq,567088994.0,1880337.0,GSM4666857 r4,0:150.84 1:150.75,A:202451049;C:79290317;G:109339678;T:175945650;N:62300,150,150,,,202451049,79290317,109339678,175945650,62300,SRX8707711,SRS6984297,SRA1097340,GEO,"UMR MARBEC, INRAE",2,9e-05,3e-05,7e-05,2e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60421,SRR12194815,SRX8707710,SRS6984298,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A6,GSM4666856,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A6,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666856,GSM4666856: adult whole brain A6; Danio rerio; Bisulfite Seq,GSM4666856,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666856,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-6_S6_L001_R1_001.fastq.gz P1-6_S6_L001_R2_001.fastq.gz,fastq fastq,489634420.0,1623466.0,GSM4666856 r1,0:150.84 1:150.76,A:169904776;C:71730566;G:104670501;T:143242668;N:85909,150,150,,,169904776,71730566,104670501,143242668,85909,SRX8707710,SRS6984298,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,4e-05,0.00011,3e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60422,SRR12194816,SRX8707710,SRS6984298,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A6,GSM4666856,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A6,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666856,GSM4666856: adult whole brain A6; Danio rerio; Bisulfite Seq,GSM4666856,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666856,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-6_S6_L002_R1_001.fastq.gz P1-6_S6_L002_R2_001.fastq.gz,fastq fastq,499486382.0,1656086.0,GSM4666856 r2,0:150.85 1:150.76,A:171888163;C:72895209;G:110598997;T:144029221;N:74792,150,150,,,171888163,72895209,110598997,144029221,74792,SRX8707710,SRS6984298,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,4e-05,8e-05,3e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60423,SRR12194817,SRX8707710,SRS6984298,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A6,GSM4666856,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A6,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666856,GSM4666856: adult whole brain A6; Danio rerio; Bisulfite Seq,GSM4666856,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666856,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-6_S6_L003_R1_001.fastq.gz P1-6_S6_L003_R2_001.fastq.gz,fastq fastq,470521343.0,1560012.0,GSM4666856 r3,0:150.84 1:150.77,A:163585269;C:69013684;G:99907189;T:137958321;N:56880,150,150,,,163585269,69013684,99907189,137958321,56880,SRX8707710,SRS6984298,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,6e-05,0.00013,5e-05,1.0,1.0,,,151,149,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60424,SRR12194818,SRX8707710,SRS6984298,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A6,GSM4666856,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A6,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666856,GSM4666856: adult whole brain A6; Danio rerio; Bisulfite Seq,GSM4666856,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666856,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-6_S6_L004_R1_001.fastq.gz P1-6_S6_L004_R2_001.fastq.gz,fastq fastq,483995197.0,1604628.0,GSM4666856 r4,0:150.85 1:150.78,A:167039222;C:70561144;G:106459549;T:139889902;N:45380,150,150,,,167039222,70561144,106459549,139889902,45380,SRX8707710,SRS6984298,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,7e-05,7e-05,4e-05,0.99997,0.99997,0.0,0.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60425,SRR12194811,SRX8707709,SRS6984295,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A5,GSM4666855,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A5,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666855,GSM4666855: adult whole brain A5; Danio rerio; Bisulfite Seq,GSM4666855,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666855,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-5_S5_L001_R1_001.fastq.gz P1-5_S5_L001_R2_001.fastq.gz,fastq fastq,877780260.0,2910964.0,GSM4666855 r1,0:150.79 1:150.75,A:308609985;C:131328298;G:175534425;T:262153765;N:153787,150,150,,,308609985,131328298,175534425,262153765,153787,SRX8707709,SRS6984295,SRA1097340,GEO,"UMR MARBEC, INRAE",2,6e-05,0.00011,3e-05,0.0001,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60426,SRR12194812,SRX8707709,SRS6984295,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A5,GSM4666855,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A5,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666855,GSM4666855: adult whole brain A5; Danio rerio; Bisulfite Seq,GSM4666855,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666855,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-5_S5_L002_R1_001.fastq.gz P1-5_S5_L002_R2_001.fastq.gz,fastq fastq,906544389.0,3006326.0,GSM4666855 r2,0:150.79 1:150.76,A:316664055;C:134985583;G:187530653;T:267229970;N:134128,150,150,,,316664055,134985583,187530653,267229970,134128,SRX8707709,SRS6984295,SRA1097340,GEO,"UMR MARBEC, INRAE",2,5e-05,2e-05,4e-05,1e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60427,SRR12194813,SRX8707709,SRS6984295,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A5,GSM4666855,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A5,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666855,GSM4666855: adult whole brain A5; Danio rerio; Bisulfite Seq,GSM4666855,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666855,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-5_S5_L003_R1_001.fastq.gz P1-5_S5_L003_R2_001.fastq.gz,fastq fastq,846202905.0,2806060.0,GSM4666855 r3,0:150.79 1:150.77,A:298081907;C:126636508;G:168480038;T:252900807;N:103645,150,150,,,298081907,126636508,168480038,252900807,103645,SRX8707709,SRS6984295,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,6e-05,6e-05,5e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60428,SRR12194814,SRX8707709,SRS6984295,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A5,GSM4666855,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:male,adult whole brain A5,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:M,GSM4666855,GSM4666855: adult whole brain A5; Danio rerio; Bisulfite Seq,GSM4666855,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666855,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-5_S5_L004_R1_001.fastq.gz P1-5_S5_L004_R2_001.fastq.gz,fastq fastq,880353400.0,2919271.0,GSM4666855 r4,0:150.79 1:150.77,A:308539383;C:130948816;G:180994838;T:259781089;N:89274,150,150,,,308539383,130948816,180994838,259781089,89274,SRX8707709,SRS6984295,SRA1097340,GEO,"UMR MARBEC, INRAE",2,8e-05,2e-05,5e-05,1e-05,0.99995,1.0,0.5,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60429,SRR12194807,SRX8707708,SRS6984296,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A4,GSM4666854,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666854,GSM4666854: adult whole brain A4; Danio rerio; Bisulfite Seq,GSM4666854,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666854,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-4_S4_L001_R1_001.fastq.gz P1-4_S4_L001_R2_001.fastq.gz,fastq fastq,737430312.0,2445429.0,GSM4666854 r1,0:150.80 1:150.76,A:260676055;C:109498384;G:150060776;T:217057822;N:137275,150,150,,,260676055,109498384,150060776,217057822,137275,SRX8707708,SRS6984296,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,2e-05,6e-05,1e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60430,SRR12194808,SRX8707708,SRS6984296,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A4,GSM4666854,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666854,GSM4666854: adult whole brain A4; Danio rerio; Bisulfite Seq,GSM4666854,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666854,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-4_S4_L002_R1_001.fastq.gz P1-4_S4_L002_R2_001.fastq.gz,fastq fastq,765749034.0,2539327.0,GSM4666854 r2,0:150.80 1:150.76,A:269190178;C:112988673;G:161626782;T:221820763;N:122638,150,150,,,269190178,112988673,161626782,221820763,122638,SRX8707708,SRS6984296,SRA1097340,GEO,"UMR MARBEC, INRAE",2,8e-05,4e-05,7e-05,3e-05,1.0,1.0,,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60431,SRR12194809,SRX8707708,SRS6984296,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A4,GSM4666854,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666854,GSM4666854: adult whole brain A4; Danio rerio; Bisulfite Seq,GSM4666854,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666854,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-4_S4_L003_R1_001.fastq.gz P1-4_S4_L003_R2_001.fastq.gz,fastq fastq,711503553.0,2359291.0,GSM4666854 r3,0:150.80 1:150.78,A:252019664;C:105669770;G:144162151;T:209562610;N:89358,150,150,,,252019664,105669770,144162151,209562610,89358,SRX8707708,SRS6984296,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,0.0001,9e-05,7e-05,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60432,SRR12194810,SRX8707708,SRS6984296,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A4,GSM4666854,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A4,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666854,GSM4666854: adult whole brain A4; Danio rerio; Bisulfite Seq,GSM4666854,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666854,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-4_S4_L004_R1_001.fastq.gz P1-4_S4_L004_R2_001.fastq.gz,fastq fastq,745537173.0,2472098.0,GSM4666854 r4,0:150.80 1:150.78,A:263030957;C:109923652;G:156233032;T:216273154;N:76378,150,150,,,263030957,109923652,156233032,216273154,76378,SRX8707708,SRS6984296,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,5e-05,6e-05,4e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60433,SRR12194803,SRX8707707,SRS6984293,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A3,GSM4666853,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666853,GSM4666853: adult whole brain A3; Danio rerio; Bisulfite Seq,GSM4666853,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666853,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-3_S3_L001_R1_001.fastq.gz P1-3_S3_L001_R2_001.fastq.gz,fastq fastq,646807540.0,2144570.0,GSM4666853 r1,0:150.85 1:150.75,A:224617528;C:93801236;G:137614309;T:190660229;N:114238,150,150,,,224617528,93801236,137614309,190660229,114238,SRX8707707,SRS6984293,SRA1097340,GEO,"UMR MARBEC, INRAE",2,6e-05,8e-05,5e-05,7e-05,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60434,SRR12194804,SRX8707707,SRS6984293,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A3,GSM4666853,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666853,GSM4666853: adult whole brain A3; Danio rerio; Bisulfite Seq,GSM4666853,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666853,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-3_S3_L002_R1_001.fastq.gz P1-3_S3_L002_R2_001.fastq.gz,fastq fastq,653902746.0,2168053.0,GSM4666853 r2,0:150.85 1:150.76,A:225479903;C:94737251;G:143111777;T:190476413;N:97402,150,150,,,225479903,94737251,143111777,190476413,97402,SRX8707707,SRS6984293,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,4e-05,0.00013,3e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60435,SRR12194805,SRX8707707,SRS6984293,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A3,GSM4666853,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666853,GSM4666853: adult whole brain A3; Danio rerio; Bisulfite Seq,GSM4666853,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666853,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-3_S3_L003_R1_001.fastq.gz P1-3_S3_L003_R2_001.fastq.gz,fastq fastq,621576186.0,2060766.0,GSM4666853 r3,0:150.85 1:150.77,A:216203295;C:90251819;G:131484669;T:183565315;N:71088,150,150,,,216203295,90251819,131484669,183565315,71088,SRX8707707,SRS6984293,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,0.00012,6e-05,7e-05,1.0,0.99995,,1.0,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60436,SRR12194806,SRX8707707,SRS6984293,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A3,GSM4666853,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A3,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666853,GSM4666853: adult whole brain A3; Danio rerio; Bisulfite Seq,GSM4666853,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666853,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-3_S3_L004_R1_001.fastq.gz P1-3_S3_L004_R2_001.fastq.gz,fastq fastq,634384753.0,2103173.0,GSM4666853 r4,0:150.85 1:150.78,A:219261165;C:91765652;G:138134079;T:185161568;N:62289,150,150,,,219261165,91765652,138134079,185161568,62289,SRX8707707,SRS6984293,SRA1097340,GEO,"UMR MARBEC, INRAE",2,7e-05,3e-05,6e-05,2e-05,1.0,1.0,,,150,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60437,SRR12194799,SRX8707706,SRS6984292,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A2,GSM4666852,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666852,GSM4666852: adult whole brain A2; Danio rerio; Bisulfite Seq,GSM4666852,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666852,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-2_S2_L001_R1_001.fastq.gz P1-2_S2_L001_R2_001.fastq.gz,fastq fastq,674312084.0,2235920.0,GSM4666852 r1,0:150.83 1:150.75,A:233471238;C:98626549;G:139882191;T:202216602;N:115504,150,150,,,233471238,98626549,139882191,202216602,115504,SRX8707706,SRS6984292,SRA1097340,GEO,"UMR MARBEC, INRAE",2,8e-05,5e-05,5e-05,2e-05,0.99995,0.99997,0.5,0.0,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60438,SRR12194800,SRX8707706,SRS6984292,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A2,GSM4666852,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666852,GSM4666852: adult whole brain A2; Danio rerio; Bisulfite Seq,GSM4666852,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666852,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-2_S2_L002_R1_001.fastq.gz P1-2_S2_L002_R2_001.fastq.gz,fastq fastq,685535725.0,2273149.0,GSM4666852 r2,0:150.83 1:150.75,A:235196480;C:100001970;G:147523309;T:202710409;N:103557,150,150,,,235196480,100001970,147523309,202710409,103557,SRX8707706,SRS6984292,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,6e-05,0.00013,3e-05,0.99995,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60439,SRR12194801,SRX8707706,SRS6984292,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A2,GSM4666852,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666852,GSM4666852: adult whole brain A2; Danio rerio; Bisulfite Seq,GSM4666852,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666852,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-2_S2_L003_R1_001.fastq.gz P1-2_S2_L003_R2_001.fastq.gz,fastq fastq,649874864.0,2154785.0,GSM4666852 r3,0:150.83 1:150.76,A:225328142;C:95087428;G:134167545;T:195210744;N:81005,150,150,,,225328142,95087428,134167545,195210744,81005,SRX8707706,SRS6984292,SRA1097340,GEO,"UMR MARBEC, INRAE",2,6e-05,3e-05,5e-05,2e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60440,SRR12194802,SRX8707706,SRS6984292,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A2,GSM4666852,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A2,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666852,GSM4666852: adult whole brain A2; Danio rerio; Bisulfite Seq,GSM4666852,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666852,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-2_S2_L004_R1_001.fastq.gz P1-2_S2_L004_R2_001.fastq.gz,fastq fastq,667039830.0,2211665.0,GSM4666852 r4,0:150.83 1:150.77,A:229300148;C:97169102;G:142943693;T:197557082;N:69805,150,150,,,229300148,97169102,142943693,197557082,69805,SRX8707706,SRS6984292,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0001,5e-05,8e-05,4e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60441,SRR12194795,SRX8707705,SRS6984294,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A1,GSM4666851,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666851,GSM4666851: adult whole brain A1; Danio rerio; Bisulfite Seq,GSM4666851,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666851,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-1_S1_L001_R1_001.fastq.gz P1-1_S1_L001_R2_001.fastq.gz,fastq fastq,421741776.0,1398549.0,GSM4666851 r1,0:150.80 1:150.76,A:146413784;C:62322273;G:86992891;T:125941006;N:71822,150,150,,,146413784,62322273,86992891,125941006,71822,SRX8707705,SRS6984294,SRA1097340,GEO,"UMR MARBEC, INRAE",2,4e-05,7e-05,3e-05,6e-05,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60442,SRR12194796,SRX8707705,SRS6984294,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A1,GSM4666851,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666851,GSM4666851: adult whole brain A1; Danio rerio; Bisulfite Seq,GSM4666851,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666851,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-1_S1_L002_R1_001.fastq.gz P1-1_S1_L002_R2_001.fastq.gz,fastq fastq,427738309.0,1418439.0,GSM4666851 r2,0:150.80 1:150.76,A:147231548;C:62922192;G:91488053;T:126029401;N:67115,150,150,,,147231548,62922192,91488053,126029401,67115,SRX8707705,SRS6984294,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,4e-05,9e-05,3e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60443,SRR12194797,SRX8707705,SRS6984294,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A1,GSM4666851,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666851,GSM4666851: adult whole brain A1; Danio rerio; Bisulfite Seq,GSM4666851,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666851,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-1_S1_L003_R1_001.fastq.gz P1-1_S1_L003_R2_001.fastq.gz,fastq fastq,406395478.0,1347584.0,GSM4666851 r3,0:150.80 1:150.77,A:141318076;C:60076033;G:83431577;T:121517303;N:52489,150,150,,,141318076,60076033,83431577,121517303,52489,SRX8707705,SRS6984294,SRA1097340,GEO,"UMR MARBEC, INRAE",2,5e-05,4e-05,2e-05,3e-05,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60444,SRR12194798,SRX8707705,SRS6984294,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain A1,GSM4666851,,tissue:adult whole brain|strain:AB line|generation:F0|Sex:female,adult whole brain A1,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F0|Sex:F,GSM4666851,GSM4666851: adult whole brain A1; Danio rerio; Bisulfite Seq,GSM4666851,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666851,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P1-1_S1_L004_R1_001.fastq.gz P1-1_S1_L004_R2_001.fastq.gz,fastq fastq,417294088.0,1383697.0,GSM4666851 r4,0:150.80 1:150.78,A:144035710;C:61366274;G:88744512;T:123101060;N:46532,150,150,,,144035710,61366274,88744512,123101060,46532,SRX8707705,SRS6984294,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,0.0,8e-05,0.0,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System