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96 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Reduced Representation" and tissue_curation_coarse = "Nervous System"

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tissue_curation_coarse 1

  • Nervous System · 96 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Reduced Representation · 96 ✖

experiment.library_layout 1

  • SINGLE · 96 ✖

devstage_curation_coarse 1

devstage_curation 1

Link 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
60289 60289 SRR12194947 SRX8707743 SRS6984330 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 B8 GSM4666889   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B8 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 GSM4666889 GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq GSM4666889   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:GSM4666889 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-6_S21_L001_R1_001.fastq.gz fastq 417626188.0 2629267.0 GSM4666889 r1 0:158.84 1:0 A:125329533;C:27957391;G:102415231;T:161892676;N:31357 158 0     125329533 27957391 102415231 161892676 31357 SRX8707743 SRS6984330 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   1.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60290 60290 SRR12194948 SRX8707743 SRS6984330 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 B8 GSM4666889   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B8 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 GSM4666889 GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq GSM4666889   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:GSM4666889 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-6_S21_L002_R1_001.fastq.gz fastq 415442115.0 2616087.0 GSM4666889 r2 0:158.80 1:0 A:122606292;C:27299099;G:106611577;T:158894919;N:30228 158 0     122606292 27299099 106611577 158894919 30228 SRX8707743 SRS6984330 SRA1097340 GEO UMR MARBEC, INRAE 1 8e-05   7e-05   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60291 60291 SRR12194949 SRX8707743 SRS6984330 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 B8 GSM4666889   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B8 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 GSM4666889 GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq GSM4666889   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:GSM4666889 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-6_S21_L003_R1_001.fastq.gz fastq 406171247.0 2557027.0 GSM4666889 r3 0:158.85 1:0 A:122039816;C:27029008;G:99485556;T:157596787;N:20080 158 0     122039816 27029008 99485556 157596787 20080 SRX8707743 SRS6984330 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00015   0.99993   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60292 60292 SRR12194950 SRX8707743 SRS6984330 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 B8 GSM4666889   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B8 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 GSM4666889 GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq GSM4666889   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:GSM4666889 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-6_S21_L004_R1_001.fastq.gz fastq 403012952.0 2537671.0 GSM4666889 r4 0:158.81 1:0 A:119320681;C:26563373;G:102739543;T:154371029;N:18326 158 0     119320681 26563373 102739543 154371029 18326 SRX8707743 SRS6984330 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00015   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60293 60293 SRR12194943 SRX8707742 SRS6984329 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 B7 GSM4666888   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B7 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 GSM4666888 GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq GSM4666888   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:GSM4666888 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-5_S20_L001_R1_001.fastq.gz fastq 453584090.0 2854818.0 GSM4666888 r1 0:158.88 1:0 A:134523251;C:27892399;G:113216536;T:177918076;N:33828 158 0     134523251 27892399 113216536 177918076 33828 SRX8707742 SRS6984329 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00012   0.99997   0.0   156   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60294 60294 SRR12194944 SRX8707742 SRS6984329 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 B7 GSM4666888   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B7 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 GSM4666888 GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq GSM4666888   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:GSM4666888 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-5_S20_L002_R1_001.fastq.gz fastq 448807947.0 2824868.0 GSM4666888 r2 0:158.88 1:0 A:130879549;C:27153648;G:117060555;T:173683407;N:30788 158 0     130879549 27153648 117060555 173683407 30788 SRX8707742 SRS6984329 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00024   0.00021   0.99995   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60295 60295 SRR12194945 SRX8707742 SRS6984329 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 B7 GSM4666888   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B7 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 GSM4666888 GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq GSM4666888   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:GSM4666888 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-5_S20_L003_R1_001.fastq.gz fastq 441209232.0 2776904.0 GSM4666888 r3 0:158.89 1:0 A:130998380;C:26957645;G:109964778;T:173264823;N:23606 158 0     130998380 26957645 109964778 173264823 23606 SRX8707742 SRS6984329 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   0.00011   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60296 60296 SRR12194946 SRX8707742 SRS6984329 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 B7 GSM4666888   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B7 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 GSM4666888 GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq GSM4666888   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:GSM4666888 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-5_S20_L004_R1_001.fastq.gz fastq 436356072.0 2746435.0 GSM4666888 r4 0:158.88 1:0 A:127599502;C:26472498;G:112912306;T:169350791;N:20975 158 0     127599502 26472498 112912306 169350791 20975 SRX8707742 SRS6984329 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00018   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60297 60297 SRR12194939 SRX8707741 SRS6984328 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 B6 GSM4666887   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B6 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 GSM4666887 GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq GSM4666887   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:GSM4666887 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-4_S19_L001_R1_001.fastq.gz fastq 459581878.0 2892480.0 GSM4666887 r1 0:158.89 1:0 A:136418528;C:26773883;G:120246272;T:176109118;N:34077 158 0     136418528 26773883 120246272 176109118 34077 SRX8707741 SRS6984328 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00018   0.00016   0.99997   0.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60298 60298 SRR12194940 SRX8707741 SRS6984328 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 B6 GSM4666887   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B6 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 GSM4666887 GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq GSM4666887   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:GSM4666887 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-4_S19_L002_R1_001.fastq.gz fastq 454682038.0 2861730.0 GSM4666887 r2 0:158.88 1:0 A:132773130;C:26007993;G:124098378;T:171770508;N:32029 158 0     132773130 26007993 124098378 171770508 32029 SRX8707741 SRS6984328 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00015   0.99993   0.33333   151   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60299 60299 SRR12194941 SRX8707741 SRS6984328 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 B6 GSM4666887   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B6 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 GSM4666887 GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq GSM4666887   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:GSM4666887 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-4_S19_L003_R1_001.fastq.gz fastq 441949571.0 2781476.0 GSM4666887 r3 0:158.89 1:0 A:131402848;C:25700491;G:115149715;T:169675287;N:21230 158 0     131402848 25700491 115149715 169675287 21230 SRX8707741 SRS6984328 SRA1097340 GEO UMR MARBEC, INRAE 1 6e-05   5e-05   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60300 60300 SRR12194942 SRX8707741 SRS6984328 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 B6 GSM4666887   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B6 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 GSM4666887 GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq GSM4666887   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:GSM4666887 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-4_S19_L004_R1_001.fastq.gz fastq 436607676.0 2747936.0 GSM4666887 r4 0:158.89 1:0 A:127862911;C:25195779;G:117992550;T:165538093;N:18343 158 0     127862911 25195779 117992550 165538093 18343 SRX8707741 SRS6984328 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.00013   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60301 60301 SRR12194935 SRX8707740 SRS6984327 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 B5 GSM4666886   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B5 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 GSM4666886 GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq GSM4666886   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:GSM4666886 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-3_S18_L001_R1_001.fastq.gz fastq 302829362.0 1906514.0 GSM4666886 r1 0:158.84 1:0 A:89694994;C:19460989;G:76993935;T:116656111;N:23333 158 0     89694994 19460989 76993935 116656111 23333 SRX8707740 SRS6984327 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00022   0.00021   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60302 60302 SRR12194936 SRX8707740 SRS6984327 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 B5 GSM4666886   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B5 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 GSM4666886 GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq GSM4666886   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:GSM4666886 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-3_S18_L002_R1_001.fastq.gz fastq 299893208.0 1888319.0 GSM4666886 r2 0:158.81 1:0 A:87157111;C:18870988;G:80083677;T:113760899;N:20533 158 0     87157111 18870988 80083677 113760899 20533 SRX8707740 SRS6984327 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0003   0.00028   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60303 60303 SRR12194937 SRX8707740 SRS6984327 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 B5 GSM4666886   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B5 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 GSM4666886 GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq GSM4666886   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:GSM4666886 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-3_S18_L003_R1_001.fastq.gz fastq 294808074.0 1855987.0 GSM4666886 r3 0:158.84 1:0 A:87400489;C:18832328;G:74835505;T:113724113;N:15639 158 0     87400489 18832328 74835505 113724113 15639 SRX8707740 SRS6984327 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   0.00012   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60304 60304 SRR12194938 SRX8707740 SRS6984327 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 B5 GSM4666886   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B5 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 GSM4666886 GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq GSM4666886   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:GSM4666886 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-3_S18_L004_R1_001.fastq.gz fastq 290930278.0 1831782.0 GSM4666886 r4 0:158.82 1:0 A:84789368;C:18396243;G:77012622;T:110719520;N:12525 158 0     84789368 18396243 77012622 110719520 12525 SRX8707740 SRS6984327 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00024   0.0002   0.99995   0.33333   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60305 60305 SRR12194931 SRX8707739 SRS6984326 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 B4 GSM4666885   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B4 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 GSM4666885 GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq GSM4666885   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:GSM4666885 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-2_S17_L001_R1_001.fastq.gz fastq 375215607.0 2361864.0 GSM4666885 r1 0:158.86 1:0 A:112024323;C:24781235;G:92436169;T:145945302;N:28578 158 0     112024323 24781235 92436169 145945302 28578 SRX8707739 SRS6984326 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   0.0001   0.99995   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60306 60306 SRR12194932 SRX8707739 SRS6984326 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 B4 GSM4666885   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B4 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 GSM4666885 GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq GSM4666885   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:GSM4666885 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-2_S17_L002_R1_001.fastq.gz fastq 370428283.0 2331824.0 GSM4666885 r2 0:158.86 1:0 A:108805681;C:24009319;G:95364944;T:142223301;N:25038 158 0     108805681 24009319 95364944 142223301 25038 SRX8707739 SRS6984326 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60307 60307 SRR12194933 SRX8707739 SRS6984326 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 B4 GSM4666885   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B4 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 GSM4666885 GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq GSM4666885   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:GSM4666885 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-2_S17_L003_R1_001.fastq.gz fastq 364134844.0 2292107.0 GSM4666885 r3 0:158.86 1:0 A:108842586;C:23917958;G:89584932;T:141770665;N:18703 158 0     108842586 23917958 89584932 141770665 18703 SRX8707739 SRS6984326 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00014   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60308 60308 SRR12194934 SRX8707739 SRS6984326 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 B4 GSM4666885   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B4 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 GSM4666885 GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq GSM4666885   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:GSM4666885 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-2_S17_L004_R1_001.fastq.gz fastq 359261298.0 2261503.0 GSM4666885 r4 0:158.86 1:0 A:105806137;C:23327442;G:91805038;T:138304777;N:17904 158 0     105806137 23327442 91805038 138304777 17904 SRX8707739 SRS6984326 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00021   0.00019   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60309 60309 SRR12194927 SRX8707738 SRS6984325 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 B3 GSM4666884   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B3 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 GSM4666884 GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq GSM4666884   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:GSM4666884 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-1_S16_L001_R1_001.fastq.gz fastq 519733754.0 3271474.0 GSM4666884 r1 0:158.87 1:0 A:155037427;C:33300575;G:128899352;T:202457471;N:38929 158 0     155037427 33300575 128899352 202457471 38929 SRX8707738 SRS6984325 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00012   0.99995   0.33333   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60310 60310 SRR12194928 SRX8707738 SRS6984325 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 B3 GSM4666884   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B3 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 GSM4666884 GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq GSM4666884   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:GSM4666884 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-1_S16_L002_R1_001.fastq.gz fastq 514851816.0 3240814.0 GSM4666884 r2 0:158.86 1:0 A:151014256;C:32338266;G:133641006;T:197823476;N:34812 158 0     151014256 32338266 133641006 197823476 34812 SRX8707738 SRS6984325 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60311 60311 SRR12194929 SRX8707738 SRS6984325 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 B3 GSM4666884   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B3 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 GSM4666884 GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq GSM4666884   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:GSM4666884 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-1_S16_L003_R1_001.fastq.gz fastq 505305764.0 3180622.0 GSM4666884 r3 0:158.87 1:0 A:150924986;C:32216951;G:125139306;T:196997199;N:27322 158 0     150924986 32216951 125139306 196997199 27322 SRX8707738 SRS6984325 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00017   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60312 60312 SRR12194930 SRX8707738 SRS6984325 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 B3 GSM4666884   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B3 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 GSM4666884 GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq GSM4666884   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:GSM4666884 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P4-1_S16_L004_R1_001.fastq.gz fastq 500262064.0 3148948.0 GSM4666884 r4 0:158.87 1:0 A:147195579;C:31493012;G:128890060;T:192659641;N:23772 158 0     147195579 31493012 128890060 192659641 23772 SRX8707738 SRS6984325 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0001   9e-05   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60313 60313 SRR12194923 SRX8707737 SRS6984324 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 B2 GSM4666883   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B2 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 GSM4666883 GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq GSM4666883   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:GSM4666883 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-6_S15_L001_R1_001.fastq.gz fastq 517956360.0 3260092.0 GSM4666883 r1 0:158.88 1:0 A:150448706;C:32858153;G:137976678;T:196634454;N:38369 158 0     150448706 32858153 137976678 196634454 38369 SRX8707737 SRS6984324 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.00014   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60314 60314 SRR12194924 SRX8707737 SRS6984324 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 B2 GSM4666883   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B2 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 GSM4666883 GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq GSM4666883   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:GSM4666883 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-6_S15_L002_R1_001.fastq.gz fastq 509673976.0 3208134.0 GSM4666883 r2 0:158.87 1:0 A:145524541;C:31734648;G:141519088;T:190860914;N:34785 158 0     145524541 31734648 141519088 190860914 34785 SRX8707737 SRS6984324 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00017   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60315 60315 SRR12194925 SRX8707737 SRS6984324 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 B2 GSM4666883   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B2 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 GSM4666883 GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq GSM4666883   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:GSM4666883 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-6_S15_L003_R1_001.fastq.gz fastq 503140482.0 3166780.0 GSM4666883 r3 0:158.88 1:0 A:146286862;C:31831570;G:133486316;T:191509945;N:25789 158 0     146286862 31831570 133486316 191509945 25789 SRX8707737 SRS6984324 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00015   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60316 60316 SRR12194926 SRX8707737 SRS6984324 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 B2 GSM4666883   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B2 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 GSM4666883 GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq GSM4666883   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:GSM4666883 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-6_S15_L004_R1_001.fastq.gz fastq 493961726.0 3109154.0 GSM4666883 r4 0:158.87 1:0 A:141543659;C:30970461;G:135682865;T:185742190;N:22551 158 0     141543659 30970461 135682865 185742190 22551 SRX8707737 SRS6984324 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00018   0.00017   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60317 60317 SRR12194919 SRX8707736 SRS6984322 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 B1 GSM4666882   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B1 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 GSM4666882 GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq GSM4666882   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:GSM4666882 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-5_S14_L001_R1_001.fastq.gz fastq 644565105.0 4057680.0 GSM4666882 r1 0:158.85 1:0 A:189377017;C:44153618;G:160972875;T:250013345;N:48250 158 0     189377017 44153618 160972875 250013345 48250 SRX8707736 SRS6984322 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   0.0001   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60318 60318 SRR12194920 SRX8707736 SRS6984322 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 B1 GSM4666882   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B1 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 GSM4666882 GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq GSM4666882   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:GSM4666882 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-5_S14_L002_R1_001.fastq.gz fastq 638463567.0 4019714.0 GSM4666882 r2 0:158.83 1:0 A:184509132;C:42923906;G:166717116;T:244267791;N:45622 158 0     184509132 42923906 166717116 244267791 45622 SRX8707736 SRS6984322 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00012   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60319 60319 SRR12194921 SRX8707736 SRS6984322 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 B1 GSM4666882   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B1 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 GSM4666882 GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq GSM4666882   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:GSM4666882 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-5_S14_L003_R1_001.fastq.gz fastq 626116922.0 3941475.0 GSM4666882 r3 0:158.85 1:0 A:184234800;C:42706665;G:156104866;T:243035941;N:34650 158 0     184234800 42706665 156104866 243035941 34650 SRX8707736 SRS6984322 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0002   0.00018   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60320 60320 SRR12194922 SRX8707736 SRS6984322 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 B1 GSM4666882   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B1 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 GSM4666882 GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq GSM4666882   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:GSM4666882 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-5_S14_L004_R1_001.fastq.gz fastq 619633878.0 3900997.0 GSM4666882 r4 0:158.84 1:0 A:179600621;C:41804166;G:160698591;T:237500321;N:30179 158 0     179600621 41804166 160698591 237500321 30179 SRX8707736 SRS6984322 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00012   0.99993   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60321 60321 SRR12194915 SRX8707735 SRS6984323 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 C16 GSM4666881   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C16 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:M GSM4666881 GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq GSM4666881   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:GSM4666881 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-6_S33_L001_R1_001.fastq.gz fastq 293820485.0 1849388.0 GSM4666881 r1 0:158.87 1:0 A:86678903;C:19266888;G:74424764;T:113427237;N:22693 158 0     86678903 19266888 74424764 113427237 22693 SRX8707735 SRS6984323 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.00012   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60322 60322 SRR12194916 SRX8707735 SRS6984323 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 C16 GSM4666881   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C16 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:M GSM4666881 GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq GSM4666881   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:GSM4666881 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-6_S33_L002_R1_001.fastq.gz fastq 290054720.0 1825735.0 GSM4666881 r2 0:158.87 1:0 A:84128360;C:18660250;G:76750691;T:110494636;N:20783 158 0     84128360 18660250 76750691 110494636 20783 SRX8707735 SRS6984323 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60323 60323 SRR12194917 SRX8707735 SRS6984323 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 C16 GSM4666881   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C16 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:M GSM4666881 GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq GSM4666881   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:GSM4666881 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-6_S33_L003_R1_001.fastq.gz fastq 285222008.0 1795272.0 GSM4666881 r3 0:158.87 1:0 A:84271091;C:18587085;G:72126787;T:110222855;N:14190 158 0     84271091 18587085 72126787 110222855 14190 SRX8707735 SRS6984323 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00014   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60324 60324 SRR12194918 SRX8707735 SRS6984323 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 C16 GSM4666881   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C16 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:M GSM4666881 GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq GSM4666881   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:GSM4666881 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-6_S33_L004_R1_001.fastq.gz fastq 281043981.0 1769013.0 GSM4666881 r4 0:158.87 1:0 A:81695659;C:18172870;G:73847131;T:107315179;N:13142 158 0     81695659 18172870 73847131 107315179 13142 SRX8707735 SRS6984323 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00021   0.00018   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60325 60325 SRR12194911 SRX8707734 SRS6984321 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 C15 GSM4666880   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C15 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:M GSM4666880 GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq GSM4666880   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:GSM4666880 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-5_S32_L001_R1_001.fastq.gz fastq 407927114.0 2567613.0 GSM4666880 r1 0:158.87 1:0 A:121216665;C:26341281;G:102882256;T:157456714;N:30198 158 0     121216665 26341281 102882256 157456714 30198 SRX8707734 SRS6984321 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0002   0.00018   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60326 60326 SRR12194912 SRX8707734 SRS6984321 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 C15 GSM4666880   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C15 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:M GSM4666880 GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq GSM4666880   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:GSM4666880 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-5_S32_L002_R1_001.fastq.gz fastq 402652470.0 2534477.0 GSM4666880 r2 0:158.87 1:0 A:117634138;C:25467360;G:106127698;T:153394332;N:28942 158 0     117634138 25467360 106127698 153394332 28942 SRX8707734 SRS6984321 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00014   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60327 60327 SRR12194913 SRX8707734 SRS6984321 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 C15 GSM4666880   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C15 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:M GSM4666880 GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq GSM4666880   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:GSM4666880 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-5_S32_L003_R1_001.fastq.gz fastq 397486480.0 2501849.0 GSM4666880 r3 0:158.88 1:0 A:118276499;C:25546701;G:100107393;T:153534109;N:21778 158 0     118276499 25546701 100107393 153534109 21778 SRX8707734 SRS6984321 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00013   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60328 60328 SRR12194914 SRX8707734 SRS6984321 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 C15 GSM4666880   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C15 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:M GSM4666880 GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq GSM4666880   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:GSM4666880 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-5_S32_L004_R1_001.fastq.gz fastq 392040128.0 2467658.0 GSM4666880 r4 0:158.87 1:0 A:114883310;C:24890978;G:102581367;T:149666668;N:17805 158 0     114883310 24890978 102581367 149666668 17805 SRX8707734 SRS6984321 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   0.00011   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60329 60329 SRR12194907 SRX8707733 SRS6984320 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 C14 GSM4666879   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C14 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:M GSM4666879 GSM4666879: adult whole brain C14; Danio rerio; Bisulfite Seq GSM4666879   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:GSM4666879 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-4_S31_L001_R1_001.fastq.gz fastq 353064855.0 2222156.0 GSM4666879 r1 0:158.88 1:0 A:104513530;C:22147087;G:91009846;T:135368042;N:26350 158 0     104513530 22147087 91009846 135368042 26350 SRX8707733 SRS6984320 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00029   0.00025   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60330 60330 SRR12194908 SRX8707733 SRS6984320 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 C14 GSM4666879   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C14 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:M GSM4666879 GSM4666879: adult whole brain C14; Danio rerio; Bisulfite Seq GSM4666879   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:GSM4666879 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-4_S31_L002_R1_001.fastq.gz fastq 351276576.0 2210926.0 GSM4666879 r2 0:158.88 1:0 A:102282891;C:21642108;G:94394894;T:132930782;N:25901 158 0     102282891 21642108 94394894 132930782 25901 SRX8707733 SRS6984320 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0002   0.00015   0.99993   0.25   155   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60331 60331 SRR12194909 SRX8707733 SRS6984320 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 C14 GSM4666879   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C14 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:M GSM4666879 GSM4666879: adult whole brain C14; Danio rerio; Bisulfite Seq GSM4666879   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:GSM4666879 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-4_S31_L003_R1_001.fastq.gz fastq 343212925.0 2160132.0 GSM4666879 r3 0:158.89 1:0 A:101732957;C:21417428;G:88158805;T:131886359;N:17376 158 0     101732957 21417428 88158805 131886359 17376 SRX8707733 SRS6984320 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00025   0.00023   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60332 60332 SRR12194910 SRX8707733 SRS6984320 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 C14 GSM4666879   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C14 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:M GSM4666879 GSM4666879: adult whole brain C14; Danio rerio; Bisulfite Seq GSM4666879   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:GSM4666879 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-4_S31_L004_R1_001.fastq.gz fastq 341256657.0 2147834.0 GSM4666879 r4 0:158.88 1:0 A:99646106;C:21129955;G:90846599;T:129617419;N:16578 158 0     99646106 21129955 90846599 129617419 16578 SRX8707733 SRS6984320 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00013   1.0       158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60333 60333 SRR12194903 SRX8707732 SRS6984319 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 C13 GSM4666878   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C13 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:M GSM4666878 GSM4666878: adult whole brain C13; Danio rerio; Bisulfite Seq GSM4666878   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:GSM4666878 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-3_S30_L001_R1_001.fastq.gz fastq 485597617.0 3056533.0 GSM4666878 r1 0:158.87 1:0 A:143980404;C:30580061;G:119295036;T:191704763;N:37353 158 0     143980404 30580061 119295036 191704763 37353 SRX8707732 SRS6984319 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0002   0.00018   0.99995   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60334 60334 SRR12194904 SRX8707732 SRS6984319 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 C13 GSM4666878   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C13 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:M GSM4666878 GSM4666878: adult whole brain C13; Danio rerio; Bisulfite Seq GSM4666878   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:GSM4666878 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-3_S30_L002_R1_001.fastq.gz fastq 469628995.0 2956090.0 GSM4666878 r2 0:158.87 1:0 A:137163280;C:28944601;G:120359197;T:183126393;N:35524 158 0     137163280 28944601 120359197 183126393 35524 SRX8707732 SRS6984319 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00018   0.00017   1.0       157   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60335 60335 SRR12194905 SRX8707732 SRS6984319 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 C13 GSM4666878   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C13 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:M GSM4666878 GSM4666878: adult whole brain C13; Danio rerio; Bisulfite Seq GSM4666878   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:GSM4666878 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-3_S30_L003_R1_001.fastq.gz fastq 472950780.0 2976902.0 GSM4666878 r3 0:158.87 1:0 A:140414817;C:29605788;G:116008980;T:186896397;N:24798 158 0     140414817 29605788 116008980 186896397 24798 SRX8707732 SRS6984319 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00022   0.0002   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60336 60336 SRR12194906 SRX8707732 SRS6984319 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 C13 GSM4666878   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C13 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:M GSM4666878 GSM4666878: adult whole brain C13; Danio rerio; Bisulfite Seq GSM4666878   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:GSM4666878 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-3_S30_L004_R1_001.fastq.gz fastq 456803955.0 2875316.0 GSM4666878 r4 0:158.87 1:0 A:133760578;C:28259216;G:116392120;T:178370154;N:21887 158 0     133760578 28259216 116392120 178370154 21887 SRX8707732 SRS6984319 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00016   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60337 60337 SRR12194899 SRX8707731 SRS6984318 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 C12 GSM4666877   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C12 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 GSM4666877 GSM4666877: adult whole brain C12; Danio rerio; Bisulfite Seq GSM4666877   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:GSM4666877 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-2_S29_L001_R1_001.fastq.gz fastq 445534772.0 2804465.0 GSM4666877 r1 0:158.87 1:0 A:133612781;C:27522254;G:109353006;T:175012186;N:34545 158 0     133612781 27522254 109353006 175012186 34545 SRX8707731 SRS6984318 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00016   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60338 60338 SRR12194900 SRX8707731 SRS6984318 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 C12 GSM4666877   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C12 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 GSM4666877 GSM4666877: adult whole brain C12; Danio rerio; Bisulfite Seq GSM4666877   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:GSM4666877 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-2_S29_L002_R1_001.fastq.gz fastq 441745440.0 2780874.0 GSM4666877 r2 0:158.85 1:0 A:130252837;C:26720888;G:113550957;T:171188873;N:31885 158 0     130252837 26720888 113550957 171188873 31885 SRX8707731 SRS6984318 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   8e-05   0.99995   0.75   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60339 60339 SRR12194901 SRX8707731 SRS6984318 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 C12 GSM4666877   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C12 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 GSM4666877 GSM4666877: adult whole brain C12; Danio rerio; Bisulfite Seq GSM4666877   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:GSM4666877 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-2_S29_L003_R1_001.fastq.gz fastq 433881978.0 2731058.0 GSM4666877 r3 0:158.87 1:0 A:130303289;C:26665502;G:106372691;T:170516024;N:24472 158 0     130303289 26665502 106372691 170516024 24472 SRX8707731 SRS6984318 SRA1097340 GEO UMR MARBEC, INRAE 1 9e-05   8e-05   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60340 60340 SRR12194902 SRX8707731 SRS6984318 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 C12 GSM4666877   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C12 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 GSM4666877 GSM4666877: adult whole brain C12; Danio rerio; Bisulfite Seq GSM4666877   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:GSM4666877 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-2_S29_L004_R1_001.fastq.gz fastq 430083625.0 2707299.0 GSM4666877 r4 0:158.86 1:0 A:127216281;C:26070400;G:109807729;T:166969346;N:19869 158 0     127216281 26070400 109807729 166969346 19869 SRX8707731 SRS6984318 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00013   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60341 60341 SRR12194895 SRX8707730 SRS6984317 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 C11 GSM4666876   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C11 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 GSM4666876 GSM4666876: adult whole brain C11; Danio rerio; Bisulfite Seq GSM4666876   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:GSM4666876 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-1_S28_L001_R1_001.fastq.gz fastq 390763441.0 2459521.0 GSM4666876 r1 0:158.88 1:0 A:115878018;C:24466254;G:101456635;T:148931279;N:31255 158 0     115878018 24466254 101456635 148931279 31255 SRX8707730 SRS6984317 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   9e-05   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60342 60342 SRR12194896 SRX8707730 SRS6984317 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 C11 GSM4666876   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C11 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 GSM4666876 GSM4666876: adult whole brain C11; Danio rerio; Bisulfite Seq GSM4666876   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:GSM4666876 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-1_S28_L002_R1_001.fastq.gz fastq 386653820.0 2433806.0 GSM4666876 r2 0:158.87 1:0 A:112748519;C:23827291;G:104589609;T:145459942;N:28459 158 0     112748519 23827291 104589609 145459942 28459 SRX8707730 SRS6984317 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   0.0001   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60343 60343 SRR12194897 SRX8707730 SRS6984317 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 C11 GSM4666876   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C11 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 GSM4666876 GSM4666876: adult whole brain C11; Danio rerio; Bisulfite Seq GSM4666876   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:GSM4666876 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-1_S28_L003_R1_001.fastq.gz fastq 380317441.0 2393754.0 GSM4666876 r3 0:158.88 1:0 A:112915106;C:23708822;G:98403695;T:145269293;N:20525 158 0     112915106 23708822 98403695 145269293 20525 SRX8707730 SRS6984317 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   9e-05   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60344 60344 SRR12194898 SRX8707730 SRS6984317 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 C11 GSM4666876   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C11 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 GSM4666876 GSM4666876: adult whole brain C11; Danio rerio; Bisulfite Seq GSM4666876   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:GSM4666876 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P8-1_S28_L004_R1_001.fastq.gz fastq 375571793.0 2363988.0 GSM4666876 r4 0:158.87 1:0 A:109850893;C:23315154;G:100624445;T:141764059;N:17242 158 0     109850893 23315154 100624445 141764059 17242 SRX8707730 SRS6984317 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0001   8e-05   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60345 60345 SRR12194891 SRX8707729 SRS6984316 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 C10 GSM4666875   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C10 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 GSM4666875 GSM4666875: adult whole brain C10; Danio rerio; Bisulfite Seq GSM4666875   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:GSM4666875 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-6_S27_L001_R1_001.fastq.gz fastq 447741142.0 2818422.0 GSM4666875 r1 0:158.86 1:0 A:132227648;C:28721642;G:111605477;T:175150599;N:35776 158 0     132227648 28721642 111605477 175150599 35776 SRX8707729 SRS6984316 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   0.00011   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60346 60346 SRR12194892 SRX8707729 SRS6984316 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 C10 GSM4666875   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C10 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 GSM4666875 GSM4666875: adult whole brain C10; Danio rerio; Bisulfite Seq GSM4666875   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:GSM4666875 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-6_S27_L002_R1_001.fastq.gz fastq 440729494.0 2774364.0 GSM4666875 r2 0:158.86 1:0 A:128001555;C:27669098;G:114912549;T:170114952;N:31340 158 0     128001555 27669098 114912549 170114952 31340 SRX8707729 SRS6984316 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00014   0.99995   0.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60347 60347 SRR12194893 SRX8707729 SRS6984316 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 C10 GSM4666875   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C10 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 GSM4666875 GSM4666875: adult whole brain C10; Danio rerio; Bisulfite Seq GSM4666875   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:GSM4666875 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-6_S27_L003_R1_001.fastq.gz fastq 435566573.0 2741716.0 GSM4666875 r3 0:158.87 1:0 A:128746294;C:27829922;G:108424722;T:170542086;N:23549 158 0     128746294 27829922 108424722 170542086 23549 SRX8707729 SRS6984316 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   0.0001   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60348 60348 SRR12194894 SRX8707729 SRS6984316 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 C10 GSM4666875   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C10 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 GSM4666875 GSM4666875: adult whole brain C10; Danio rerio; Bisulfite Seq GSM4666875   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:GSM4666875 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-6_S27_L004_R1_001.fastq.gz fastq 427498288.0 2691000.0 GSM4666875 r4 0:158.86 1:0 A:124522617;C:26924291;G:110757433;T:165273747;N:20200 158 0     124522617 26924291 110757433 165273747 20200 SRX8707729 SRS6984316 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   0.0001   1.0       158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60349 60349 SRR12194887 SRX8707728 SRS6984315 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 C9 GSM4666874   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C9 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 GSM4666874 GSM4666874: adult whole brain C9; Danio rerio; Bisulfite Seq GSM4666874   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:GSM4666874 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-5_S26_L001_R1_001.fastq.gz fastq 349783641.0 2201717.0 GSM4666874 r1 0:158.87 1:0 A:102701594;C:22632391;G:88063333;T:136359733;N:26590 158 0     102701594 22632391 88063333 136359733 26590 SRX8707728 SRS6984315 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   9e-05   0.99993   0.33333   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60350 60350 SRR12194888 SRX8707728 SRS6984315 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 C9 GSM4666874   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C9 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 GSM4666874 GSM4666874: adult whole brain C9; Danio rerio; Bisulfite Seq GSM4666874   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:GSM4666874 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-5_S26_L002_R1_001.fastq.gz fastq 344622908.0 2169270.0 GSM4666874 r2 0:158.87 1:0 A:99438832;C:21808331;G:90870468;T:132481551;N:23726 158 0     99438832 21808331 90870468 132481551 23726 SRX8707728 SRS6984315 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60351 60351 SRR12194889 SRX8707728 SRS6984315 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 C9 GSM4666874   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C9 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 GSM4666874 GSM4666874: adult whole brain C9; Danio rerio; Bisulfite Seq GSM4666874   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:GSM4666874 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-5_S26_L003_R1_001.fastq.gz fastq 341160840.0 2147418.0 GSM4666874 r3 0:158.87 1:0 A:100266987;C:21990788;G:85828984;T:133055843;N:18238 158 0     100266987 21990788 85828984 133055843 18238 SRX8707728 SRS6984315 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   0.00011   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60352 60352 SRR12194890 SRX8707728 SRS6984315 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 C9 GSM4666874   tissue:adult whole brain|strain:AB line|generation:F2|Sex:female adult whole brain C9 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 GSM4666874 GSM4666874: adult whole brain C9; Danio rerio; Bisulfite Seq GSM4666874   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:GSM4666874 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-5_S26_L004_R1_001.fastq.gz fastq 334749648.0 2107096.0 GSM4666874 r4 0:158.87 1:0 A:96876210;C:21224218;G:87738246;T:128896105;N:14869 158 0     96876210 21224218 87738246 128896105 14869 SRX8707728 SRS6984315 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   0.0001   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60353 60353 SRR12194883 SRX8707727 SRS6984314 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 C8 GSM4666873   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C8 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:M GSM4666873 GSM4666873: adult whole brain C8; Danio rerio; Bisulfite Seq GSM4666873   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:GSM4666873 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-4_S25_L001_R1_001.fastq.gz fastq 367179684.0 2310944.0 GSM4666873 r1 0:158.89 1:0 A:108387100;C:22533917;G:95615269;T:140615389;N:28009 158 0     108387100 22533917 95615269 140615389 28009 SRX8707727 SRS6984314 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60354 60354 SRR12194884 SRX8707727 SRS6984314 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 C8 GSM4666873   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C8 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:M GSM4666873 GSM4666873: adult whole brain C8; Danio rerio; Bisulfite Seq GSM4666873   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:GSM4666873 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-4_S25_L002_R1_001.fastq.gz fastq 363113715.0 2285411.0 GSM4666873 r2 0:158.88 1:0 A:105466521;C:21922644;G:98373713;T:137324677;N:26160 158 0     105466521 21922644 98373713 137324677 26160 SRX8707727 SRS6984314 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   9e-05   0.99993   0.33333   157   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60355 60355 SRR12194885 SRX8707727 SRS6984314 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 C8 GSM4666873   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C8 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:M GSM4666873 GSM4666873: adult whole brain C8; Danio rerio; Bisulfite Seq GSM4666873   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:GSM4666873 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-4_S25_L003_R1_001.fastq.gz fastq 357335658.0 2248967.0 GSM4666873 r3 0:158.89 1:0 A:105614730;C:21856793;G:92703497;T:137141999;N:18639 158 0     105614730 21856793 92703497 137141999 18639 SRX8707727 SRS6984314 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   9e-05   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60356 60356 SRR12194886 SRX8707727 SRS6984314 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 C8 GSM4666873   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C8 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:M GSM4666873 GSM4666873: adult whole brain C8; Danio rerio; Bisulfite Seq GSM4666873   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:GSM4666873 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-4_S25_L004_R1_001.fastq.gz fastq 353077077.0 2222198.0 GSM4666873 r4 0:158.89 1:0 A:102842329;C:21438123;G:94843754;T:133936647;N:16224 158 0     102842329 21438123 94843754 133936647 16224 SRX8707727 SRS6984314 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   0.0001   1.0       158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60357 60357 SRR12194879 SRX8707726 SRS6984313 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 C7 GSM4666872   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C7 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:M GSM4666872 GSM4666872: adult whole brain C7; Danio rerio; Bisulfite Seq GSM4666872   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:GSM4666872 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-3_S24_L001_R1_001.fastq.gz fastq 399756481.0 2516343.0 GSM4666872 r1 0:158.86 1:0 A:118237358;C:26081912;G:98561591;T:156845680;N:29940 158 0     118237358 26081912 98561591 156845680 29940 SRX8707726 SRS6984313 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0001   9e-05   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60358 60358 SRR12194880 SRX8707726 SRS6984313 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 C7 GSM4666872   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C7 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:M GSM4666872 GSM4666872: adult whole brain C7; Danio rerio; Bisulfite Seq GSM4666872   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:GSM4666872 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-3_S24_L002_R1_001.fastq.gz fastq 396127431.0 2493602.0 GSM4666872 r2 0:158.86 1:0 A:115214780;C:25275842;G:102362471;T:153246596;N:27742 158 0     115214780 25275842 102362471 153246596 27742 SRX8707726 SRS6984313 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00011   0.0001   0.99997   1.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60359 60359 SRR12194881 SRX8707726 SRS6984313 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 C7 GSM4666872   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C7 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:M GSM4666872 GSM4666872: adult whole brain C7; Danio rerio; Bisulfite Seq GSM4666872   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:GSM4666872 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-3_S24_L003_R1_001.fastq.gz fastq 389004313.0 2448635.0 GSM4666872 r3 0:158.87 1:0 A:115229990;C:25251186;G:95770612;T:152732390;N:20135 158 0     115229990 25251186 95770612 152732390 20135 SRX8707726 SRS6984313 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00016   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60360 60360 SRR12194882 SRX8707726 SRS6984313 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 C7 GSM4666872   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C7 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:M GSM4666872 GSM4666872: adult whole brain C7; Danio rerio; Bisulfite Seq GSM4666872   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:GSM4666872 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-3_S24_L004_R1_001.fastq.gz fastq 384663393.0 2421377.0 GSM4666872 r4 0:158.86 1:0 A:112225329;C:24613712;G:98738353;T:149068065;N:17934 158 0     112225329 24613712 98738353 149068065 17934 SRX8707726 SRS6984313 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00013   0.99993   0.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60361 60361 SRR12194875 SRX8707725 SRS6984312 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 C6 GSM4666871   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C6 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:M GSM4666871 GSM4666871: adult whole brain C6; Danio rerio; Bisulfite Seq GSM4666871   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:GSM4666871 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-2_S23_L001_R1_001.fastq.gz fastq 325067614.0 2046204.0 GSM4666871 r1 0:158.86 1:0 A:95450820;C:20939443;G:81181140;T:127471342;N:24869 158 0     95450820 20939443 81181140 127471342 24869 SRX8707725 SRS6984312 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00021   0.00019   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60362 60362 SRR12194876 SRX8707725 SRS6984312 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 C6 GSM4666871   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C6 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:M GSM4666871 GSM4666871: adult whole brain C6; Danio rerio; Bisulfite Seq GSM4666871   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:GSM4666871 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-2_S23_L002_R1_001.fastq.gz fastq 320319950.0 2016427.0 GSM4666871 r2 0:158.86 1:0 A:92486172;C:20198381;G:83651952;T:123960477;N:22968 158 0     92486172 20198381 83651952 123960477 22968 SRX8707725 SRS6984312 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00012   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60363 60363 SRR12194877 SRX8707725 SRS6984312 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 C6 GSM4666871   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C6 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:M GSM4666871 GSM4666871: adult whole brain C6; Danio rerio; Bisulfite Seq GSM4666871   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:GSM4666871 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-2_S23_L003_R1_001.fastq.gz fastq 316364136.0 1991396.0 GSM4666871 r3 0:158.87 1:0 A:92983629;C:20280380;G:78951240;T:124131696;N:17191 158 0     92983629 20280380 78951240 124131696 17191 SRX8707725 SRS6984312 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00012   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60364 60364 SRR12194878 SRX8707725 SRS6984312 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 C6 GSM4666871   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C6 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:M GSM4666871 GSM4666871: adult whole brain C6; Danio rerio; Bisulfite Seq GSM4666871   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:GSM4666871 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-2_S23_L004_R1_001.fastq.gz fastq 311015025.0 1957808.0 GSM4666871 r4 0:158.86 1:0 A:90033225;C:19681379;G:80716796;T:120569654;N:13971 158 0     90033225 19681379 80716796 120569654 13971 SRX8707725 SRS6984312 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0001   8e-05   0.99995   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60365 60365 SRR12194871 SRX8707724 SRS6984311 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 C5 GSM4666870   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C5 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:M GSM4666870 GSM4666870: adult whole brain C5; Danio rerio; Bisulfite Seq GSM4666870   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:GSM4666870 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-1_S22_L001_R1_001.fastq.gz fastq 315943762.0 1988605.0 GSM4666870 r1 0:158.88 1:0 A:93723864;C:18954342;G:80459863;T:122782937;N:22756 158 0     93723864 18954342 80459863 122782937 22756 SRX8707724 SRS6984311 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00013   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60366 60366 SRR12194872 SRX8707724 SRS6984311 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 C5 GSM4666870   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C5 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:M GSM4666870 GSM4666870: adult whole brain C5; Danio rerio; Bisulfite Seq GSM4666870   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:GSM4666870 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-1_S22_L002_R1_001.fastq.gz fastq 310504031.0 1954502.0 GSM4666870 r2 0:158.87 1:0 A:90486065;C:18296279;G:82704207;T:118994604;N:22876 158 0     90486065 18296279 82704207 118994604 22876 SRX8707724 SRS6984311 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00014   0.99997   1.0   156   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60367 60367 SRR12194873 SRX8707724 SRS6984311 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 C5 GSM4666870   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C5 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:M GSM4666870 GSM4666870: adult whole brain C5; Danio rerio; Bisulfite Seq GSM4666870   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:GSM4666870 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-1_S22_L003_R1_001.fastq.gz fastq 307897943.0 1937946.0 GSM4666870 r3 0:158.88 1:0 A:91452182;C:18358073;G:78256247;T:119814774;N:16667 158 0     91452182 18358073 78256247 119814774 16667 SRX8707724 SRS6984311 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00011   0.99995   0.5   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60368 60368 SRR12194874 SRX8707724 SRS6984311 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 C5 GSM4666870   tissue:adult whole brain|strain:AB line|generation:F2|Sex:male adult whole brain C5 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:M GSM4666870 GSM4666870: adult whole brain C5; Danio rerio; Bisulfite Seq GSM4666870   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:GSM4666870 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P7-1_S22_L004_R1_001.fastq.gz fastq 302471183.0 1903940.0 GSM4666870 r4 0:158.87 1:0 A:88449452;C:17899861;G:79818103;T:116289565;N:14202 158 0     88449452 17899861 79818103 116289565 14202 SRX8707724 SRS6984311 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   0.00011   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60385 60385 SRR12194851 SRX8707719 SRS6984305 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 A16 GSM4666865   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A16 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 GSM4666865 GSM4666865: adult whole brain A16; Danio rerio; Bisulfite Seq GSM4666865   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:GSM4666865 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-4_S13_L001_R1_001.fastq.gz fastq 689809617.0 4342121.0 GSM4666865 r1 0:158.86 1:0 A:204801275;C:45250604;G:172351276;T:267354920;N:51542 158 0     204801275 45250604 172351276 267354920 51542 SRX8707719 SRS6984305 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00011   0.99993   0.75   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60386 60386 SRR12194852 SRX8707719 SRS6984305 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 A16 GSM4666865   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A16 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 GSM4666865 GSM4666865: adult whole brain A16; Danio rerio; Bisulfite Seq GSM4666865   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:GSM4666865 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-4_S13_L002_R1_001.fastq.gz fastq 686687820.0 4322753.0 GSM4666865 r2 0:158.85 1:0 A:200353753;C:44245206;G:179745865;T:262293092;N:49904 158 0     200353753 44245206 179745865 262293092 49904 SRX8707719 SRS6984305 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00018   0.00014   0.99995   0.33333   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60387 60387 SRR12194853 SRX8707719 SRS6984305 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 A16 GSM4666865   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A16 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 GSM4666865 GSM4666865: adult whole brain A16; Danio rerio; Bisulfite Seq GSM4666865   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:GSM4666865 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-4_S13_L003_R1_001.fastq.gz fastq 671069788.0 4224077.0 GSM4666865 r3 0:158.87 1:0 A:199544822;C:43797434;G:167299291;T:260393222;N:35019 158 0     199544822 43797434 167299291 260393222 35019 SRX8707719 SRS6984305 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.0001   0.99993   0.2   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60388 60388 SRR12194854 SRX8707719 SRS6984305 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 A16 GSM4666865   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A16 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 GSM4666865 GSM4666865: adult whole brain A16; Danio rerio; Bisulfite Seq GSM4666865   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:GSM4666865 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-4_S13_L004_R1_001.fastq.gz fastq 667703665.0 4203131.0 GSM4666865 r4 0:158.86 1:0 A:195451578;C:43118340;G:173582806;T:255518344;N:32597 158 0     195451578 43118340 173582806 255518344 32597 SRX8707719 SRS6984305 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00012   9e-05   0.99993   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60389 60389 SRR12194847 SRX8707718 SRS6984306 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 A15 GSM4666864   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A15 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 GSM4666864 GSM4666864: adult whole brain A15; Danio rerio; Bisulfite Seq GSM4666864   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:GSM4666864 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-3_S12_L001_R1_001.fastq.gz fastq 355015325.0 2234389.0 GSM4666864 r1 0:158.89 1:0 A:103483498;C:22414222;G:93489185;T:135601273;N:27147 158 0     103483498 22414222 93489185 135601273 27147 SRX8707718 SRS6984306 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00014   0.00012   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60390 60390 SRR12194848 SRX8707718 SRS6984306 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 A15 GSM4666864   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A15 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 GSM4666864 GSM4666864: adult whole brain A15; Danio rerio; Bisulfite Seq GSM4666864   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:GSM4666864 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-3_S12_L002_R1_001.fastq.gz fastq 344540591.0 2168598.0 GSM4666864 r2 0:158.88 1:0 A:98888829;C:21494277;G:94039139;T:130093467;N:24879 158 0     98888829 21494277 94039139 130093467 24879 SRX8707718 SRS6984306 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00012   0.99993   0.0   154   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60391 60391 SRR12194849 SRX8707718 SRS6984306 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 A15 GSM4666864   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A15 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 GSM4666864 GSM4666864: adult whole brain A15; Danio rerio; Bisulfite Seq GSM4666864   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:GSM4666864 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-3_S12_L003_R1_001.fastq.gz fastq 343972942.0 2164884.0 GSM4666864 r3 0:158.89 1:0 A:100374272;C:21615694;G:90311565;T:131653845;N:17566 158 0     100374272 21615694 90311565 131653845 17566 SRX8707718 SRS6984306 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00017   0.00015   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60392 60392 SRR12194850 SRX8707718 SRS6984306 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 A15 GSM4666864   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A15 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 GSM4666864 GSM4666864: adult whole brain A15; Danio rerio; Bisulfite Seq GSM4666864   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:GSM4666864 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-3_S12_L004_R1_001.fastq.gz fastq 333191247.0 2097119.0 GSM4666864 r4 0:158.88 1:0 A:95922078;C:20917222;G:90090985;T:126245639;N:15323 158 0     95922078 20917222 90090985 126245639 15323 SRX8707718 SRS6984306 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00013   0.00011   0.99997   0.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60393 60393 SRR12194843 SRX8707717 SRS6984304 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 A14 GSM4666863   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A14 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 GSM4666863 GSM4666863: adult whole brain A14; Danio rerio; Bisulfite Seq GSM4666863   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:GSM4666863 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-2_S11_L001_R1_001.fastq.gz fastq 743810165.0 4681255.0 GSM4666863 r1 0:158.89 1:0 A:217243361;C:45701715;G:189898434;T:290907157;N:59498 158 0     217243361 45701715 189898434 290907157 59498 SRX8707717 SRS6984304 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00016   0.00015   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60394 60394 SRR12194844 SRX8707717 SRS6984304 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 A14 GSM4666863   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A14 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 GSM4666863 GSM4666863: adult whole brain A14; Danio rerio; Bisulfite Seq GSM4666863   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:GSM4666863 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-2_S11_L002_R1_001.fastq.gz fastq 730002043.0 4594488.0 GSM4666863 r2 0:158.89 1:0 A:209558957;C:43963309;G:194931384;T:281497288;N:51105 158 0     209558957 43963309 194931384 281497288 51105 SRX8707717 SRS6984304 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.00013   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60395 60395 SRR12194845 SRX8707717 SRS6984304 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 A14 GSM4666863   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A14 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 GSM4666863 GSM4666863: adult whole brain A14; Danio rerio; Bisulfite Seq GSM4666863   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:GSM4666863 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-2_S11_L003_R1_001.fastq.gz fastq 725703528.0 4567274.0 GSM4666863 r3 0:158.89 1:0 A:212245753;C:44330620;G:184996112;T:284092198;N:38845 158 0     212245753 44330620 184996112 284092198 38845 SRX8707717 SRS6984304 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00026   0.00024   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60396 60396 SRR12194846 SRX8707717 SRS6984304 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 A14 GSM4666863   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A14 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 GSM4666863 GSM4666863: adult whole brain A14; Danio rerio; Bisulfite Seq GSM4666863   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:GSM4666863 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-2_S11_L004_R1_001.fastq.gz fastq 707809263.0 4454746.0 GSM4666863 r4 0:158.89 1:0 A:203710504;C:42797792;G:187665310;T:273602813;N:32844 158 0     203710504 42797792 187665310 273602813 32844 SRX8707717 SRS6984304 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00021   0.0002   1.0       159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60397 60397 SRR12194839 SRX8707716 SRS6984303 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 A13 GSM4666862   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A13 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 GSM4666862 GSM4666862: adult whole brain A13; Danio rerio; Bisulfite Seq GSM4666862   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:GSM4666862 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-1_S10_L001_R1_001.fastq.gz fastq 340997897.0 2146311.0 GSM4666862 r1 0:158.88 1:0 A:100329490;C:21676681;G:86956335;T:132008442;N:26949 158 0     100329490 21676681 86956335 132008442 26949 SRX8707716 SRS6984303 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00022   0.0002   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60398 60398 SRR12194840 SRX8707716 SRS6984303 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 A13 GSM4666862   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A13 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 GSM4666862 GSM4666862: adult whole brain A13; Danio rerio; Bisulfite Seq GSM4666862   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:GSM4666862 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-1_S10_L002_R1_001.fastq.gz fastq 333808156.0 2101103.0 GSM4666862 r2 0:158.87 1:0 A:96653159;C:20788816;G:88898866;T:127443522;N:23793 158 0     96653159 20788816 88898866 127443522 23793 SRX8707716 SRS6984303 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00019   0.00017   0.99997   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60399 60399 SRR12194841 SRX8707716 SRS6984303 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 A13 GSM4666862   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A13 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 GSM4666862 GSM4666862: adult whole brain A13; Danio rerio; Bisulfite Seq GSM4666862   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:GSM4666862 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-1_S10_L003_R1_001.fastq.gz fastq 331975171.0 2089484.0 GSM4666862 r3 0:158.88 1:0 A:97828615;C:21019525;G:84521164;T:128587307;N:18560 158 0     97828615 21019525 84521164 128587307 18560 SRX8707716 SRS6984303 SRA1097340 GEO UMR MARBEC, INRAE 1 0.0002   0.00016   0.99995   0.0   159   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60400 60400 SRR12194842 SRX8707716 SRS6984303 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 A13 GSM4666862   tissue:adult whole brain|strain:AB line|generation:F0|Sex:male adult whole brain A13 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 GSM4666862 GSM4666862: adult whole brain A13; Danio rerio; Bisulfite Seq GSM4666862   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:GSM4666862 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation SINGLE ILLUMINA NextSeq 550   SRP271280     P3-1_S10_L004_R1_001.fastq.gz fastq 323207612.0 2034349.0 GSM4666862 r4 0:158.88 1:0 A:93834118;C:20161426;G:85585275;T:123610648;N:16145 158 0     93834118 20161426 85585275 123610648 16145 SRX8707716 SRS6984303 SRA1097340 GEO UMR MARBEC, INRAE 1 0.00015   0.00013   0.99997   0.0   158   T   under 1.2% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;