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run_metadata

200 rows where devstage_curation = "Adult" and experiment.library_strategy = "Bisulfite-Seq"

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tissue_curation_coarse 2

tissue_curation 2

experiment.library_selection 2

experiment.library_layout 2

technology 1

experiment.platform 1

experiment.library_strategy 1

  • Bisulfite-Seq · 200 ✖

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 200 ✖
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
29641 29641 SRR27397714 SRX23073965 SRS20033317 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library10 PG2   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 10|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS10 RRBS10 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG2_L7_1.fq.gz PG2_L7_2.fq.gz fastq fastq 981695400.0 3272318.0 PG2 L7 1.fq.gz 0:150 1:150 A:253124715;C:152724975;G:341105704;T:234698202;N:41804 150 150     253124715 152724975 341105704 234698202 41804 SRX23073965 SRS20033317 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0164 0.00047 0.01505 0.00036 0.9961 0.99965 0.58102 0.47058 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29642 29642 SRR27397715 SRX23073964 SRS20033316 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library9 PG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 9|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS9 RRBS9 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG1_L7_1.fq.gz PG1_L7_2.fq.gz fastq fastq 1157067600.0 3856892.0 PG1 L7 1.fq.gz 0:150 1:150 A:278308283;C:162228777;G:432676687;T:283803806;N:50047 150 150     278308283 162228777 432676687 283803806 50047 SRX23073964 SRS20033316 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02347 0.02319 0.02188 0.02162 0.99517 0.99519 0.50342 0.51027 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29643 29643 SRR27397716 SRX23073963 SRS20033315 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library8 LG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 8|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS8 RRBS8 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG4_L7_1.fq.gz LG4_L7_2.fq.gz fastq fastq 1080684300.0 3602281.0 LG4 L7 1.fq.gz 0:150 1:150 A:270759422;C:159278390;G:387693215;T:262907381;N:45892 150 150     270759422 159278390 387693215 262907381 45892 SRX23073963 SRS20033315 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01698 0.00033 0.01593 0.00026 0.99675 0.99979 0.4974 0.2 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29644 29644 SRR27397717 SRX23073962 SRS20033314 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library7 LG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 7|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS7 RRBS7 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG3_L7_1.fq.gz LG3_L7_2.fq.gz fastq fastq 1223063700.0 4076879.0 LG3 L7 1.fq.gz 0:150 1:150 A:301167012;C:182106743;G:443329321;T:296409064;N:51560 150 150     301167012 182106743 443329321 296409064 51560 SRX23073962 SRS20033314 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01787 0.01759 0.01644 0.01622 0.99545 0.99582 0.56826 0.56126 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29645 29645 SRR27397718 SRX23073961 SRS20033313 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library6 LG2   strain:ab|age:adult|collection date:2023 02 07|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 6|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS6 RRBS6 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG2_L7_1.fq.gz LG2_L7_2.fq.gz fastq fastq 1188600300.0 3962001.0 LG2 L7 1.fq.gz 0:150 1:150 A:294477343;C:172669379;G:418732939;T:302669966;N:50673 150 150     294477343 172669379 418732939 302669966 50673 SRX23073961 SRS20033313 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0205 0.02042 0.01903 0.01894 0.99584 0.99577 0.51685 0.51824 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29646 29646 SRR27397719 SRX23073960 SRS20033312 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library5 LG1   strain:ab|age:adult|collection date:2023 02 06|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 5|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS5 RRBS5 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     LG1_L7_1.fq.gz LG1_L7_2.fq.gz fastq fastq 1048183200.0 3493944.0 LG1 L7 1.fq.gz 0:150 1:150 A:260330612;C:163890192;G:372783427;T:251133569;N:45400 150 150     260330612 163890192 372783427 251133569 45400 SRX23073960 SRS20033312 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01999 0.00059 0.01851 0.00045 0.99563 0.99961 0.49816 0.36842 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29647 29647 SRR27397720 SRX23073959 SRS20033311 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library4 CG4   strain:ab|age:adult|collection date:2023 02 05|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 4|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS4 RRBS4 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG4_L7_1.fq.gz CG4_L7_2.fq.gz fastq fastq 1547200200.0 5157334.0 CG4 L7 1.fq.gz 0:150 1:150 A:389261224;C:230650937;G:559928386;T:367293552;N:66101 150 150     389261224 230650937 559928386 367293552 66101 SRX23073959 SRS20033311 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01121 0.00022 0.01024 0.00018 0.99713 0.99991 0.56111 1.0 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29648 29648 SRR27397721 SRX23073958 SRS20033310 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library3 CG3   strain:ab|age:adult|collection date:2023 02 04|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 3|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS3 RRBS3 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG3_L7_1.fq.gz CG3_L7_2.fq.gz fastq fastq 1164022500.0 3880075.0 CG3 L7 1.fq.gz 0:150 1:150 A:281490630;C:172929357;G:423757698;T:285795200;N:49615 150 150     281490630 172929357 423757698 285795200 49615 SRX23073958 SRS20033310 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.0188 0.00046 0.01744 0.00039 0.99626 0.99981 0.55421 0.6 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29649 29649 SRR27397722 SRX23073957 SRS20033309 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library12 PG4   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 12|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS12 RRBS12 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG4_L7_1.fq.gz PG4_L7_2.fq.gz fastq fastq 937521000.0 3125070.0 PG4 L7 1.fq.gz 0:150 1:150 A:230277419;C:145742183;G:328432893;T:233027715;N:40790 150 150     230277419 145742183 328432893 233027715 40790 SRX23073957 SRS20033309 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01943 0.01926 0.01799 0.01786 0.99575 0.99588 0.51136 0.48062 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29650 29650 SRR27397723 SRX23073956 SRS20033308 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library11 PG3   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 11|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS11 RRBS11 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     PG3_L7_1.fq.gz PG3_L7_2.fq.gz fastq fastq 1256812500.0 4189375.0 PG3 L7 1.fq.gz 0:150 1:150 A:318736087;C:194540494;G:434374337;T:309107761;N:53821 150 150     318736087 194540494 434374337 309107761 53821 SRX23073956 SRS20033308 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.01424 0.00046 0.01316 0.00036 0.99683 0.99975 0.49746 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29651 29651 SRR27397724 SRX23073955 SRS20033307 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library2 CG2   strain:ab|age:adult|collection date:2023 02 03|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 2|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS2 RRBS2 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG2_L7_1.fq.gz CG2_L7_2.fq.gz fastq fastq 1157888400.0 3859628.0 CG2 L7 1.fq.gz 0:150 1:150 A:292628434;C:171796176;G:406707172;T:286706357;N:50261 150 150     292628434 171796176 406707172 286706357 50261 SRX23073955 SRS20033307 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02036 0.02023 0.01903 0.01889 0.99616 0.99614 0.55102 0.57894 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
29652 29652 SRR27397725 SRX23073954 SRS20033306 SRP480899 PRJNA1060279 EPIFISH PRJNA1060279 Other Epigenetic changes in fish during domestication       RRBS library1 CG1   strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 1|BioSampleModel:Model organism or animal                 RNA seq of danio rerio RRBS1 RRBS1 Library preparation kit used Zymo Seq RRBS Library Kit     Bisulfite-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP480899     CG1_L7_1.fq.gz CG1_L7_2.fq.gz fastq fastq 1004867700.0 3349559.0 CG1 L7 1.fq.gz 0:150 1:150 A:247727849;C:158203386;G:350367173;T:248526527;N:42765 150 150     247727849 158203386 350367173 248526527 42765 SRX23073954 SRS20033306 SRA1777947 Nord University|Bioscience and Aquaculture Nord University 2 0.02764 0.00147 0.0252 0.00121 0.99233 0.99926 0.51541 0.5 150 150 T T mates < 9% mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Norway 2024-01-02 Adult Adult Muscle Muscular System
60257 60257 SRR12194979 SRX8707751 SRS6984337 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B15 GSM4666897   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B15 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666897 GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq GSM4666897   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666897 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-1_S19_L001_R1_001.fastq.gz P6-1_S19_L001_R2_001.fastq.gz fastq fastq 626505630.0 2077251.0 GSM4666897 r1 0:150.88 1:150.72 A:231784841;C:80425574;G:110085227;T:204102624;N:107364 150 150     231784841 80425574 110085227 204102624 107364 SRX8707751 SRS6984337 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00014 0.00014 0.00013 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60258 60258 SRR12194980 SRX8707751 SRS6984337 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B15 GSM4666897   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B15 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666897 GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq GSM4666897   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666897 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-1_S19_L002_R1_001.fastq.gz P6-1_S19_L002_R2_001.fastq.gz fastq fastq 646447345.0 2143304.0 GSM4666897 r2 0:150.88 1:150.73 A:237189853;C:82748065;G:118625007;T:207787390;N:97030 150 150     237189853 82748065 118625007 207787390 97030 SRX8707751 SRS6984337 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00023 0.0002 0.00022 0.00019 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60259 60259 SRR12194981 SRX8707751 SRS6984337 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B15 GSM4666897   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B15 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666897 GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq GSM4666897   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666897 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-1_S19_L003_R1_001.fastq.gz P6-1_S19_L003_R2_001.fastq.gz fastq fastq 603701501.0 2001537.0 GSM4666897 r3 0:150.88 1:150.74 A:223744015;C:77591778;G:105364702;T:196924362;N:76644 150 150     223744015 77591778 105364702 196924362 76644 SRX8707751 SRS6984337 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00017 0.00018 0.00016 0.00017 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60260 60260 SRR12194982 SRX8707751 SRS6984337 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B15 GSM4666897   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B15 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666897 GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq GSM4666897   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666897 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-1_S19_L004_R1_001.fastq.gz P6-1_S19_L004_R2_001.fastq.gz fastq fastq 626999718.0 2078709.0 GSM4666897 r4 0:150.89 1:150.74 A:230679756;C:80184689;G:114353798;T:201714990;N:66485 150 150     230679756 80184689 114353798 201714990 66485 SRX8707751 SRS6984337 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00023 0.00014 0.00022 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60261 60261 SRR12194975 SRX8707750 SRS6984338 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B14 GSM4666896   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B14 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666896 GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq GSM4666896   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666896 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-6_S18_L001_R1_001.fastq.gz P5-6_S18_L001_R2_001.fastq.gz fastq fastq 362632647.0 1202487.0 GSM4666896 r1 0:150.85 1:150.72 A:134187427;C:47593733;G:60920059;T:119870940;N:60488 150 150     134187427 47593733 60920059 119870940 60488 SRX8707750 SRS6984338 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00012 0.00018 0.0001 0.00015 0.99997 0.99997 0.0 0.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60262 60262 SRR12194976 SRX8707750 SRS6984338 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B14 GSM4666896   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B14 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666896 GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq GSM4666896   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666896 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-6_S18_L002_R2_001.fastq.gz P5-6_S18_L002_R1_001.fastq.gz fastq fastq 371328815.0 1231316.0 GSM4666896 r2 0:150.85 1:150.72 A:136045457;C:48493148;G:65714953;T:121017397;N:57860 150 150     136045457 48493148 65714953 121017397 57860 SRX8707750 SRS6984338 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00017 0.00014 0.00015 1.0 0.99997   1.0 149 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60263 60263 SRR12194977 SRX8707750 SRS6984338 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B14 GSM4666896   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B14 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666896 GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq GSM4666896   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666896 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-6_S18_L003_R1_001.fastq.gz P5-6_S18_L003_R2_001.fastq.gz fastq fastq 349651276.0 1159376.0 GSM4666896 r3 0:150.85 1:150.74 A:129571477;C:45879693;G:58514844;T:115645628;N:39634 150 150     129571477 45879693 58514844 115645628 39634 SRX8707750 SRS6984338 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00011 0.00018 0.0001 0.00017 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60264 60264 SRR12194978 SRX8707750 SRS6984338 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B14 GSM4666896   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B14 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666896 GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq GSM4666896   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666896 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-6_S18_L004_R1_001.fastq.gz P5-6_S18_L004_R2_001.fastq.gz fastq fastq 359741298.0 1192811.0 GSM4666896 r4 0:150.85 1:150.74 A:132192036;C:47006274;G:63129910;T:117375509;N:37569 150 150     132192036 47006274 63129910 117375509 37569 SRX8707750 SRS6984338 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00017 0.00015 0.00014 0.00014 0.99995 1.0 0.0   150 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60265 60265 SRR12194971 SRX8707749 SRS6984336 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B16 GSM4666895   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B16 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666895 GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq GSM4666895   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666895 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-2_S20_L001_R1_001.fastq.gz P6-2_S20_L001_R2_001.fastq.gz fastq fastq 767379925.0 2544544.0 GSM4666895 r1 0:150.86 1:150.72 A:285185142;C:99053157;G:127959880;T:255052821;N:128925 150 150     285185142 99053157 127959880 255052821 128925 SRX8707749 SRS6984336 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.0002 0.00014 0.00019 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60266 60266 SRR12194972 SRX8707749 SRS6984336 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B16 GSM4666895   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B16 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666895 GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq GSM4666895   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666895 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-2_S20_L002_R1_001.fastq.gz P6-2_S20_L002_R2_001.fastq.gz fastq fastq 801048716.0 2656168.0 GSM4666895 r2 0:150.86 1:150.72 A:294948276;C:103019861;G:140485071;T:262473164;N:122344 150 150     294948276 103019861 140485071 262473164 122344 SRX8707749 SRS6984336 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00021 0.00014 0.0002 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60267 60267 SRR12194973 SRX8707749 SRS6984336 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B16 GSM4666895   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B16 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666895 GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq GSM4666895   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666895 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-2_S20_L003_R1_001.fastq.gz P6-2_S20_L003_R2_001.fastq.gz fastq fastq 740955391.0 2456791.0 GSM4666895 r3 0:150.86 1:150.73 A:275837928;C:95675216;G:123037692;T:246311396;N:93159 150 150     275837928 95675216 123037692 246311396 93159 SRX8707749 SRS6984336 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00014 0.0003 0.00013 0.00029 1.0 1.0     151 150 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60268 60268 SRR12194974 SRX8707749 SRS6984336 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B16 GSM4666895   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B16 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666895 GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq GSM4666895   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666895 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P6-2_S20_L004_R1_001.fastq.gz P6-2_S20_L004_R2_001.fastq.gz fastq fastq 776243814.0 2573716.0 GSM4666895 r4 0:150.86 1:150.74 A:286702347;C:99810593;G:135079256;T:254574374;N:77244 150 150     286702347 99810593 135079256 254574374 77244 SRX8707749 SRS6984336 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00029 0.00021 0.00026 0.0002 0.99997 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60269 60269 SRR12194967 SRX8707748 SRS6984335 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B13 GSM4666894   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B13 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666894 GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq GSM4666894   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666894 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-5_S17_L001_R2_001.fastq.gz P5-5_S17_L001_R1_001.fastq.gz fastq fastq 818338842.0 2713477.0 GSM4666894 r1 0:150.86 1:150.72 A:301830002;C:107389155;G:139489598;T:269496153;N:133934 150 150     301830002 107389155 139489598 269496153 133934 SRX8707748 SRS6984335 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00019 0.00014 0.00018 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60270 60270 SRR12194968 SRX8707748 SRS6984335 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B13 GSM4666894   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B13 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666894 GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq GSM4666894   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666894 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-5_S17_L002_R1_001.fastq.gz P5-5_S17_L002_R2_001.fastq.gz fastq fastq 846228975.0 2805930.0 GSM4666894 r2 0:150.86 1:150.72 A:308870822;C:110466773;G:152421867;T:274347549;N:121964 150 150     308870822 110466773 152421867 274347549 121964 SRX8707748 SRS6984335 SRA1097340 GEO UMR MARBEC, INRAE 2 0.0002 0.00015 0.00018 0.00011 0.99997 0.99997 0.0 1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60271 60271 SRR12194969 SRX8707748 SRS6984335 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B13 GSM4666894   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B13 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666894 GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq GSM4666894   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666894 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-5_S17_L003_R2_001.fastq.gz P5-5_S17_L003_R1_001.fastq.gz fastq fastq 790658387.0 2621591.0 GSM4666894 r3 0:150.86 1:150.73 A:292027450;C:103748394;G:134258887;T:260520383;N:103273 150 150     292027450 103748394 134258887 260520383 103273 SRX8707748 SRS6984335 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00016 0.00014 0.00013 0.00013 0.99995 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60272 60272 SRR12194970 SRX8707748 SRS6984335 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B13 GSM4666894   tissue:adult whole brain|strain:AB line|generation:F1|Sex:male adult whole brain B13 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:M GSM4666894 GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq GSM4666894   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666894 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-5_S17_L004_R1_001.fastq.gz P5-5_S17_L004_R2_001.fastq.gz fastq fastq 815907660.0 2705210.0 GSM4666894 r4 0:150.86 1:150.74 A:298609755;C:106483104;G:145958694;T:264775944;N:80163 150 150     298609755 106483104 145958694 264775944 80163 SRX8707748 SRS6984335 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00029 0.00012 0.00028 0.99997 1.0 0.0   151 150 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60273 60273 SRR12194963 SRX8707747 SRS6984334 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B12 GSM4666893   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B12 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666893 GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq GSM4666893   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666893 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-4_S16_L001_R1_001.fastq.gz P5-4_S16_L001_R2_001.fastq.gz fastq fastq 700559459.0 2322745.0 GSM4666893 r1 0:150.89 1:150.72 A:258008915;C:91134331;G:124267705;T:227032496;N:116012 150 150     258008915 91134331 124267705 227032496 116012 SRX8707747 SRS6984334 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00013 0.00017 0.00012 0.00016 1.0 1.0     151 150 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60274 60274 SRR12194964 SRX8707747 SRS6984334 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B12 GSM4666893   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B12 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666893 GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq GSM4666893   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666893 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-4_S16_L002_R2_001.fastq.gz P5-4_S16_L002_R1_001.fastq.gz fastq fastq 728622859.0 2415726.0 GSM4666893 r2 0:150.89 1:150.73 A:265918573;C:94480694;G:135330434;T:232783961;N:109197 150 150     265918573 94480694 135330434 232783961 109197 SRX8707747 SRS6984334 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00017 0.00022 0.00014 0.00021 0.99995 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60275 60275 SRR12194965 SRX8707747 SRS6984334 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B12 GSM4666893   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B12 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666893 GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq GSM4666893   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666893 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-4_S16_L003_R1_001.fastq.gz P5-4_S16_L003_R2_001.fastq.gz fastq fastq 676046027.0 2241356.0 GSM4666893 r3 0:150.89 1:150.74 A:249345303;C:88016423;G:119300461;T:219299203;N:84637 150 150     249345303 88016423 119300461 219299203 84637 SRX8707747 SRS6984334 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00022 0.00024 0.00021 0.00023 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60276 60276 SRR12194966 SRX8707747 SRS6984334 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B12 GSM4666893   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B12 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666893 GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq GSM4666893   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666893 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-4_S16_L004_R1_001.fastq.gz P5-4_S16_L004_R2_001.fastq.gz fastq fastq 703809171.0 2333304.0 GSM4666893 r4 0:150.89 1:150.75 A:257462138;C:91215734;G:129931298;T:225132059;N:67942 150 150     257462138 91215734 129931298 225132059 67942 SRX8707747 SRS6984334 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00022 0.00014 0.00021 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60277 60277 SRR12194959 SRX8707746 SRS6984333 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B11 GSM4666892   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B11 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666892 GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq GSM4666892   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666892 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-3_S15_L001_R1_001.fastq.gz P5-3_S15_L001_R2_001.fastq.gz fastq fastq 875916606.0 2904546.0 GSM4666892 r1 0:150.85 1:150.72 A:323769382;C:115778670;G:148157089;T:288058377;N:153088 150 150     323769382 115778670 148157089 288058377 153088 SRX8707746 SRS6984333 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 9e-05 0.00014 6e-05 1.0 0.99997   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60278 60278 SRR12194960 SRX8707746 SRS6984333 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B11 GSM4666892   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B11 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666892 GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq GSM4666892   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666892 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-3_S15_L002_R1_001.fastq.gz P5-3_S15_L002_R2_001.fastq.gz fastq fastq 906266878.0 3005123.0 GSM4666892 r2 0:150.85 1:150.73 A:331841540;C:119200098;G:161492735;T:293597000;N:135505 150 150     331841540 119200098 161492735 293597000 135505 SRX8707746 SRS6984333 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00015 0.00013 0.00012 0.99997 0.99997 0.0 1.0 150 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60279 60279 SRR12194961 SRX8707746 SRS6984333 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B11 GSM4666892   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B11 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666892 GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq GSM4666892   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666892 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-3_S15_L003_R1_001.fastq.gz P5-3_S15_L003_R2_001.fastq.gz fastq fastq 845425773.0 2803262.0 GSM4666892 r3 0:150.85 1:150.74 A:312923215;C:111769611;G:142528786;T:278100796;N:103365 150 150     312923215 111769611 142528786 278100796 103365 SRX8707746 SRS6984333 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00019 0.00017 0.00018 0.00015 1.0 0.99997   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60280 60280 SRR12194962 SRX8707746 SRS6984333 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B11 GSM4666892   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B11 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666892 GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq GSM4666892   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666892 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-3_S15_L004_R1_001.fastq.gz P5-3_S15_L004_R2_001.fastq.gz fastq fastq 879089154.0 2914795.0 GSM4666892 r4 0:150.85 1:150.74 A:322802592;C:115646186;G:155527621;T:285023759;N:88996 150 150     322802592 115646186 155527621 285023759 88996 SRX8707746 SRS6984333 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00016 0.00014 0.00013 0.00013 0.99993 1.0 0.0   151 150 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60281 60281 SRR12194955 SRX8707745 SRS6984332 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B10 GSM4666891   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B10 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666891 GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq GSM4666891   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666891 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-2_S14_L001_R1_001.fastq.gz P5-2_S14_L001_R2_001.fastq.gz fastq fastq 612289518.0 2030276.0 GSM4666891 r1 0:150.86 1:150.72 A:225461166;C:80840857;G:104624118;T:201255710;N:107667 150 150     225461166 80840857 104624118 201255710 107667 SRX8707745 SRS6984332 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00017 0.00021 0.00014 0.00019 0.99995 0.99997 0.5 1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60282 60282 SRR12194956 SRX8707745 SRS6984332 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B10 GSM4666891   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B10 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666891 GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq GSM4666891   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666891 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-2_S14_L002_R1_001.fastq.gz P5-2_S14_L002_R2_001.fastq.gz fastq fastq 634607694.0 2104258.0 GSM4666891 r2 0:150.86 1:150.73 A:231299105;C:83482957;G:114131270;T:205602870;N:91492 150 150     231299105 83482957 114131270 205602870 91492 SRX8707745 SRS6984332 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00028 0.00014 0.00027 0.00013 1.0 1.0     150 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60283 60283 SRR12194957 SRX8707745 SRS6984332 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B10 GSM4666891   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B10 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666891 GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq GSM4666891   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666891 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-2_S14_L003_R1_001.fastq.gz P5-2_S14_L003_R2_001.fastq.gz fastq fastq 590348631.0 1957422.0 GSM4666891 r3 0:150.86 1:150.74 A:217666345;C:77986590;G:100434245;T:194187946;N:73505 150 150     217666345 77986590 100434245 194187946 73505 SRX8707745 SRS6984332 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00015 0.00017 0.00014 0.00016 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60284 60284 SRR12194958 SRX8707745 SRS6984332 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B10 GSM4666891   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B10 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666891 GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq GSM4666891   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666891 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-2_S14_L004_R1_001.fastq.gz P5-2_S14_L004_R2_001.fastq.gz fastq fastq 613280111.0 2033405.0 GSM4666891 r4 0:150.86 1:150.74 A:224142863;C:80650974;G:109510542;T:198916747;N:58985 150 150     224142863 80650974 109510542 198916747 58985 SRX8707745 SRS6984332 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00019 0.00015 0.00016 0.00014 0.99995 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60285 60285 SRR12194951 SRX8707744 SRS6984331 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B9 GSM4666890   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B9 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666890 GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq GSM4666890   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666890 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-1_S13_L001_R1_001.fastq.gz P5-1_S13_L001_R2_001.fastq.gz fastq fastq 871269001.0 2888776.0 GSM4666890 r1 0:150.89 1:150.72 A:314795365;C:112414599;G:160314482;T:283594068;N:150487 150 150     314795365 112414599 160314482 283594068 150487 SRX8707744 SRS6984331 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00013 0.00015 0.00012 0.00014 1.0 1.0     151 150 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60286 60286 SRR12194952 SRX8707744 SRS6984331 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B9 GSM4666890   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B9 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666890 GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq GSM4666890   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666890 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-1_S13_L002_R1_001.fastq.gz P5-1_S13_L002_R2_001.fastq.gz fastq fastq 902501754.0 2992248.0 GSM4666890 r2 0:150.89 1:150.72 A:322645331;C:115934758;G:174818254;T:288967241;N:136170 150 150     322645331 115934758 174818254 288967241 136170 SRX8707744 SRS6984331 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00012 0.00026 0.0001 0.00025 0.99997 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60287 60287 SRR12194953 SRX8707744 SRS6984331 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B9 GSM4666890   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B9 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666890 GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq GSM4666890   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666890 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-1_S13_L003_R1_001.fastq.gz P5-1_S13_L003_R2_001.fastq.gz fastq fastq 839686349.0 2783900.0 GSM4666890 r3 0:150.89 1:150.73 A:303601399;C:108395743;G:153892840;T:273690404;N:105963 150 150     303601399 108395743 153892840 273690404 105963 SRX8707744 SRS6984331 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00012 0.00018 0.00011 0.00017 1.0 1.0     151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
60288 60288 SRR12194954 SRX8707744 SRS6984331 SRP271280 PRJNA645421 Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L GSE154206 Other In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0   pubmed:33752003   adult whole brain B9 GSM4666890   tissue:adult whole brain|strain:AB line|generation:F1|Sex:female adult whole brain B9 Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction adult whole brain   Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS   strain:AB line|generation:F1|Sex:F GSM4666890 GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq GSM4666890   1 Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS GEO Accession:GSM4666890 Bisulfite-Seq TRANSCRIPTOMIC Reduced Representation PAIRED ILLUMINA NextSeq 550   SRP271280     P5-1_S13_L004_R1_001.fastq.gz P5-1_S13_L004_R2_001.fastq.gz fastq fastq 872412889.0 2892296.0 GSM4666890 r4 0:150.89 1:150.74 A:312195512;C:111967601;G:168316892;T:279843866;N:89018 150 150     312195512 111967601 168316892 279843866 89018 SRX8707744 SRS6984331 SRA1097340 GEO UMR MARBEC, INRAE 2 0.00021 0.00034 0.00018 0.00033 0.99995 1.0 0.0   151 151 T T mates < 9% mapping rate illumina nextseq unknown other unknown bulk unknown unknown   France 2020-07-10 Adult Adult Brain Nervous System
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

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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");;