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,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,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,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,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,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,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,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,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,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,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,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,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,SRR12194979,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L001_R1_001.fastq.gz P6-1_S19_L001_R2_001.fastq.gz,fastq fastq,626505630.0,2077251.0,GSM4666897 r1,0:150.88 1:150.72,A:231784841;C:80425574;G:110085227;T:204102624;N:107364,150,150,,,231784841,80425574,110085227,204102624,107364,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00014,0.00014,0.00013,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60258,SRR12194980,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L002_R1_001.fastq.gz P6-1_S19_L002_R2_001.fastq.gz,fastq fastq,646447345.0,2143304.0,GSM4666897 r2,0:150.88 1:150.73,A:237189853;C:82748065;G:118625007;T:207787390;N:97030,150,150,,,237189853,82748065,118625007,207787390,97030,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00023,0.0002,0.00022,0.00019,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60259,SRR12194981,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L003_R1_001.fastq.gz P6-1_S19_L003_R2_001.fastq.gz,fastq fastq,603701501.0,2001537.0,GSM4666897 r3,0:150.88 1:150.74,A:223744015;C:77591778;G:105364702;T:196924362;N:76644,150,150,,,223744015,77591778,105364702,196924362,76644,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00018,0.00016,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60260,SRR12194982,SRX8707751,SRS6984337,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B15,GSM4666897,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B15,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666897,GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq,GSM4666897,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666897,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-1_S19_L004_R1_001.fastq.gz P6-1_S19_L004_R2_001.fastq.gz,fastq fastq,626999718.0,2078709.0,GSM4666897 r4,0:150.89 1:150.74,A:230679756;C:80184689;G:114353798;T:201714990;N:66485,150,150,,,230679756,80184689,114353798,201714990,66485,SRX8707751,SRS6984337,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00023,0.00014,0.00022,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60261,SRR12194975,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L001_R1_001.fastq.gz P5-6_S18_L001_R2_001.fastq.gz,fastq fastq,362632647.0,1202487.0,GSM4666896 r1,0:150.85 1:150.72,A:134187427;C:47593733;G:60920059;T:119870940;N:60488,150,150,,,134187427,47593733,60920059,119870940,60488,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00018,0.0001,0.00015,0.99997,0.99997,0.0,0.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60262,SRR12194976,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L002_R2_001.fastq.gz P5-6_S18_L002_R1_001.fastq.gz,fastq fastq,371328815.0,1231316.0,GSM4666896 r2,0:150.85 1:150.72,A:136045457;C:48493148;G:65714953;T:121017397;N:57860,150,150,,,136045457,48493148,65714953,121017397,57860,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00017,0.00014,0.00015,1.0,0.99997,,1.0,149,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60263,SRR12194977,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L003_R1_001.fastq.gz P5-6_S18_L003_R2_001.fastq.gz,fastq fastq,349651276.0,1159376.0,GSM4666896 r3,0:150.85 1:150.74,A:129571477;C:45879693;G:58514844;T:115645628;N:39634,150,150,,,129571477,45879693,58514844,115645628,39634,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00011,0.00018,0.0001,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60264,SRR12194978,SRX8707750,SRS6984338,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B14,GSM4666896,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B14,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666896,GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq,GSM4666896,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666896,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-6_S18_L004_R1_001.fastq.gz P5-6_S18_L004_R2_001.fastq.gz,fastq fastq,359741298.0,1192811.0,GSM4666896 r4,0:150.85 1:150.74,A:132192036;C:47006274;G:63129910;T:117375509;N:37569,150,150,,,132192036,47006274,63129910,117375509,37569,SRX8707750,SRS6984338,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00015,0.00014,0.00014,0.99995,1.0,0.0,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60265,SRR12194971,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L001_R1_001.fastq.gz P6-2_S20_L001_R2_001.fastq.gz,fastq fastq,767379925.0,2544544.0,GSM4666895 r1,0:150.86 1:150.72,A:285185142;C:99053157;G:127959880;T:255052821;N:128925,150,150,,,285185142,99053157,127959880,255052821,128925,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.0002,0.00014,0.00019,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60266,SRR12194972,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L002_R1_001.fastq.gz P6-2_S20_L002_R2_001.fastq.gz,fastq fastq,801048716.0,2656168.0,GSM4666895 r2,0:150.86 1:150.72,A:294948276;C:103019861;G:140485071;T:262473164;N:122344,150,150,,,294948276,103019861,140485071,262473164,122344,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00021,0.00014,0.0002,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60267,SRR12194973,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L003_R1_001.fastq.gz P6-2_S20_L003_R2_001.fastq.gz,fastq fastq,740955391.0,2456791.0,GSM4666895 r3,0:150.86 1:150.73,A:275837928;C:95675216;G:123037692;T:246311396;N:93159,150,150,,,275837928,95675216,123037692,246311396,93159,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00014,0.0003,0.00013,0.00029,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60268,SRR12194974,SRX8707749,SRS6984336,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B16,GSM4666895,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B16,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666895,GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq,GSM4666895,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666895,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P6-2_S20_L004_R1_001.fastq.gz P6-2_S20_L004_R2_001.fastq.gz,fastq fastq,776243814.0,2573716.0,GSM4666895 r4,0:150.86 1:150.74,A:286702347;C:99810593;G:135079256;T:254574374;N:77244,150,150,,,286702347,99810593,135079256,254574374,77244,SRX8707749,SRS6984336,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00029,0.00021,0.00026,0.0002,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60269,SRR12194967,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L001_R2_001.fastq.gz P5-5_S17_L001_R1_001.fastq.gz,fastq fastq,818338842.0,2713477.0,GSM4666894 r1,0:150.86 1:150.72,A:301830002;C:107389155;G:139489598;T:269496153;N:133934,150,150,,,301830002,107389155,139489598,269496153,133934,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00019,0.00014,0.00018,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60270,SRR12194968,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L002_R1_001.fastq.gz P5-5_S17_L002_R2_001.fastq.gz,fastq fastq,846228975.0,2805930.0,GSM4666894 r2,0:150.86 1:150.72,A:308870822;C:110466773;G:152421867;T:274347549;N:121964,150,150,,,308870822,110466773,152421867,274347549,121964,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.0002,0.00015,0.00018,0.00011,0.99997,0.99997,0.0,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60271,SRR12194969,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L003_R2_001.fastq.gz P5-5_S17_L003_R1_001.fastq.gz,fastq fastq,790658387.0,2621591.0,GSM4666894 r3,0:150.86 1:150.73,A:292027450;C:103748394;G:134258887;T:260520383;N:103273,150,150,,,292027450,103748394,134258887,260520383,103273,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00016,0.00014,0.00013,0.00013,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60272,SRR12194970,SRX8707748,SRS6984335,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B13,GSM4666894,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:male,adult whole brain B13,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:M,GSM4666894,GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq,GSM4666894,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666894,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-5_S17_L004_R1_001.fastq.gz P5-5_S17_L004_R2_001.fastq.gz,fastq fastq,815907660.0,2705210.0,GSM4666894 r4,0:150.86 1:150.74,A:298609755;C:106483104;G:145958694;T:264775944;N:80163,150,150,,,298609755,106483104,145958694,264775944,80163,SRX8707748,SRS6984335,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00029,0.00012,0.00028,0.99997,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60273,SRR12194963,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L001_R1_001.fastq.gz P5-4_S16_L001_R2_001.fastq.gz,fastq fastq,700559459.0,2322745.0,GSM4666893 r1,0:150.89 1:150.72,A:258008915;C:91134331;G:124267705;T:227032496;N:116012,150,150,,,258008915,91134331,124267705,227032496,116012,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00017,0.00012,0.00016,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60274,SRR12194964,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L002_R2_001.fastq.gz P5-4_S16_L002_R1_001.fastq.gz,fastq fastq,728622859.0,2415726.0,GSM4666893 r2,0:150.89 1:150.73,A:265918573;C:94480694;G:135330434;T:232783961;N:109197,150,150,,,265918573,94480694,135330434,232783961,109197,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00022,0.00014,0.00021,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60275,SRR12194965,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L003_R1_001.fastq.gz P5-4_S16_L003_R2_001.fastq.gz,fastq fastq,676046027.0,2241356.0,GSM4666893 r3,0:150.89 1:150.74,A:249345303;C:88016423;G:119300461;T:219299203;N:84637,150,150,,,249345303,88016423,119300461,219299203,84637,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00022,0.00024,0.00021,0.00023,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60276,SRR12194966,SRX8707747,SRS6984334,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B12,GSM4666893,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B12,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666893,GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq,GSM4666893,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666893,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-4_S16_L004_R1_001.fastq.gz P5-4_S16_L004_R2_001.fastq.gz,fastq fastq,703809171.0,2333304.0,GSM4666893 r4,0:150.89 1:150.75,A:257462138;C:91215734;G:129931298;T:225132059;N:67942,150,150,,,257462138,91215734,129931298,225132059,67942,SRX8707747,SRS6984334,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00022,0.00014,0.00021,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60277,SRR12194959,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L001_R1_001.fastq.gz P5-3_S15_L001_R2_001.fastq.gz,fastq fastq,875916606.0,2904546.0,GSM4666892 r1,0:150.85 1:150.72,A:323769382;C:115778670;G:148157089;T:288058377;N:153088,150,150,,,323769382,115778670,148157089,288058377,153088,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,9e-05,0.00014,6e-05,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60278,SRR12194960,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L002_R1_001.fastq.gz P5-3_S15_L002_R2_001.fastq.gz,fastq fastq,906266878.0,3005123.0,GSM4666892 r2,0:150.85 1:150.73,A:331841540;C:119200098;G:161492735;T:293597000;N:135505,150,150,,,331841540,119200098,161492735,293597000,135505,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00015,0.00013,0.00012,0.99997,0.99997,0.0,1.0,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60279,SRR12194961,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L003_R1_001.fastq.gz P5-3_S15_L003_R2_001.fastq.gz,fastq fastq,845425773.0,2803262.0,GSM4666892 r3,0:150.85 1:150.74,A:312923215;C:111769611;G:142528786;T:278100796;N:103365,150,150,,,312923215,111769611,142528786,278100796,103365,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00017,0.00018,0.00015,1.0,0.99997,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60280,SRR12194962,SRX8707746,SRS6984333,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B11,GSM4666892,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B11,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666892,GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq,GSM4666892,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666892,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-3_S15_L004_R1_001.fastq.gz P5-3_S15_L004_R2_001.fastq.gz,fastq fastq,879089154.0,2914795.0,GSM4666892 r4,0:150.85 1:150.74,A:322802592;C:115646186;G:155527621;T:285023759;N:88996,150,150,,,322802592,115646186,155527621,285023759,88996,SRX8707746,SRS6984333,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00016,0.00014,0.00013,0.00013,0.99993,1.0,0.0,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60281,SRR12194955,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L001_R1_001.fastq.gz P5-2_S14_L001_R2_001.fastq.gz,fastq fastq,612289518.0,2030276.0,GSM4666891 r1,0:150.86 1:150.72,A:225461166;C:80840857;G:104624118;T:201255710;N:107667,150,150,,,225461166,80840857,104624118,201255710,107667,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00017,0.00021,0.00014,0.00019,0.99995,0.99997,0.5,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60282,SRR12194956,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L002_R1_001.fastq.gz P5-2_S14_L002_R2_001.fastq.gz,fastq fastq,634607694.0,2104258.0,GSM4666891 r2,0:150.86 1:150.73,A:231299105;C:83482957;G:114131270;T:205602870;N:91492,150,150,,,231299105,83482957,114131270,205602870,91492,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00028,0.00014,0.00027,0.00013,1.0,1.0,,,150,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60283,SRR12194957,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L003_R1_001.fastq.gz P5-2_S14_L003_R2_001.fastq.gz,fastq fastq,590348631.0,1957422.0,GSM4666891 r3,0:150.86 1:150.74,A:217666345;C:77986590;G:100434245;T:194187946;N:73505,150,150,,,217666345,77986590,100434245,194187946,73505,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00015,0.00017,0.00014,0.00016,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60284,SRR12194958,SRX8707745,SRS6984332,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B10,GSM4666891,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B10,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666891,GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq,GSM4666891,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666891,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-2_S14_L004_R1_001.fastq.gz P5-2_S14_L004_R2_001.fastq.gz,fastq fastq,613280111.0,2033405.0,GSM4666891 r4,0:150.86 1:150.74,A:224142863;C:80650974;G:109510542;T:198916747;N:58985,150,150,,,224142863,80650974,109510542,198916747,58985,SRX8707745,SRS6984332,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00019,0.00015,0.00016,0.00014,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60285,SRR12194951,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L001_R1_001.fastq.gz P5-1_S13_L001_R2_001.fastq.gz,fastq fastq,871269001.0,2888776.0,GSM4666890 r1,0:150.89 1:150.72,A:314795365;C:112414599;G:160314482;T:283594068;N:150487,150,150,,,314795365,112414599,160314482,283594068,150487,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00013,0.00015,0.00012,0.00014,1.0,1.0,,,151,150,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60286,SRR12194952,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L002_R1_001.fastq.gz P5-1_S13_L002_R2_001.fastq.gz,fastq fastq,902501754.0,2992248.0,GSM4666890 r2,0:150.89 1:150.72,A:322645331;C:115934758;G:174818254;T:288967241;N:136170,150,150,,,322645331,115934758,174818254,288967241,136170,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00026,0.0001,0.00025,0.99997,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60287,SRR12194953,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L003_R1_001.fastq.gz P5-1_S13_L003_R2_001.fastq.gz,fastq fastq,839686349.0,2783900.0,GSM4666890 r3,0:150.89 1:150.73,A:303601399;C:108395743;G:153892840;T:273690404;N:105963,150,150,,,303601399,108395743,153892840,273690404,105963,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00012,0.00018,0.00011,0.00017,1.0,1.0,,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
60288,SRR12194954,SRX8707744,SRS6984331,SRP271280,PRJNA645421,Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L,GSE154206,Other,In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0,,pubmed:33752003,,adult whole brain B9,GSM4666890,,tissue:adult whole brain|strain:AB line|generation:F1|Sex:female,adult whole brain B9,"Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with ""L 0  0.6"". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction",adult whole brain,,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,,strain:AB line|generation:F1|Sex:F,GSM4666890,GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq,GSM4666890,,1,Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS,GEO Accession:GSM4666890,Bisulfite-Seq,TRANSCRIPTOMIC,Reduced Representation,PAIRED,ILLUMINA,NextSeq 550,,SRP271280,,,P5-1_S13_L004_R1_001.fastq.gz P5-1_S13_L004_R2_001.fastq.gz,fastq fastq,872412889.0,2892296.0,GSM4666890 r4,0:150.89 1:150.74,A:312195512;C:111967601;G:168316892;T:279843866;N:89018,150,150,,,312195512,111967601,168316892,279843866,89018,SRX8707744,SRS6984331,SRA1097340,GEO,"UMR MARBEC, INRAE",2,0.00021,0.00034,0.00018,0.00033,0.99995,1.0,0.0,,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,France,2020-07-10,Adult,Adult,Brain,Nervous System
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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