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 51269,SRR8663334,SRX5460031,SRS4433921,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 48hpf rep2,GSM3638675,,source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,ZF 48hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,GSM3638675,GSM3638675: ZF 48hpf rep2; Danio rerio; Bisulfite Seq,GSM3638675,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638675,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21257043600.0,70856812.0,GSM3638675 r1,0:150 1:150,A:7462169931;C:3151216767;G:3428144480;T:7214024902;N:1487520,150,150,,,7462169931,3151216767,3428144480,7214024902,1487520,SRX5460031,SRS4433921,SRA855736,GEO,Sun Yat-sen University,2,0.00062,0.00055,0.00017,0.00013,0.99949,0.99945,0.67901,0.75362,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures 51270,SRR8663333,SRX5460030,SRS4433920,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 48hpf rep1,GSM3638674,,source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,ZF 48hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,GSM3638674,GSM3638674: ZF 48hpf rep1; Danio rerio; Bisulfite Seq,GSM3638674,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638674,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,20408177400.0,68027258.0,GSM3638674 r1,0:150 1:150,A:6990585654;C:3225159172;G:3562240517;T:6628764661;N:1427396,150,150,,,6990585654,3225159172,3562240517,6628764661,1427396,SRX5460030,SRS4433920,SRA855736,GEO,Sun Yat-sen University,2,0.0009,0.00071,0.0003,0.00019,0.99928,0.99941,0.6,0.64367,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures 51271,SRR8663332,SRX5460029,SRS4433919,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 24hpf rep2,GSM3638673,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638673,GSM3638673: ZF 24hpf rep2; Danio rerio; Bisulfite Seq,GSM3638673,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638673,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21961409700.0,73204699.0,GSM3638673 r1,0:150 1:150,A:7568027843;C:3406881222;G:3795216487;T:7190249641;N:1034507,150,150,,,7568027843,3406881222,3795216487,7190249641,1034507,SRX5460029,SRS4433919,SRA855736,GEO,Sun Yat-sen University,2,0.00082,0.0007,0.00032,0.00023,0.99945,0.99947,0.65517,0.65,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 51272,SRR8663331,SRX5460028,SRS4433918,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 24hpf rep1,GSM3638672,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638672,GSM3638672: ZF 24hpf rep1; Danio rerio; Bisulfite Seq,GSM3638672,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638672,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,22998615300.0,76662051.0,GSM3638672 r1,0:150 1:150,A:7938674920;C:3553518327;G:3950127781;T:7555207157;N:1087115,150,150,,,7938674920,3553518327,3950127781,7555207157,1087115,SRX5460028,SRS4433918,SRA855736,GEO,Sun Yat-sen University,2,0.00076,0.00067,0.00027,0.00021,0.99926,0.99937,0.53658,0.58666,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 51273,SRR8663330,SRX5460027,SRS4433917,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 16hpf rep2,GSM3638671,,source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,ZF 16hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,GSM3638671,GSM3638671: ZF 16hpf rep2; Danio rerio; Bisulfite Seq,GSM3638671,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638671,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,25701246300.0,85670821.0,GSM3638671 r1,0:150 1:150,A:8976132831;C:3855344207;G:4201042226;T:8667517583;N:1209453,150,150,,,8976132831,3855344207,4201042226,8667517583,1209453,SRX5460027,SRS4433917,SRA855736,GEO,Sun Yat-sen University,2,0.00117,0.00107,0.00036,0.00034,0.99928,0.99941,0.73571,0.75206,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 51274,SRR8663329,SRX5460026,SRS4433916,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 16hpf rep1,GSM3638670,,source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,ZF 16hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,GSM3638670,GSM3638670: ZF 16hpf rep1; Danio rerio; Bisulfite Seq,GSM3638670,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638670,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21585057600.0,71950192.0,GSM3638670 r1,0:150 1:150,A:7493903581;C:3312864799;G:3567558230;T:7209728977;N:1002013,150,150,,,7493903581,3312864799,3567558230,7209728977,1002013,SRX5460026,SRS4433916,SRA855736,GEO,Sun Yat-sen University,2,0.00125,0.00119,0.00039,0.00034,0.99945,0.99947,0.7551,0.76865,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 51275,SRR8663328,SRX5460025,SRS4433915,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 10hpf rep2,GSM3638669,,source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish,ZF 10hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish,GSM3638669,GSM3638669: ZF 10hpf rep2; Danio rerio; Bisulfite Seq,GSM3638669,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638669,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,18449316900.0,61497723.0,GSM3638669 r1,0:150 1:150,A:6508135454;C:2695665097;G:2948776234;T:6296104735;N:635380,150,150,,,6508135454,2695665097,2948776234,6296104735,635380,SRX5460025,SRS4433915,SRA855736,GEO,Sun Yat-sen University,2,0.00092,0.00073,0.00035,0.00017,0.99931,0.99933,0.66019,0.6129,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51276,SRR8663327,SRX5460024,SRS4433914,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 10hpf rep1,GSM3638668,,source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish,ZF 10hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish,GSM3638668,GSM3638668: ZF 10hpf rep1; Danio rerio; Bisulfite Seq,GSM3638668,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638668,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,35064552300.0,116881841.0,GSM3638668 r1,0:150 1:150,A:12442483305;C:5073538954;G:5489080636;T:12058238019;N:1211386,150,150,,,12442483305,5073538954,5489080636,12058238019,1211386,SRX5460024,SRS4433914,SRA855736,GEO,Sun Yat-sen University,2,0.0009,0.00072,0.00028,0.00019,0.99926,0.99945,0.61403,0.67045,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51277,SRR8663326,SRX5460023,SRS4433913,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 8hpf rep2,GSM3638667,,source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish,ZF 8hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish,GSM3638667,GSM3638667: ZF 8hpf rep2; Danio rerio; Bisulfite Seq,GSM3638667,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638667,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,14346635400.0,47822118.0,GSM3638667 r1,0:150 1:150,A:5096565523;C:2082957184;G:2242869596;T:4923737869;N:505228,150,150,,,5096565523,2082957184,2242869596,4923737869,505228,SRX5460023,SRS4433913,SRA855736,GEO,Sun Yat-sen University,2,0.00107,0.00102,0.00035,0.00021,0.99884,0.99884,0.61068,0.71428,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51278,SRR8663325,SRX5460022,SRS4433912,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 8hpf rep1,GSM3638666,,source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish,ZF 8hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish,GSM3638666,GSM3638666: ZF 8hpf rep1; Danio rerio; Bisulfite Seq,GSM3638666,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638666,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,22564435500.0,75214785.0,GSM3638666 r1,0:150 1:150,A:8037530388;C:3263669666;G:3467393764;T:7794998569;N:843113,150,150,,,8037530388,3263669666,3467393764,7794998569,843113,SRX5460022,SRS4433912,SRA855736,GEO,Sun Yat-sen University,2,0.00089,0.00082,0.00026,0.0002,0.99939,0.99939,0.71171,0.73267,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51279,SRR8663324,SRX5460021,SRS4433911,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 6hpf rep2,GSM3638665,,source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish,ZF 6hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish,GSM3638665,GSM3638665: ZF 6hpf rep2; Danio rerio; Bisulfite Seq,GSM3638665,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638665,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,15663840300.0,52212801.0,GSM3638665 r1,0:150 1:150,A:5036459488;C:2768054214;G:3109386160;T:4747198752;N:2741686,150,150,,,5036459488,2768054214,3109386160,4747198752,2741686,SRX5460021,SRS4433911,SRA855736,GEO,Sun Yat-sen University,2,0.00121,0.0008,0.00062,0.00035,0.99922,0.99924,0.41509,0.40789,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51280,SRR8663323,SRX5460020,SRS4433910,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 6hpf rep1,GSM3638664,,source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish,ZF 6hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish,GSM3638664,GSM3638664: ZF 6hpf rep1; Danio rerio; Bisulfite Seq,GSM3638664,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638664,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,13146289500.0,43820965.0,GSM3638664 r1,0:150 1:150,A:4440608717;C:2140855274;G:2250243580;T:4312362152;N:2219777,150,150,,,4440608717,2140855274,2250243580,4312362152,2219777,SRX5460020,SRS4433910,SRA855736,GEO,Sun Yat-sen University,2,0.00073,0.00047,0.00038,0.00014,0.99945,0.99941,0.32812,0.5,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 51281,SRR8663322,SRX5460019,SRS4433909,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 4hpf rep2,GSM3638663,,source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,ZF 4hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,GSM3638663,GSM3638663: ZF 4hpf rep2; Danio rerio; Bisulfite Seq,GSM3638663,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638663,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,14505809700.0,48352699.0,GSM3638663 r1,0:150 1:150,A:4877194269;C:2388898572;G:2560124505;T:4676340810;N:3251544,150,150,,,4877194269,2388898572,2560124505,4676340810,3251544,SRX5460019,SRS4433909,SRA855736,GEO,Sun Yat-sen University,2,0.00065,0.00045,0.00027,0.00016,0.99928,0.99945,0.46376,0.54166,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51282,SRR8663321,SRX5460018,SRS4433908,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 4hpf rep1,GSM3638662,,source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,ZF 4hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,GSM3638662,GSM3638662: ZF 4hpf rep1; Danio rerio; Bisulfite Seq,GSM3638662,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638662,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,13666257000.0,45554190.0,GSM3638662 r1,0:150 1:150,A:4616947793;C:2221382014;G:2373430205;T:4451384606;N:3112382,150,150,,,4616947793,2221382014,2373430205,4451384606,3112382,SRX5460018,SRS4433908,SRA855736,GEO,Sun Yat-sen University,2,0.00094,0.00054,0.00044,0.00022,0.99928,0.99939,0.38888,0.50943,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51283,SRR8663320,SRX5460017,SRS4433907,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 2hpf rep2,GSM3638661,,source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,ZF 2hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,GSM3638661,GSM3638661: ZF 2hpf rep2; Danio rerio; Bisulfite Seq,GSM3638661,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638661,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,14619051000.0,48730170.0,GSM3638661 r1,0:150 1:150,A:4888878605;C:2423468919;G:2611005028;T:4692396498;N:3301950,150,150,,,4888878605,2423468919,2611005028,4692396498,3301950,SRX5460017,SRS4433907,SRA855736,GEO,Sun Yat-sen University,2,0.00069,0.00053,0.00032,0.00019,0.99943,0.99953,0.28358,0.375,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 51284,SRR8663319,SRX5460016,SRS4433906,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 2hpf rep1,GSM3638660,,source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,ZF 2hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,GSM3638660,GSM3638660: ZF 2hpf rep1; Danio rerio; Bisulfite Seq,GSM3638660,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638660,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,13281290400.0,44270968.0,GSM3638660 r1,0:150 1:150,A:4501039678;C:2150810078;G:2278027624;T:4348527287;N:2885733,150,150,,,4501039678,2150810078,2278027624,4348527287,2885733,SRX5460016,SRS4433906,SRA855736,GEO,Sun Yat-sen University,2,0.00064,0.00039,0.00025,0.00013,0.99949,0.99963,0.46478,0.63414,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 51285,SRR8663318,SRX5460015,SRS4433905,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 0hpf rep2,GSM3638659,,source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,ZF 0hpf rep2,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,GSM3638659,GSM3638659: ZF 0hpf rep2; Danio rerio; Bisulfite Seq,GSM3638659,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638659,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,11732143200.0,39107144.0,GSM3638659 r1,0:150 1:150,A:4048603242;C:1827111316;G:1904770606;T:3949005244;N:2652792,150,150,,,4048603242,1827111316,1904770606,3949005244,2652792,SRX5460015,SRS4433905,SRA855736,GEO,Sun Yat-sen University,2,0.00152,0.00115,0.00043,0.00016,0.99928,0.99943,0.24509,0.81645,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Zygote,Embryo,Embryo Imprecise,All anatomical structures 51286,SRR8663317,SRX5460014,SRS4433904,SRP187415,PRJNA525392,Whole transcriptome bisufilte sequencing for multiple species [Zebrafish],GSE127779,Other,We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.,parent bioproject:PRJNA525389,pubmed:35513466,,ZF 0hpf rep1,GSM3638658,,source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,ZF 0hpf rep1,Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites,embryo,,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,GSM3638658,GSM3638658: ZF 0hpf rep1; Danio rerio; Bisulfite Seq,GSM3638658,,1,For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.,GEO Accession:GSM3638658,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,9931664700.0,33105549.0,GSM3638658 r1,0:150 1:150,A:3401474427;C:1566218806;G:1670547045;T:3291140367;N:2284055,150,150,,,3401474427,1566218806,1670547045,3291140367,2284055,SRX5460014,SRS4433904,SRA855736,GEO,Sun Yat-sen University,2,0.00196,0.00154,0.00071,0.00027,0.99928,0.99935,0.80263,0.85024,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Zygote,Embryo,Embryo Imprecise,All anatomical structures 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