metadata: run_metadata: 92 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "Bisulfite-Seq" and tissue_curation

92 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "Bisulfite-Seq" and tissue_curation_coarse = "Nervous System"

descending

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

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