metadata: run_metadata: 218 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "Bisulfite-Seq" and technology = "unknown"

218 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "Bisulfite-Seq" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.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
29641	29641	SRR27397714	SRX23073965	SRS20033317	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library10	PG2	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 10\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS10	RRBS10	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	PG2_L7_1.fq.gz PG2_L7_2.fq.gz	fastq fastq	981695400.0	3272318.0	PG2 L7 1.fq.gz	0:150 1:150	A:253124715;C:152724975;G:341105704;T:234698202;N:41804	150	150	253124715	152724975	341105704	234698202	41804	SRX23073965	SRS20033317	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.0164	0.00047	0.01505	0.00036	0.9961	0.99965	0.58102	0.47058	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29642	29642	SRR27397715	SRX23073964	SRS20033316	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library9	PG1	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 9\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS9	RRBS9	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	PG1_L7_1.fq.gz PG1_L7_2.fq.gz	fastq fastq	1157067600.0	3856892.0	PG1 L7 1.fq.gz	0:150 1:150	A:278308283;C:162228777;G:432676687;T:283803806;N:50047	150	150	278308283	162228777	432676687	283803806	50047	SRX23073964	SRS20033316	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.02347	0.02319	0.02188	0.02162	0.99517	0.99519	0.50342	0.51027	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29643	29643	SRR27397716	SRX23073963	SRS20033315	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library8	LG4	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 8\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS8	RRBS8	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	LG4_L7_1.fq.gz LG4_L7_2.fq.gz	fastq fastq	1080684300.0	3602281.0	LG4 L7 1.fq.gz	0:150 1:150	A:270759422;C:159278390;G:387693215;T:262907381;N:45892	150	150	270759422	159278390	387693215	262907381	45892	SRX23073963	SRS20033315	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01698	0.00033	0.01593	0.00026	0.99675	0.99979	0.4974	0.2	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29644	29644	SRR27397717	SRX23073962	SRS20033314	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library7	LG3	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 7\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS7	RRBS7	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	LG3_L7_1.fq.gz LG3_L7_2.fq.gz	fastq fastq	1223063700.0	4076879.0	LG3 L7 1.fq.gz	0:150 1:150	A:301167012;C:182106743;G:443329321;T:296409064;N:51560	150	150	301167012	182106743	443329321	296409064	51560	SRX23073962	SRS20033314	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01787	0.01759	0.01644	0.01622	0.99545	0.99582	0.56826	0.56126	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29645	29645	SRR27397718	SRX23073961	SRS20033313	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library6	LG2	strain:ab\|age:adult\|collection date:2023 02 07\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 6\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS6	RRBS6	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	LG2_L7_1.fq.gz LG2_L7_2.fq.gz	fastq fastq	1188600300.0	3962001.0	LG2 L7 1.fq.gz	0:150 1:150	A:294477343;C:172669379;G:418732939;T:302669966;N:50673	150	150	294477343	172669379	418732939	302669966	50673	SRX23073961	SRS20033313	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.0205	0.02042	0.01903	0.01894	0.99584	0.99577	0.51685	0.51824	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29646	29646	SRR27397719	SRX23073960	SRS20033312	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library5	LG1	strain:ab\|age:adult\|collection date:2023 02 06\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 5\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS5	RRBS5	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	LG1_L7_1.fq.gz LG1_L7_2.fq.gz	fastq fastq	1048183200.0	3493944.0	LG1 L7 1.fq.gz	0:150 1:150	A:260330612;C:163890192;G:372783427;T:251133569;N:45400	150	150	260330612	163890192	372783427	251133569	45400	SRX23073960	SRS20033312	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01999	0.00059	0.01851	0.00045	0.99563	0.99961	0.49816	0.36842	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29647	29647	SRR27397720	SRX23073959	SRS20033311	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library4	CG4	strain:ab\|age:adult\|collection date:2023 02 05\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 4\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS4	RRBS4	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	CG4_L7_1.fq.gz CG4_L7_2.fq.gz	fastq fastq	1547200200.0	5157334.0	CG4 L7 1.fq.gz	0:150 1:150	A:389261224;C:230650937;G:559928386;T:367293552;N:66101	150	150	389261224	230650937	559928386	367293552	66101	SRX23073959	SRS20033311	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01121	0.00022	0.01024	0.00018	0.99713	0.99991	0.56111	1.0	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29648	29648	SRR27397721	SRX23073958	SRS20033310	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library3	CG3	strain:ab\|age:adult\|collection date:2023 02 04\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 3\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS3	RRBS3	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	CG3_L7_1.fq.gz CG3_L7_2.fq.gz	fastq fastq	1164022500.0	3880075.0	CG3 L7 1.fq.gz	0:150 1:150	A:281490630;C:172929357;G:423757698;T:285795200;N:49615	150	150	281490630	172929357	423757698	285795200	49615	SRX23073958	SRS20033310	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.0188	0.00046	0.01744	0.00039	0.99626	0.99981	0.55421	0.6	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29649	29649	SRR27397722	SRX23073957	SRS20033309	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library12	PG4	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 12\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS12	RRBS12	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	PG4_L7_1.fq.gz PG4_L7_2.fq.gz	fastq fastq	937521000.0	3125070.0	PG4 L7 1.fq.gz	0:150 1:150	A:230277419;C:145742183;G:328432893;T:233027715;N:40790	150	150	230277419	145742183	328432893	233027715	40790	SRX23073957	SRS20033309	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01943	0.01926	0.01799	0.01786	0.99575	0.99588	0.51136	0.48062	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29650	29650	SRR27397723	SRX23073956	SRS20033308	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library11	PG3	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 11\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS11	RRBS11	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	PG3_L7_1.fq.gz PG3_L7_2.fq.gz	fastq fastq	1256812500.0	4189375.0	PG3 L7 1.fq.gz	0:150 1:150	A:318736087;C:194540494;G:434374337;T:309107761;N:53821	150	150	318736087	194540494	434374337	309107761	53821	SRX23073956	SRS20033308	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.01424	0.00046	0.01316	0.00036	0.99683	0.99975	0.49746	0.5	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29651	29651	SRR27397724	SRX23073955	SRS20033307	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library2	CG2	strain:ab\|age:adult\|collection date:2023 02 03\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 2\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS2	RRBS2	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	CG2_L7_1.fq.gz CG2_L7_2.fq.gz	fastq fastq	1157888400.0	3859628.0	CG2 L7 1.fq.gz	0:150 1:150	A:292628434;C:171796176;G:406707172;T:286706357;N:50261	150	150	292628434	171796176	406707172	286706357	50261	SRX23073955	SRS20033307	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.02036	0.02023	0.01903	0.01889	0.99616	0.99614	0.55102	0.57894	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
29652	29652	SRR27397725	SRX23073954	SRS20033306	SRP480899	PRJNA1060279	EPIFISH	PRJNA1060279	Other	Epigenetic changes in fish during domestication			RRBS library1	CG1	strain:ab\|age:adult\|collection date:2023 02 02\|geo loc name:Italy\|sex:male\|tissue:Muscle\|Source materail identifiers:day 1\|BioSampleModel:Model organism or animal								RNA seq of danio rerio	RRBS1	RRBS1	Library preparation kit used Zymo Seq RRBS Library Kit			Bisulfite-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480899	CG1_L7_1.fq.gz CG1_L7_2.fq.gz	fastq fastq	1004867700.0	3349559.0	CG1 L7 1.fq.gz	0:150 1:150	A:247727849;C:158203386;G:350367173;T:248526527;N:42765	150	150	247727849	158203386	350367173	248526527	42765	SRX23073954	SRS20033306	SRA1777947	Nord University\|Bioscience and Aquaculture	Nord University	2	0.02764	0.00147	0.0252	0.00121	0.99233	0.99926	0.51541	0.5	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	Norway	2024-01-02	Adult	Adult	Muscle	Muscular System
51269	51269	SRR8663334	SRX5460031	SRS4433921	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 48hpf rep2	GSM3638675	source name:embryo\|tissue:embryo\|developmental stage:48 hpf\|strain:wild type AB fish	ZF 48hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:48 hpf\|strain:wild type AB fish	GSM3638675	GSM3638675: ZF 48hpf rep2; Danio rerio; Bisulfite Seq	GSM3638675		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638675	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			21257043600.0	70856812.0	GSM3638675 r1	0:150 1:150	A:7462169931;C:3151216767;G:3428144480;T:7214024902;N:1487520	150	150	7462169931	3151216767	3428144480	7214024902	1487520	SRX5460031	SRS4433921	SRA855736	GEO	Sun Yat-sen University	2	0.00062	0.00055	0.00017	0.00013	0.99949	0.99945	0.67901	0.75362	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
51270	51270	SRR8663333	SRX5460030	SRS4433920	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 48hpf rep1	GSM3638674	source name:embryo\|tissue:embryo\|developmental stage:48 hpf\|strain:wild type AB fish	ZF 48hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:48 hpf\|strain:wild type AB fish	GSM3638674	GSM3638674: ZF 48hpf rep1; Danio rerio; Bisulfite Seq	GSM3638674		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638674	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			20408177400.0	68027258.0	GSM3638674 r1	0:150 1:150	A:6990585654;C:3225159172;G:3562240517;T:6628764661;N:1427396	150	150	6990585654	3225159172	3562240517	6628764661	1427396	SRX5460030	SRS4433920	SRA855736	GEO	Sun Yat-sen University	2	0.0009	0.00071	0.0003	0.00019	0.99928	0.99941	0.6	0.64367	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
51271	51271	SRR8663332	SRX5460029	SRS4433919	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 24hpf rep2	GSM3638673	source name:embryo\|tissue:embryo\|developmental stage:24 hpf\|strain:wild type AB fish	ZF 24hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:24 hpf\|strain:wild type AB fish	GSM3638673	GSM3638673: ZF 24hpf rep2; Danio rerio; Bisulfite Seq	GSM3638673		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638673	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			21961409700.0	73204699.0	GSM3638673 r1	0:150 1:150	A:7568027843;C:3406881222;G:3795216487;T:7190249641;N:1034507	150	150	7568027843	3406881222	3795216487	7190249641	1034507	SRX5460029	SRS4433919	SRA855736	GEO	Sun Yat-sen University	2	0.00082	0.0007	0.00032	0.00023	0.99945	0.99947	0.65517	0.65	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
51272	51272	SRR8663331	SRX5460028	SRS4433918	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 24hpf rep1	GSM3638672	source name:embryo\|tissue:embryo\|developmental stage:24 hpf\|strain:wild type AB fish	ZF 24hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:24 hpf\|strain:wild type AB fish	GSM3638672	GSM3638672: ZF 24hpf rep1; Danio rerio; Bisulfite Seq	GSM3638672		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638672	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			22998615300.0	76662051.0	GSM3638672 r1	0:150 1:150	A:7938674920;C:3553518327;G:3950127781;T:7555207157;N:1087115	150	150	7938674920	3553518327	3950127781	7555207157	1087115	SRX5460028	SRS4433918	SRA855736	GEO	Sun Yat-sen University	2	0.00076	0.00067	0.00027	0.00021	0.99926	0.99937	0.53658	0.58666	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
51273	51273	SRR8663330	SRX5460027	SRS4433917	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 16hpf rep2	GSM3638671	source name:embryo\|tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	ZF 16hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	GSM3638671	GSM3638671: ZF 16hpf rep2; Danio rerio; Bisulfite Seq	GSM3638671		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638671	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			25701246300.0	85670821.0	GSM3638671 r1	0:150 1:150	A:8976132831;C:3855344207;G:4201042226;T:8667517583;N:1209453	150	150	8976132831	3855344207	4201042226	8667517583	1209453	SRX5460027	SRS4433917	SRA855736	GEO	Sun Yat-sen University	2	0.00117	0.00107	0.00036	0.00034	0.99928	0.99941	0.73571	0.75206	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
51274	51274	SRR8663329	SRX5460026	SRS4433916	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 16hpf rep1	GSM3638670	source name:embryo\|tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	ZF 16hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	GSM3638670	GSM3638670: ZF 16hpf rep1; Danio rerio; Bisulfite Seq	GSM3638670		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638670	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			21585057600.0	71950192.0	GSM3638670 r1	0:150 1:150	A:7493903581;C:3312864799;G:3567558230;T:7209728977;N:1002013	150	150	7493903581	3312864799	3567558230	7209728977	1002013	SRX5460026	SRS4433916	SRA855736	GEO	Sun Yat-sen University	2	0.00125	0.00119	0.00039	0.00034	0.99945	0.99947	0.7551	0.76865	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
51275	51275	SRR8663328	SRX5460025	SRS4433915	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 10hpf rep2	GSM3638669	source name:embryo\|tissue:embryo\|developmental stage:10 hpf\|strain:wild type AB fish	ZF 10hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:10 hpf\|strain:wild type AB fish	GSM3638669	GSM3638669: ZF 10hpf rep2; Danio rerio; Bisulfite Seq	GSM3638669		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638669	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			18449316900.0	61497723.0	GSM3638669 r1	0:150 1:150	A:6508135454;C:2695665097;G:2948776234;T:6296104735;N:635380	150	150	6508135454	2695665097	2948776234	6296104735	635380	SRX5460025	SRS4433915	SRA855736	GEO	Sun Yat-sen University	2	0.00092	0.00073	0.00035	0.00017	0.99931	0.99933	0.66019	0.6129	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51276	51276	SRR8663327	SRX5460024	SRS4433914	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 10hpf rep1	GSM3638668	source name:embryo\|tissue:embryo\|developmental stage:10 hpf\|strain:wild type AB fish	ZF 10hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:10 hpf\|strain:wild type AB fish	GSM3638668	GSM3638668: ZF 10hpf rep1; Danio rerio; Bisulfite Seq	GSM3638668		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638668	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			35064552300.0	116881841.0	GSM3638668 r1	0:150 1:150	A:12442483305;C:5073538954;G:5489080636;T:12058238019;N:1211386	150	150	12442483305	5073538954	5489080636	12058238019	1211386	SRX5460024	SRS4433914	SRA855736	GEO	Sun Yat-sen University	2	0.0009	0.00072	0.00028	0.00019	0.99926	0.99945	0.61403	0.67045	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51277	51277	SRR8663326	SRX5460023	SRS4433913	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 8hpf rep2	GSM3638667	source name:embryo\|tissue:embryo\|developmental stage:8 hpf\|strain:wild type AB fish	ZF 8hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:8 hpf\|strain:wild type AB fish	GSM3638667	GSM3638667: ZF 8hpf rep2; Danio rerio; Bisulfite Seq	GSM3638667		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638667	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			14346635400.0	47822118.0	GSM3638667 r1	0:150 1:150	A:5096565523;C:2082957184;G:2242869596;T:4923737869;N:505228	150	150	5096565523	2082957184	2242869596	4923737869	505228	SRX5460023	SRS4433913	SRA855736	GEO	Sun Yat-sen University	2	0.00107	0.00102	0.00035	0.00021	0.99884	0.99884	0.61068	0.71428	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51278	51278	SRR8663325	SRX5460022	SRS4433912	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 8hpf rep1	GSM3638666	source name:embryo\|tissue:embryo\|developmental stage:8 hpf\|strain:wild type AB fish	ZF 8hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:8 hpf\|strain:wild type AB fish	GSM3638666	GSM3638666: ZF 8hpf rep1; Danio rerio; Bisulfite Seq	GSM3638666		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638666	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			22564435500.0	75214785.0	GSM3638666 r1	0:150 1:150	A:8037530388;C:3263669666;G:3467393764;T:7794998569;N:843113	150	150	8037530388	3263669666	3467393764	7794998569	843113	SRX5460022	SRS4433912	SRA855736	GEO	Sun Yat-sen University	2	0.00089	0.00082	0.00026	0.0002	0.99939	0.99939	0.71171	0.73267	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51279	51279	SRR8663324	SRX5460021	SRS4433911	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 6hpf rep2	GSM3638665	source name:embryo\|tissue:embryo\|developmental stage:6 hpf\|strain:wild type AB fish	ZF 6hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:6 hpf\|strain:wild type AB fish	GSM3638665	GSM3638665: ZF 6hpf rep2; Danio rerio; Bisulfite Seq	GSM3638665		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638665	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			15663840300.0	52212801.0	GSM3638665 r1	0:150 1:150	A:5036459488;C:2768054214;G:3109386160;T:4747198752;N:2741686	150	150	5036459488	2768054214	3109386160	4747198752	2741686	SRX5460021	SRS4433911	SRA855736	GEO	Sun Yat-sen University	2	0.00121	0.0008	0.00062	0.00035	0.99922	0.99924	0.41509	0.40789	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51280	51280	SRR8663323	SRX5460020	SRS4433910	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 6hpf rep1	GSM3638664	source name:embryo\|tissue:embryo\|developmental stage:6 hpf\|strain:wild type AB fish	ZF 6hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:6 hpf\|strain:wild type AB fish	GSM3638664	GSM3638664: ZF 6hpf rep1; Danio rerio; Bisulfite Seq	GSM3638664		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638664	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			13146289500.0	43820965.0	GSM3638664 r1	0:150 1:150	A:4440608717;C:2140855274;G:2250243580;T:4312362152;N:2219777	150	150	4440608717	2140855274	2250243580	4312362152	2219777	SRX5460020	SRS4433910	SRA855736	GEO	Sun Yat-sen University	2	0.00073	0.00047	0.00038	0.00014	0.99945	0.99941	0.32812	0.5	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
51281	51281	SRR8663322	SRX5460019	SRS4433909	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 4hpf rep2	GSM3638663	source name:embryo\|tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	ZF 4hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	GSM3638663	GSM3638663: ZF 4hpf rep2; Danio rerio; Bisulfite Seq	GSM3638663		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638663	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			14505809700.0	48352699.0	GSM3638663 r1	0:150 1:150	A:4877194269;C:2388898572;G:2560124505;T:4676340810;N:3251544	150	150	4877194269	2388898572	2560124505	4676340810	3251544	SRX5460019	SRS4433909	SRA855736	GEO	Sun Yat-sen University	2	0.00065	0.00045	0.00027	0.00016	0.99928	0.99945	0.46376	0.54166	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51282	51282	SRR8663321	SRX5460018	SRS4433908	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 4hpf rep1	GSM3638662	source name:embryo\|tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	ZF 4hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	GSM3638662	GSM3638662: ZF 4hpf rep1; Danio rerio; Bisulfite Seq	GSM3638662		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638662	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			13666257000.0	45554190.0	GSM3638662 r1	0:150 1:150	A:4616947793;C:2221382014;G:2373430205;T:4451384606;N:3112382	150	150	4616947793	2221382014	2373430205	4451384606	3112382	SRX5460018	SRS4433908	SRA855736	GEO	Sun Yat-sen University	2	0.00094	0.00054	0.00044	0.00022	0.99928	0.99939	0.38888	0.50943	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51283	51283	SRR8663320	SRX5460017	SRS4433907	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 2hpf rep2	GSM3638661	source name:embryo\|tissue:embryo\|developmental stage:2 hpf\|strain:wild type AB fish	ZF 2hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:2 hpf\|strain:wild type AB fish	GSM3638661	GSM3638661: ZF 2hpf rep2; Danio rerio; Bisulfite Seq	GSM3638661		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638661	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			14619051000.0	48730170.0	GSM3638661 r1	0:150 1:150	A:4888878605;C:2423468919;G:2611005028;T:4692396498;N:3301950	150	150	4888878605	2423468919	2611005028	4692396498	3301950	SRX5460017	SRS4433907	SRA855736	GEO	Sun Yat-sen University	2	0.00069	0.00053	0.00032	0.00019	0.99943	0.99953	0.28358	0.375	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51284	51284	SRR8663319	SRX5460016	SRS4433906	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 2hpf rep1	GSM3638660	source name:embryo\|tissue:embryo\|developmental stage:2 hpf\|strain:wild type AB fish	ZF 2hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:2 hpf\|strain:wild type AB fish	GSM3638660	GSM3638660: ZF 2hpf rep1; Danio rerio; Bisulfite Seq	GSM3638660		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638660	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			13281290400.0	44270968.0	GSM3638660 r1	0:150 1:150	A:4501039678;C:2150810078;G:2278027624;T:4348527287;N:2885733	150	150	4501039678	2150810078	2278027624	4348527287	2885733	SRX5460016	SRS4433906	SRA855736	GEO	Sun Yat-sen University	2	0.00064	0.00039	0.00025	0.00013	0.99949	0.99963	0.46478	0.63414	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
51285	51285	SRR8663318	SRX5460015	SRS4433905	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 0hpf rep2	GSM3638659	source name:embryo\|tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	ZF 0hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	GSM3638659	GSM3638659: ZF 0hpf rep2; Danio rerio; Bisulfite Seq	GSM3638659		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638659	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			11732143200.0	39107144.0	GSM3638659 r1	0:150 1:150	A:4048603242;C:1827111316;G:1904770606;T:3949005244;N:2652792	150	150	4048603242	1827111316	1904770606	3949005244	2652792	SRX5460015	SRS4433905	SRA855736	GEO	Sun Yat-sen University	2	0.00152	0.00115	0.00043	0.00016	0.99928	0.99943	0.24509	0.81645	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Zygote	Embryo	Embryo Imprecise	All anatomical structures
51286	51286	SRR8663317	SRX5460014	SRS4433904	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466	ZF 0hpf rep1	GSM3638658	source name:embryo\|tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	ZF 0hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:0 hpf\|strain:wild type AB fish	GSM3638658	GSM3638658: ZF 0hpf rep1; Danio rerio; Bisulfite Seq	GSM3638658		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638658	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			9931664700.0	33105549.0	GSM3638658 r1	0:150 1:150	A:3401474427;C:1566218806;G:1670547045;T:3291140367;N:2284055	150	150	3401474427	1566218806	1670547045	3291140367	2284055	SRX5460014	SRS4433904	SRA855736	GEO	Sun Yat-sen University	2	0.00196	0.00154	0.00071	0.00027	0.99928	0.99935	0.80263	0.85024	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Zygote	Embryo	Embryo Imprecise	All anatomical structures
60257	60257	SRR12194979	SRX8707751	SRS6984337	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B15	GSM4666897	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666897	GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq	GSM4666897		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666897	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-1_S19_L001_R1_001.fastq.gz P6-1_S19_L001_R2_001.fastq.gz	fastq fastq	626505630.0	2077251.0	GSM4666897 r1	0:150.88 1:150.72	A:231784841;C:80425574;G:110085227;T:204102624;N:107364	150	150	231784841	80425574	110085227	204102624	107364	SRX8707751	SRS6984337	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00014	0.00014	0.00013	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60258	60258	SRR12194980	SRX8707751	SRS6984337	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B15	GSM4666897	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666897	GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq	GSM4666897		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666897	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-1_S19_L002_R1_001.fastq.gz P6-1_S19_L002_R2_001.fastq.gz	fastq fastq	646447345.0	2143304.0	GSM4666897 r2	0:150.88 1:150.73	A:237189853;C:82748065;G:118625007;T:207787390;N:97030	150	150	237189853	82748065	118625007	207787390	97030	SRX8707751	SRS6984337	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00023	0.0002	0.00022	0.00019	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60259	60259	SRR12194981	SRX8707751	SRS6984337	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B15	GSM4666897	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666897	GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq	GSM4666897		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666897	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-1_S19_L003_R1_001.fastq.gz P6-1_S19_L003_R2_001.fastq.gz	fastq fastq	603701501.0	2001537.0	GSM4666897 r3	0:150.88 1:150.74	A:223744015;C:77591778;G:105364702;T:196924362;N:76644	150	150	223744015	77591778	105364702	196924362	76644	SRX8707751	SRS6984337	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00017	0.00018	0.00016	0.00017	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60260	60260	SRR12194982	SRX8707751	SRS6984337	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B15	GSM4666897	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666897	GSM4666897: adult whole brain B15; Danio rerio; Bisulfite Seq	GSM4666897		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666897	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-1_S19_L004_R1_001.fastq.gz P6-1_S19_L004_R2_001.fastq.gz	fastq fastq	626999718.0	2078709.0	GSM4666897 r4	0:150.89 1:150.74	A:230679756;C:80184689;G:114353798;T:201714990;N:66485	150	150	230679756	80184689	114353798	201714990	66485	SRX8707751	SRS6984337	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00023	0.00014	0.00022	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60261	60261	SRR12194975	SRX8707750	SRS6984338	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B14	GSM4666896	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B14	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666896	GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq	GSM4666896		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666896	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-6_S18_L001_R1_001.fastq.gz P5-6_S18_L001_R2_001.fastq.gz	fastq fastq	362632647.0	1202487.0	GSM4666896 r1	0:150.85 1:150.72	A:134187427;C:47593733;G:60920059;T:119870940;N:60488	150	150	134187427	47593733	60920059	119870940	60488	SRX8707750	SRS6984338	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00012	0.00018	0.0001	0.00015	0.99997	0.99997	0.0	0.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60262	60262	SRR12194976	SRX8707750	SRS6984338	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B14	GSM4666896	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B14	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666896	GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq	GSM4666896		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666896	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-6_S18_L002_R2_001.fastq.gz P5-6_S18_L002_R1_001.fastq.gz	fastq fastq	371328815.0	1231316.0	GSM4666896 r2	0:150.85 1:150.72	A:136045457;C:48493148;G:65714953;T:121017397;N:57860	150	150	136045457	48493148	65714953	121017397	57860	SRX8707750	SRS6984338	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00017	0.00014	0.00015	1.0	0.99997		1.0	149	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60263	60263	SRR12194977	SRX8707750	SRS6984338	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B14	GSM4666896	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B14	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666896	GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq	GSM4666896		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666896	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-6_S18_L003_R1_001.fastq.gz P5-6_S18_L003_R2_001.fastq.gz	fastq fastq	349651276.0	1159376.0	GSM4666896 r3	0:150.85 1:150.74	A:129571477;C:45879693;G:58514844;T:115645628;N:39634	150	150	129571477	45879693	58514844	115645628	39634	SRX8707750	SRS6984338	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00011	0.00018	0.0001	0.00017	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60264	60264	SRR12194978	SRX8707750	SRS6984338	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B14	GSM4666896	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B14	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666896	GSM4666896: adult whole brain B14; Danio rerio; Bisulfite Seq	GSM4666896		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666896	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-6_S18_L004_R1_001.fastq.gz P5-6_S18_L004_R2_001.fastq.gz	fastq fastq	359741298.0	1192811.0	GSM4666896 r4	0:150.85 1:150.74	A:132192036;C:47006274;G:63129910;T:117375509;N:37569	150	150	132192036	47006274	63129910	117375509	37569	SRX8707750	SRS6984338	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00017	0.00015	0.00014	0.00014	0.99995	1.0	0.0		150	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60265	60265	SRR12194971	SRX8707749	SRS6984336	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B16	GSM4666895	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666895	GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq	GSM4666895		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666895	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-2_S20_L001_R1_001.fastq.gz P6-2_S20_L001_R2_001.fastq.gz	fastq fastq	767379925.0	2544544.0	GSM4666895 r1	0:150.86 1:150.72	A:285185142;C:99053157;G:127959880;T:255052821;N:128925	150	150	285185142	99053157	127959880	255052821	128925	SRX8707749	SRS6984336	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.0002	0.00014	0.00019	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60266	60266	SRR12194972	SRX8707749	SRS6984336	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B16	GSM4666895	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666895	GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq	GSM4666895		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666895	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-2_S20_L002_R1_001.fastq.gz P6-2_S20_L002_R2_001.fastq.gz	fastq fastq	801048716.0	2656168.0	GSM4666895 r2	0:150.86 1:150.72	A:294948276;C:103019861;G:140485071;T:262473164;N:122344	150	150	294948276	103019861	140485071	262473164	122344	SRX8707749	SRS6984336	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00021	0.00014	0.0002	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60267	60267	SRR12194973	SRX8707749	SRS6984336	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B16	GSM4666895	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666895	GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq	GSM4666895		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666895	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-2_S20_L003_R1_001.fastq.gz P6-2_S20_L003_R2_001.fastq.gz	fastq fastq	740955391.0	2456791.0	GSM4666895 r3	0:150.86 1:150.73	A:275837928;C:95675216;G:123037692;T:246311396;N:93159	150	150	275837928	95675216	123037692	246311396	93159	SRX8707749	SRS6984336	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00014	0.0003	0.00013	0.00029	1.0	1.0			151	150	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60268	60268	SRR12194974	SRX8707749	SRS6984336	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B16	GSM4666895	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666895	GSM4666895: adult whole brain B16; Danio rerio; Bisulfite Seq	GSM4666895		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666895	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P6-2_S20_L004_R1_001.fastq.gz P6-2_S20_L004_R2_001.fastq.gz	fastq fastq	776243814.0	2573716.0	GSM4666895 r4	0:150.86 1:150.74	A:286702347;C:99810593;G:135079256;T:254574374;N:77244	150	150	286702347	99810593	135079256	254574374	77244	SRX8707749	SRS6984336	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00029	0.00021	0.00026	0.0002	0.99997	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60269	60269	SRR12194967	SRX8707748	SRS6984335	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B13	GSM4666894	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B13	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666894	GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq	GSM4666894		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666894	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-5_S17_L001_R2_001.fastq.gz P5-5_S17_L001_R1_001.fastq.gz	fastq fastq	818338842.0	2713477.0	GSM4666894 r1	0:150.86 1:150.72	A:301830002;C:107389155;G:139489598;T:269496153;N:133934	150	150	301830002	107389155	139489598	269496153	133934	SRX8707748	SRS6984335	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00019	0.00014	0.00018	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60270	60270	SRR12194968	SRX8707748	SRS6984335	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B13	GSM4666894	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B13	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666894	GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq	GSM4666894		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666894	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-5_S17_L002_R1_001.fastq.gz P5-5_S17_L002_R2_001.fastq.gz	fastq fastq	846228975.0	2805930.0	GSM4666894 r2	0:150.86 1:150.72	A:308870822;C:110466773;G:152421867;T:274347549;N:121964	150	150	308870822	110466773	152421867	274347549	121964	SRX8707748	SRS6984335	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.0002	0.00015	0.00018	0.00011	0.99997	0.99997	0.0	1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60271	60271	SRR12194969	SRX8707748	SRS6984335	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B13	GSM4666894	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B13	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666894	GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq	GSM4666894		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666894	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-5_S17_L003_R2_001.fastq.gz P5-5_S17_L003_R1_001.fastq.gz	fastq fastq	790658387.0	2621591.0	GSM4666894 r3	0:150.86 1:150.73	A:292027450;C:103748394;G:134258887;T:260520383;N:103273	150	150	292027450	103748394	134258887	260520383	103273	SRX8707748	SRS6984335	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00016	0.00014	0.00013	0.00013	0.99995	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60272	60272	SRR12194970	SRX8707748	SRS6984335	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B13	GSM4666894	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B13	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666894	GSM4666894: adult whole brain B13; Danio rerio; Bisulfite Seq	GSM4666894		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666894	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-5_S17_L004_R1_001.fastq.gz P5-5_S17_L004_R2_001.fastq.gz	fastq fastq	815907660.0	2705210.0	GSM4666894 r4	0:150.86 1:150.74	A:298609755;C:106483104;G:145958694;T:264775944;N:80163	150	150	298609755	106483104	145958694	264775944	80163	SRX8707748	SRS6984335	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00029	0.00012	0.00028	0.99997	1.0	0.0		151	150	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60273	60273	SRR12194963	SRX8707747	SRS6984334	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B12	GSM4666893	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B12	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666893	GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq	GSM4666893		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666893	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-4_S16_L001_R1_001.fastq.gz P5-4_S16_L001_R2_001.fastq.gz	fastq fastq	700559459.0	2322745.0	GSM4666893 r1	0:150.89 1:150.72	A:258008915;C:91134331;G:124267705;T:227032496;N:116012	150	150	258008915	91134331	124267705	227032496	116012	SRX8707747	SRS6984334	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00013	0.00017	0.00012	0.00016	1.0	1.0			151	150	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60274	60274	SRR12194964	SRX8707747	SRS6984334	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B12	GSM4666893	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B12	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666893	GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq	GSM4666893		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666893	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-4_S16_L002_R2_001.fastq.gz P5-4_S16_L002_R1_001.fastq.gz	fastq fastq	728622859.0	2415726.0	GSM4666893 r2	0:150.89 1:150.73	A:265918573;C:94480694;G:135330434;T:232783961;N:109197	150	150	265918573	94480694	135330434	232783961	109197	SRX8707747	SRS6984334	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00017	0.00022	0.00014	0.00021	0.99995	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60275	60275	SRR12194965	SRX8707747	SRS6984334	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B12	GSM4666893	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B12	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666893	GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq	GSM4666893		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666893	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-4_S16_L003_R1_001.fastq.gz P5-4_S16_L003_R2_001.fastq.gz	fastq fastq	676046027.0	2241356.0	GSM4666893 r3	0:150.89 1:150.74	A:249345303;C:88016423;G:119300461;T:219299203;N:84637	150	150	249345303	88016423	119300461	219299203	84637	SRX8707747	SRS6984334	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00022	0.00024	0.00021	0.00023	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60276	60276	SRR12194966	SRX8707747	SRS6984334	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B12	GSM4666893	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B12	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666893	GSM4666893: adult whole brain B12; Danio rerio; Bisulfite Seq	GSM4666893		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666893	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-4_S16_L004_R1_001.fastq.gz P5-4_S16_L004_R2_001.fastq.gz	fastq fastq	703809171.0	2333304.0	GSM4666893 r4	0:150.89 1:150.75	A:257462138;C:91215734;G:129931298;T:225132059;N:67942	150	150	257462138	91215734	129931298	225132059	67942	SRX8707747	SRS6984334	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00022	0.00014	0.00021	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60277	60277	SRR12194959	SRX8707746	SRS6984333	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B11	GSM4666892	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B11	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666892	GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq	GSM4666892		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666892	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-3_S15_L001_R1_001.fastq.gz P5-3_S15_L001_R2_001.fastq.gz	fastq fastq	875916606.0	2904546.0	GSM4666892 r1	0:150.85 1:150.72	A:323769382;C:115778670;G:148157089;T:288058377;N:153088	150	150	323769382	115778670	148157089	288058377	153088	SRX8707746	SRS6984333	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	9e-05	0.00014	6e-05	1.0	0.99997		1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60278	60278	SRR12194960	SRX8707746	SRS6984333	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B11	GSM4666892	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B11	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666892	GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq	GSM4666892		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666892	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-3_S15_L002_R1_001.fastq.gz P5-3_S15_L002_R2_001.fastq.gz	fastq fastq	906266878.0	3005123.0	GSM4666892 r2	0:150.85 1:150.73	A:331841540;C:119200098;G:161492735;T:293597000;N:135505	150	150	331841540	119200098	161492735	293597000	135505	SRX8707746	SRS6984333	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00015	0.00013	0.00012	0.99997	0.99997	0.0	1.0	150	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60279	60279	SRR12194961	SRX8707746	SRS6984333	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B11	GSM4666892	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B11	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666892	GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq	GSM4666892		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666892	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-3_S15_L003_R1_001.fastq.gz P5-3_S15_L003_R2_001.fastq.gz	fastq fastq	845425773.0	2803262.0	GSM4666892 r3	0:150.85 1:150.74	A:312923215;C:111769611;G:142528786;T:278100796;N:103365	150	150	312923215	111769611	142528786	278100796	103365	SRX8707746	SRS6984333	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00019	0.00017	0.00018	0.00015	1.0	0.99997		1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60280	60280	SRR12194962	SRX8707746	SRS6984333	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B11	GSM4666892	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B11	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666892	GSM4666892: adult whole brain B11; Danio rerio; Bisulfite Seq	GSM4666892		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666892	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-3_S15_L004_R1_001.fastq.gz P5-3_S15_L004_R2_001.fastq.gz	fastq fastq	879089154.0	2914795.0	GSM4666892 r4	0:150.85 1:150.74	A:322802592;C:115646186;G:155527621;T:285023759;N:88996	150	150	322802592	115646186	155527621	285023759	88996	SRX8707746	SRS6984333	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00016	0.00014	0.00013	0.00013	0.99993	1.0	0.0		151	150	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60281	60281	SRR12194955	SRX8707745	SRS6984332	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B10	GSM4666891	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B10	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666891	GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq	GSM4666891		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666891	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-2_S14_L001_R1_001.fastq.gz P5-2_S14_L001_R2_001.fastq.gz	fastq fastq	612289518.0	2030276.0	GSM4666891 r1	0:150.86 1:150.72	A:225461166;C:80840857;G:104624118;T:201255710;N:107667	150	150	225461166	80840857	104624118	201255710	107667	SRX8707745	SRS6984332	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00017	0.00021	0.00014	0.00019	0.99995	0.99997	0.5	1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60282	60282	SRR12194956	SRX8707745	SRS6984332	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B10	GSM4666891	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B10	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666891	GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq	GSM4666891		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666891	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-2_S14_L002_R1_001.fastq.gz P5-2_S14_L002_R2_001.fastq.gz	fastq fastq	634607694.0	2104258.0	GSM4666891 r2	0:150.86 1:150.73	A:231299105;C:83482957;G:114131270;T:205602870;N:91492	150	150	231299105	83482957	114131270	205602870	91492	SRX8707745	SRS6984332	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00028	0.00014	0.00027	0.00013	1.0	1.0			150	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60283	60283	SRR12194957	SRX8707745	SRS6984332	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B10	GSM4666891	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B10	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666891	GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq	GSM4666891		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666891	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-2_S14_L003_R1_001.fastq.gz P5-2_S14_L003_R2_001.fastq.gz	fastq fastq	590348631.0	1957422.0	GSM4666891 r3	0:150.86 1:150.74	A:217666345;C:77986590;G:100434245;T:194187946;N:73505	150	150	217666345	77986590	100434245	194187946	73505	SRX8707745	SRS6984332	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00015	0.00017	0.00014	0.00016	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60284	60284	SRR12194958	SRX8707745	SRS6984332	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B10	GSM4666891	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B10	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666891	GSM4666891: adult whole brain B10; Danio rerio; Bisulfite Seq	GSM4666891		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666891	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-2_S14_L004_R1_001.fastq.gz P5-2_S14_L004_R2_001.fastq.gz	fastq fastq	613280111.0	2033405.0	GSM4666891 r4	0:150.86 1:150.74	A:224142863;C:80650974;G:109510542;T:198916747;N:58985	150	150	224142863	80650974	109510542	198916747	58985	SRX8707745	SRS6984332	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00019	0.00015	0.00016	0.00014	0.99995	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60285	60285	SRR12194951	SRX8707744	SRS6984331	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B9	GSM4666890	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B9	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666890	GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq	GSM4666890		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666890	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-1_S13_L001_R1_001.fastq.gz P5-1_S13_L001_R2_001.fastq.gz	fastq fastq	871269001.0	2888776.0	GSM4666890 r1	0:150.89 1:150.72	A:314795365;C:112414599;G:160314482;T:283594068;N:150487	150	150	314795365	112414599	160314482	283594068	150487	SRX8707744	SRS6984331	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00013	0.00015	0.00012	0.00014	1.0	1.0			151	150	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60286	60286	SRR12194952	SRX8707744	SRS6984331	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B9	GSM4666890	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B9	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666890	GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq	GSM4666890		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666890	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-1_S13_L002_R1_001.fastq.gz P5-1_S13_L002_R2_001.fastq.gz	fastq fastq	902501754.0	2992248.0	GSM4666890 r2	0:150.89 1:150.72	A:322645331;C:115934758;G:174818254;T:288967241;N:136170	150	150	322645331	115934758	174818254	288967241	136170	SRX8707744	SRS6984331	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00012	0.00026	0.0001	0.00025	0.99997	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60287	60287	SRR12194953	SRX8707744	SRS6984331	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B9	GSM4666890	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B9	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666890	GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq	GSM4666890		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666890	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-1_S13_L003_R1_001.fastq.gz P5-1_S13_L003_R2_001.fastq.gz	fastq fastq	839686349.0	2783900.0	GSM4666890 r3	0:150.89 1:150.73	A:303601399;C:108395743;G:153892840;T:273690404;N:105963	150	150	303601399	108395743	153892840	273690404	105963	SRX8707744	SRS6984331	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00012	0.00018	0.00011	0.00017	1.0	1.0			151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60288	60288	SRR12194954	SRX8707744	SRS6984331	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B9	GSM4666890	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B9	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666890	GSM4666890: adult whole brain B9; Danio rerio; Bisulfite Seq	GSM4666890		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666890	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	PAIRED	ILLUMINA	NextSeq 550	SRP271280	P5-1_S13_L004_R1_001.fastq.gz P5-1_S13_L004_R2_001.fastq.gz	fastq fastq	872412889.0	2892296.0	GSM4666890 r4	0:150.89 1:150.74	A:312195512;C:111967601;G:168316892;T:279843866;N:89018	150	150	312195512	111967601	168316892	279843866	89018	SRX8707744	SRS6984331	SRA1097340	GEO	UMR MARBEC, INRAE	2	0.00021	0.00034	0.00018	0.00033	0.99995	1.0	0.0		151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60289	60289	SRR12194947	SRX8707743	SRS6984330	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B8	GSM4666889	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B8	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666889	GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq	GSM4666889		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666889	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-6_S21_L001_R1_001.fastq.gz	fastq	417626188.0	2629267.0	GSM4666889 r1	0:158.84 1:0	A:125329533;C:27957391;G:102415231;T:161892676;N:31357	158	0	125329533	27957391	102415231	161892676	31357	SRX8707743	SRS6984330	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00017		0.00015		0.99997		1.0		158		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60290	60290	SRR12194948	SRX8707743	SRS6984330	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B8	GSM4666889	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B8	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666889	GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq	GSM4666889		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666889	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-6_S21_L002_R1_001.fastq.gz	fastq	415442115.0	2616087.0	GSM4666889 r2	0:158.80 1:0	A:122606292;C:27299099;G:106611577;T:158894919;N:30228	158	0	122606292	27299099	106611577	158894919	30228	SRX8707743	SRS6984330	SRA1097340	GEO	UMR MARBEC, INRAE	1	8e-05		7e-05		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60291	60291	SRR12194949	SRX8707743	SRS6984330	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B8	GSM4666889	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B8	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666889	GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq	GSM4666889		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666889	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-6_S21_L003_R1_001.fastq.gz	fastq	406171247.0	2557027.0	GSM4666889 r3	0:158.85 1:0	A:122039816;C:27029008;G:99485556;T:157596787;N:20080	158	0	122039816	27029008	99485556	157596787	20080	SRX8707743	SRS6984330	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00019		0.00015		0.99993		0.5		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60292	60292	SRR12194950	SRX8707743	SRS6984330	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B8	GSM4666889	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B8	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666889	GSM4666889: adult whole brain B8; Danio rerio; Bisulfite Seq	GSM4666889		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666889	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-6_S21_L004_R1_001.fastq.gz	fastq	403012952.0	2537671.0	GSM4666889 r4	0:158.81 1:0	A:119320681;C:26563373;G:102739543;T:154371029;N:18326	158	0	119320681	26563373	102739543	154371029	18326	SRX8707743	SRS6984330	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00015		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60293	60293	SRR12194943	SRX8707742	SRS6984329	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B7	GSM4666888	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B7	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666888	GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq	GSM4666888		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666888	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-5_S20_L001_R1_001.fastq.gz	fastq	453584090.0	2854818.0	GSM4666888 r1	0:158.88 1:0	A:134523251;C:27892399;G:113216536;T:177918076;N:33828	158	0	134523251	27892399	113216536	177918076	33828	SRX8707742	SRS6984329	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00014		0.00012		0.99997		0.0		156		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60294	60294	SRR12194944	SRX8707742	SRS6984329	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B7	GSM4666888	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B7	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666888	GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq	GSM4666888		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666888	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-5_S20_L002_R1_001.fastq.gz	fastq	448807947.0	2824868.0	GSM4666888 r2	0:158.88 1:0	A:130879549;C:27153648;G:117060555;T:173683407;N:30788	158	0	130879549	27153648	117060555	173683407	30788	SRX8707742	SRS6984329	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00024		0.00021		0.99995		0.5		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60295	60295	SRR12194945	SRX8707742	SRS6984329	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B7	GSM4666888	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B7	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666888	GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq	GSM4666888		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666888	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-5_S20_L003_R1_001.fastq.gz	fastq	441209232.0	2776904.0	GSM4666888 r3	0:158.89 1:0	A:130998380;C:26957645;G:109964778;T:173264823;N:23606	158	0	130998380	26957645	109964778	173264823	23606	SRX8707742	SRS6984329	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00012		0.00011		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60296	60296	SRR12194946	SRX8707742	SRS6984329	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B7	GSM4666888	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B7	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666888	GSM4666888: adult whole brain B7; Danio rerio; Bisulfite Seq	GSM4666888		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666888	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-5_S20_L004_R1_001.fastq.gz	fastq	436356072.0	2746435.0	GSM4666888 r4	0:158.88 1:0	A:127599502;C:26472498;G:112912306;T:169350791;N:20975	158	0	127599502	26472498	112912306	169350791	20975	SRX8707742	SRS6984329	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00019		0.00018		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60297	60297	SRR12194939	SRX8707741	SRS6984328	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B6	GSM4666887	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B6	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666887	GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq	GSM4666887		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666887	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-4_S19_L001_R1_001.fastq.gz	fastq	459581878.0	2892480.0	GSM4666887 r1	0:158.89 1:0	A:136418528;C:26773883;G:120246272;T:176109118;N:34077	158	0	136418528	26773883	120246272	176109118	34077	SRX8707741	SRS6984328	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00018		0.00016		0.99997		0.0		158		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60298	60298	SRR12194940	SRX8707741	SRS6984328	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B6	GSM4666887	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B6	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666887	GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq	GSM4666887		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666887	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-4_S19_L002_R1_001.fastq.gz	fastq	454682038.0	2861730.0	GSM4666887 r2	0:158.88 1:0	A:132773130;C:26007993;G:124098378;T:171770508;N:32029	158	0	132773130	26007993	124098378	171770508	32029	SRX8707741	SRS6984328	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00019		0.00015		0.99993		0.33333		151		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60299	60299	SRR12194941	SRX8707741	SRS6984328	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B6	GSM4666887	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B6	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666887	GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq	GSM4666887		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666887	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-4_S19_L003_R1_001.fastq.gz	fastq	441949571.0	2781476.0	GSM4666887 r3	0:158.89 1:0	A:131402848;C:25700491;G:115149715;T:169675287;N:21230	158	0	131402848	25700491	115149715	169675287	21230	SRX8707741	SRS6984328	SRA1097340	GEO	UMR MARBEC, INRAE	1	6e-05		5e-05		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60300	60300	SRR12194942	SRX8707741	SRS6984328	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B6	GSM4666887	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B6	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666887	GSM4666887: adult whole brain B6; Danio rerio; Bisulfite Seq	GSM4666887		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666887	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-4_S19_L004_R1_001.fastq.gz	fastq	436607676.0	2747936.0	GSM4666887 r4	0:158.89 1:0	A:127862911;C:25195779;G:117992550;T:165538093;N:18343	158	0	127862911	25195779	117992550	165538093	18343	SRX8707741	SRS6984328	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00015		0.00013		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60301	60301	SRR12194935	SRX8707740	SRS6984327	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B5	GSM4666886	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B5	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666886	GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq	GSM4666886		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666886	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-3_S18_L001_R1_001.fastq.gz	fastq	302829362.0	1906514.0	GSM4666886 r1	0:158.84 1:0	A:89694994;C:19460989;G:76993935;T:116656111;N:23333	158	0	89694994	19460989	76993935	116656111	23333	SRX8707740	SRS6984327	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00022		0.00021		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60302	60302	SRR12194936	SRX8707740	SRS6984327	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B5	GSM4666886	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B5	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666886	GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq	GSM4666886		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666886	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-3_S18_L002_R1_001.fastq.gz	fastq	299893208.0	1888319.0	GSM4666886 r2	0:158.81 1:0	A:87157111;C:18870988;G:80083677;T:113760899;N:20533	158	0	87157111	18870988	80083677	113760899	20533	SRX8707740	SRS6984327	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.0003		0.00028		0.99997		1.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60303	60303	SRR12194937	SRX8707740	SRS6984327	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B5	GSM4666886	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B5	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666886	GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq	GSM4666886		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666886	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-3_S18_L003_R1_001.fastq.gz	fastq	294808074.0	1855987.0	GSM4666886 r3	0:158.84 1:0	A:87400489;C:18832328;G:74835505;T:113724113;N:15639	158	0	87400489	18832328	74835505	113724113	15639	SRX8707740	SRS6984327	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00013		0.00012		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60304	60304	SRR12194938	SRX8707740	SRS6984327	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B5	GSM4666886	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:male	adult whole brain B5	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:M	GSM4666886	GSM4666886: adult whole brain B5; Danio rerio; Bisulfite Seq	GSM4666886		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666886	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-3_S18_L004_R1_001.fastq.gz	fastq	290930278.0	1831782.0	GSM4666886 r4	0:158.82 1:0	A:84789368;C:18396243;G:77012622;T:110719520;N:12525	158	0	84789368	18396243	77012622	110719520	12525	SRX8707740	SRS6984327	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00024		0.0002		0.99995		0.33333		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60305	60305	SRR12194931	SRX8707739	SRS6984326	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B4	GSM4666885	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B4	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666885	GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq	GSM4666885		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666885	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-2_S17_L001_R1_001.fastq.gz	fastq	375215607.0	2361864.0	GSM4666885 r1	0:158.86 1:0	A:112024323;C:24781235;G:92436169;T:145945302;N:28578	158	0	112024323	24781235	92436169	145945302	28578	SRX8707739	SRS6984326	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00013		0.0001		0.99995		0.5		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60306	60306	SRR12194932	SRX8707739	SRS6984326	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B4	GSM4666885	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B4	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666885	GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq	GSM4666885		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666885	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-2_S17_L002_R1_001.fastq.gz	fastq	370428283.0	2331824.0	GSM4666885 r2	0:158.86 1:0	A:108805681;C:24009319;G:95364944;T:142223301;N:25038	158	0	108805681	24009319	95364944	142223301	25038	SRX8707739	SRS6984326	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00017		0.00015		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60307	60307	SRR12194933	SRX8707739	SRS6984326	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B4	GSM4666885	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B4	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666885	GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq	GSM4666885		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666885	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-2_S17_L003_R1_001.fastq.gz	fastq	364134844.0	2292107.0	GSM4666885 r3	0:158.86 1:0	A:108842586;C:23917958;G:89584932;T:141770665;N:18703	158	0	108842586	23917958	89584932	141770665	18703	SRX8707739	SRS6984326	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00014		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60308	60308	SRR12194934	SRX8707739	SRS6984326	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B4	GSM4666885	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B4	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666885	GSM4666885: adult whole brain B4; Danio rerio; Bisulfite Seq	GSM4666885		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666885	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-2_S17_L004_R1_001.fastq.gz	fastq	359261298.0	2261503.0	GSM4666885 r4	0:158.86 1:0	A:105806137;C:23327442;G:91805038;T:138304777;N:17904	158	0	105806137	23327442	91805038	138304777	17904	SRX8707739	SRS6984326	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00021		0.00019		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60309	60309	SRR12194927	SRX8707738	SRS6984325	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B3	GSM4666884	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B3	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666884	GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq	GSM4666884		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666884	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-1_S16_L001_R1_001.fastq.gz	fastq	519733754.0	3271474.0	GSM4666884 r1	0:158.87 1:0	A:155037427;C:33300575;G:128899352;T:202457471;N:38929	158	0	155037427	33300575	128899352	202457471	38929	SRX8707738	SRS6984325	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00012		0.99995		0.33333		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60310	60310	SRR12194928	SRX8707738	SRS6984325	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B3	GSM4666884	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B3	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666884	GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq	GSM4666884		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666884	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-1_S16_L002_R1_001.fastq.gz	fastq	514851816.0	3240814.0	GSM4666884 r2	0:158.86 1:0	A:151014256;C:32338266;G:133641006;T:197823476;N:34812	158	0	151014256	32338266	133641006	197823476	34812	SRX8707738	SRS6984325	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00017		0.00015		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60311	60311	SRR12194929	SRX8707738	SRS6984325	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B3	GSM4666884	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B3	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666884	GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq	GSM4666884		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666884	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-1_S16_L003_R1_001.fastq.gz	fastq	505305764.0	3180622.0	GSM4666884 r3	0:158.87 1:0	A:150924986;C:32216951;G:125139306;T:196997199;N:27322	158	0	150924986	32216951	125139306	196997199	27322	SRX8707738	SRS6984325	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00019		0.00017		0.99997		1.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60312	60312	SRR12194930	SRX8707738	SRS6984325	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B3	GSM4666884	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B3	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666884	GSM4666884: adult whole brain B3; Danio rerio; Bisulfite Seq	GSM4666884		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666884	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P4-1_S16_L004_R1_001.fastq.gz	fastq	500262064.0	3148948.0	GSM4666884 r4	0:158.87 1:0	A:147195579;C:31493012;G:128890060;T:192659641;N:23772	158	0	147195579	31493012	128890060	192659641	23772	SRX8707738	SRS6984325	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.0001		9e-05		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60313	60313	SRR12194923	SRX8707737	SRS6984324	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B2	GSM4666883	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B2	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666883	GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq	GSM4666883		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666883	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-6_S15_L001_R1_001.fastq.gz	fastq	517956360.0	3260092.0	GSM4666883 r1	0:158.88 1:0	A:150448706;C:32858153;G:137976678;T:196634454;N:38369	158	0	150448706	32858153	137976678	196634454	38369	SRX8707737	SRS6984324	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00015		0.00014		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60314	60314	SRR12194924	SRX8707737	SRS6984324	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B2	GSM4666883	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B2	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666883	GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq	GSM4666883		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666883	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-6_S15_L002_R1_001.fastq.gz	fastq	509673976.0	3208134.0	GSM4666883 r2	0:158.87 1:0	A:145524541;C:31734648;G:141519088;T:190860914;N:34785	158	0	145524541	31734648	141519088	190860914	34785	SRX8707737	SRS6984324	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00019		0.00017		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60315	60315	SRR12194925	SRX8707737	SRS6984324	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B2	GSM4666883	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B2	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666883	GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq	GSM4666883		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666883	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-6_S15_L003_R1_001.fastq.gz	fastq	503140482.0	3166780.0	GSM4666883 r3	0:158.88 1:0	A:146286862;C:31831570;G:133486316;T:191509945;N:25789	158	0	146286862	31831570	133486316	191509945	25789	SRX8707737	SRS6984324	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00015		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60316	60316	SRR12194926	SRX8707737	SRS6984324	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B2	GSM4666883	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B2	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666883	GSM4666883: adult whole brain B2; Danio rerio; Bisulfite Seq	GSM4666883		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666883	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-6_S15_L004_R1_001.fastq.gz	fastq	493961726.0	3109154.0	GSM4666883 r4	0:158.87 1:0	A:141543659;C:30970461;G:135682865;T:185742190;N:22551	158	0	141543659	30970461	135682865	185742190	22551	SRX8707737	SRS6984324	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00018		0.00017		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60317	60317	SRR12194919	SRX8707736	SRS6984322	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B1	GSM4666882	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B1	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666882	GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq	GSM4666882		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666882	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-5_S14_L001_R1_001.fastq.gz	fastq	644565105.0	4057680.0	GSM4666882 r1	0:158.85 1:0	A:189377017;C:44153618;G:160972875;T:250013345;N:48250	158	0	189377017	44153618	160972875	250013345	48250	SRX8707736	SRS6984322	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00011		0.0001		1.0				159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60318	60318	SRR12194920	SRX8707736	SRS6984322	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B1	GSM4666882	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B1	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666882	GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq	GSM4666882		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666882	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-5_S14_L002_R1_001.fastq.gz	fastq	638463567.0	4019714.0	GSM4666882 r2	0:158.83 1:0	A:184509132;C:42923906;G:166717116;T:244267791;N:45622	158	0	184509132	42923906	166717116	244267791	45622	SRX8707736	SRS6984322	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00014		0.00012		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60319	60319	SRR12194921	SRX8707736	SRS6984322	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B1	GSM4666882	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B1	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666882	GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq	GSM4666882		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666882	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-5_S14_L003_R1_001.fastq.gz	fastq	626116922.0	3941475.0	GSM4666882 r3	0:158.85 1:0	A:184234800;C:42706665;G:156104866;T:243035941;N:34650	158	0	184234800	42706665	156104866	243035941	34650	SRX8707736	SRS6984322	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.0002		0.00018		0.99997		1.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60320	60320	SRR12194922	SRX8707736	SRS6984322	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain B1	GSM4666882	tissue:adult whole brain\|strain:AB line\|generation:F1\|Sex:female	adult whole brain B1	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F1\|Sex:F	GSM4666882	GSM4666882: adult whole brain B1; Danio rerio; Bisulfite Seq	GSM4666882		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666882	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P3-5_S14_L004_R1_001.fastq.gz	fastq	619633878.0	3900997.0	GSM4666882 r4	0:158.84 1:0	A:179600621;C:41804166;G:160698591;T:237500321;N:30179	158	0	179600621	41804166	160698591	237500321	30179	SRX8707736	SRS6984322	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00017		0.00012		0.99993		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60321	60321	SRR12194915	SRX8707735	SRS6984323	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C16	GSM4666881	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666881	GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq	GSM4666881		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666881	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-6_S33_L001_R1_001.fastq.gz	fastq	293820485.0	1849388.0	GSM4666881 r1	0:158.87 1:0	A:86678903;C:19266888;G:74424764;T:113427237;N:22693	158	0	86678903	19266888	74424764	113427237	22693	SRX8707735	SRS6984323	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00015		0.00012		0.99995		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60322	60322	SRR12194916	SRX8707735	SRS6984323	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C16	GSM4666881	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666881	GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq	GSM4666881		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666881	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-6_S33_L002_R1_001.fastq.gz	fastq	290054720.0	1825735.0	GSM4666881 r2	0:158.87 1:0	A:84128360;C:18660250;G:76750691;T:110494636;N:20783	158	0	84128360	18660250	76750691	110494636	20783	SRX8707735	SRS6984323	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00017		0.00015		0.99997		1.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60323	60323	SRR12194917	SRX8707735	SRS6984323	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C16	GSM4666881	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666881	GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq	GSM4666881		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666881	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-6_S33_L003_R1_001.fastq.gz	fastq	285222008.0	1795272.0	GSM4666881 r3	0:158.87 1:0	A:84271091;C:18587085;G:72126787;T:110222855;N:14190	158	0	84271091	18587085	72126787	110222855	14190	SRX8707735	SRS6984323	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00014		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60324	60324	SRR12194918	SRX8707735	SRS6984323	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C16	GSM4666881	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C16	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666881	GSM4666881: adult whole brain C16; Danio rerio; Bisulfite Seq	GSM4666881		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666881	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-6_S33_L004_R1_001.fastq.gz	fastq	281043981.0	1769013.0	GSM4666881 r4	0:158.87 1:0	A:81695659;C:18172870;G:73847131;T:107315179;N:13142	158	0	81695659	18172870	73847131	107315179	13142	SRX8707735	SRS6984323	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00021		0.00018		0.99995		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60325	60325	SRR12194911	SRX8707734	SRS6984321	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C15	GSM4666880	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666880	GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq	GSM4666880		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666880	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-5_S32_L001_R1_001.fastq.gz	fastq	407927114.0	2567613.0	GSM4666880 r1	0:158.87 1:0	A:121216665;C:26341281;G:102882256;T:157456714;N:30198	158	0	121216665	26341281	102882256	157456714	30198	SRX8707734	SRS6984321	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.0002		0.00018		0.99997		1.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System
60326	60326	SRR12194912	SRX8707734	SRS6984321	SRP271280	PRJNA645421	Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L	GSE154206	Other	In the present study zebrafish were exposed to permethrin during early life and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020 and here we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0 F1 and F2 generations 4 replicates treatment 4 replicates control for each sex and each generation. Except only 3 treated male F0		pubmed:33752003	adult whole brain C15	GSM4666880	tissue:adult whole brain\|strain:AB line\|generation:F2\|Sex:male	adult whole brain C15	Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L 0 0.6". Rk due to batch effects described below PE sequences were analyzed as SE. methyl calling using Bismark extractor cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor. *.tabular files before correction and corrected matrix.csv post correction	adult whole brain	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS		strain:AB line\|generation:F2\|Sex:M	GSM4666880	GSM4666880: adult whole brain C15; Danio rerio; Bisulfite Seq	GSM4666880		1	Fish were euthanized brains were dissected and flash frozen in liquid nitrogen and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE University of Perpignan France for pair ended or single ended RRBS	GEO Accession:GSM4666880	Bisulfite-Seq	TRANSCRIPTOMIC	Reduced Representation	SINGLE	ILLUMINA	NextSeq 550	SRP271280	P8-5_S32_L002_R1_001.fastq.gz	fastq	402652470.0	2534477.0	GSM4666880 r2	0:158.87 1:0	A:117634138;C:25467360;G:106127698;T:153394332;N:28942	158	0	117634138	25467360	106127698	153394332	28942	SRX8707734	SRS6984321	SRA1097340	GEO	UMR MARBEC, INRAE	1	0.00016		0.00014		0.99997		0.0		159		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	France	2020-07-10	Adult	Adult	Brain	Nervous System

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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");;