metadata: run_metadata: 31 rows where devstage_curation = "Larval" and experiment.library

31 rows where devstage_curation = "Larval" and experiment.library_strategy = "RIP-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
43454	43454	SRR7169686	SRX4087616	SRS3304345	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IN wholefishtranscriptome RNAseq rep4	GSM3143177	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep4	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM3143177	GSM3143177: IN wholefishtranscriptome RNAseq rep4; Danio rerio; RIP Seq	GSM3143177		1	RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer's instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3143177	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN3_R1.fastq.gz RiboZF_IN3_R2.fastq.gz	fastq fastq	9065897639.0	60495321.0	GSM3143177 r1	0:74.96 1:74.90	A:2375136682;C:2190164060;G:2113095817;T:2385734886;N:1766194	74	74	2375136682	2190164060	2113095817	2385734886	1766194	SRX4087616	SRS3304345	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.92807	0.92373	0.0842	0.08335	0.71754	0.72305	0.45254	0.46074	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2018-05-16	Larval	Larval	Whole Organism	All anatomical structures
43455	43455	SRR5952030	SRX3110524	SRS2445617	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IN wholefishtranscriptome RNAseq rep3	GSM2747297	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep3	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747297	GSM2747297: IN wholefishtranscriptome RNAseq rep3; Danio rerio; RIP Seq	GSM2747297		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747297	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN4_R1.fastq.gz RiboZF_IN4_R2.fastq.gz	fastq fastq	8796307376.0	58697576.0	GSM2747297 r1	0:74.96 1:74.90	A:2326140676;C:2104630190;G:2033251376;T:2330582425;N:1702709	74	74	2326140676	2104630190	2033251376	2330582425	1702709	SRX3110524	SRS2445617	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.94186	0.93847	0.08006	0.08004	0.70169	0.70778	0.46714	0.45678	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	All anatomical structures
43456	43456	SRR5952029	SRX3110523	SRS2445616	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IN wholefishtranscriptome RNAseq rep2	GSM2747296	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep2	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747296	GSM2747296: IN wholefishtranscriptome RNAseq rep2; Danio rerio; RIP Seq	GSM2747296		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747296	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN2_R1.fastq.gz RiboZF_IN2_R2.fastq.gz	fastq fastq	7407816750.0	49385445.0	GSM2747296 r1	0:75 1:75	A:1965588922;C:1772589081;G:1716538525;T:1951670484;N:1429738	75	75	1965588922	1772589081	1716538525	1951670484	1429738	SRX3110523	SRS2445616	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.93743	0.9347	0.07981	0.07938	0.69721	0.70246	0.46381	0.46767	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	All anatomical structures
43457	43457	SRR5952028	SRX3110522	SRS2445615	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IN wholefishtranscriptome RNAseq rep1	GSM2747295	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep1	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747295	GSM2747295: IN wholefishtranscriptome RNAseq rep1; Danio rerio; RIP Seq	GSM2747295		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747295	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN1_R1.fastq.gz RiboZF_IN1_R2.fastq.gz	fastq fastq	4971869342.0	33177517.0	GSM2747295 r1	0:74.96 1:74.90	A:1277896624;C:1224383725;G:1184225816;T:1284401610;N:961567	74	74	1277896624	1224383725	1184225816	1284401610	961567	SRX3110522	SRS2445615	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.94557	0.94195	0.09264	0.0931	0.69785	0.70337	0.48067	0.48526	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	All anatomical structures
43458	43458	SRR5952027	SRX3110521	SRS2445614	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep3	GSM2747294	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep3	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747294	GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq	GSM2747294		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747294	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz	fastq fastq	4994833580.0	33330363.0	GSM2747294 r1	0:74.96 1:74.90	A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588	74	74	1202677579	1288784412	1278463604	1223941397	966588	SRX3110521	SRS2445614	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.61854	0.6151	0.20328	0.19651	0.83599	0.84104	0.60632	0.59954	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
43459	43459	SRR5952026	SRX3110520	SRS2445613	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep2	GSM2747293	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep2	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747293	GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq	GSM2747293		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747293	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz	fastq fastq	4530855300.0	30205702.0	GSM2747293 r1	0:75 1:75	A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367	75	75	1112381418	1153277132	1147183468	1117133915	879367	SRX3110520	SRS2445613	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.64948	0.64878	0.15967	0.15683	0.80756	0.81288	0.56438	0.56275	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
43460	43460	SRR5952025	SRX3110519	SRS2445612	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.	pubmed:29765956	IP HCtranslatome RNAseq rep1	GSM2747292	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome RNAseq rep1	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	GSM2747292	GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq	GSM2747292		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747292	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz	fastq fastq	5261113350.0	35074089.0	GSM2747292 r1	0:75 1:75	A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927	75	75	1356848229	1276483567	1260001700	1366757927	1021927	SRX3110519	SRS2445612	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.66363	0.6599	0.15644	0.15316	0.76808	0.7725	0.48538	0.48933	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Embryo Imprecise	All anatomical structures
60025	60025	SRR12103783	SRX8627954	SRS6916259	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB4 IP	GSM4644253	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	PCB4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644253	GSM4644253: PCB4 IP; Danio rerio; RIP Seq	GSM4644253		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644253	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz	fastq fastq	2309150560.0	15191780.0	GSM4644253 r1	0:76 1:76	A:490672579;C:656568819;G:666651729;T:495020365;N:237068	76	76	490672579	656568819	666651729	495020365	237068	SRX8627954	SRS6916259	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94474	0.944	0.18094	0.18203	0.7515	0.75554	0.60771	0.6152	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60026	60026	SRR12103782	SRX8627953	SRS6916258	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB3 IP	GSM4644252	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	PCB3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644252	GSM4644252: PCB3 IP; Danio rerio; RIP Seq	GSM4644252		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644252	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz	fastq fastq	2965972504.0	19512977.0	GSM4644252 r1	0:76 1:76	A:620624207;C:853765538;G:874990332;T:616281897;N:310530	76	76	620624207	853765538	874990332	616281897	310530	SRX8627953	SRS6916258	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93433	0.93213	0.16543	0.16208	0.75043	0.753	0.62186	0.64359	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60027	60027	SRR12103781	SRX8627952	SRS6916257	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB2 IP	GSM4644251	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	PCB2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644251	GSM4644251: PCB2 IP; Danio rerio; RIP Seq	GSM4644251		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644251	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz	fastq fastq	2687973472.0	17684036.0	GSM4644251 r1	0:76 1:76	A:585901626;C:744255122;G:756993274;T:600539454;N:283996	76	76	585901626	744255122	756993274	600539454	283996	SRX8627952	SRS6916257	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9445	0.94466	0.16876	0.17035	0.74728	0.75022	0.57878	0.57933	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60028	60028	SRR12103780	SRX8627951	SRS6916256	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB1 IP	GSM4644250	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	PCB1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644250	GSM4644250: PCB1 IP; Danio rerio; RIP Seq	GSM4644250		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644250	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz	fastq fastq	2596174288.0	17080094.0	GSM4644250 r1	0:76 1:76	A:564523297;C:723443207;G:735894528;T:572044392;N:268864	76	76	564523297	723443207	735894528	572044392	268864	SRX8627951	SRS6916256	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93494	0.93528	0.17469	0.17518	0.746	0.74803	0.60114	0.60005	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60029	60029	SRR12103779	SRX8627950	SRS6916255	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB4 Input	GSM4644249	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644249	GSM4644249: PCB4 Input; Danio rerio; RIP Seq	GSM4644249		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644249	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz	fastq fastq	3655473384.0	24049167.0	GSM4644249 r1	0:76 1:76	A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960	76	76	680110064	1145409769	1179103219	650470372	379960	SRX8627950	SRS6916255	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93037	0.96319	0.21668	0.22563	0.86338	0.86385	0.77257	0.70059	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60030	60030	SRR12103778	SRX8627949	SRS6916254	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB3 Input	GSM4644248	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644248	GSM4644248: PCB3 Input; Danio rerio; RIP Seq	GSM4644248		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644248	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz	fastq fastq	4926238376.0	32409463.0	GSM4644248 r1	0:76 1:76	A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124	76	76	929043061	1530175131	1577898210	888604850	517124	SRX8627949	SRS6916254	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92875	0.95698	0.21539	0.22073	0.85253	0.85431	0.76235	0.68659	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60031	60031	SRR12103777	SRX8627948	SRS6916253	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB2 Input	GSM4644247	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644247	GSM4644247: PCB2 Input; Danio rerio; RIP Seq	GSM4644247		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644247	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz	fastq fastq	5669611400.0	37300075.0	GSM4644247 r1	0:76 1:76	A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993	76	76	1050955836	1780355588	1829450728	1008257255	591993	SRX8627948	SRS6916253	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93297	0.93791	0.21298	0.21667	0.85902	0.86302	0.7387	0.69759	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60032	60032	SRR12103776	SRX8627947	SRS6916252	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	PCB1 Input	GSM4644246	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644246	GSM4644246: PCB1 Input; Danio rerio; RIP Seq	GSM4644246		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644246	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz	fastq fastq	4154972744.0	27335347.0	GSM4644246 r1	0:76 1:76	A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109	76	76	764769282	1310937656	1344287240	734545457	433109	SRX8627947	SRS6916252	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92033	0.95428	0.21666	0.2245	0.86571	0.8678	0.74089	0.68247	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60033	60033	SRR12103775	SRX8627946	SRS6916251	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO4 IP	GSM4644245	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	DMSO4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644245	GSM4644245: DMSO4 IP; Danio rerio; RIP Seq	GSM4644245		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644245	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz	fastq fastq	2415539920.0	15891710.0	GSM4644245 r1	0:76 1:76	A:519904759;C:674887600;G:688106098;T:532387711;N:253752	76	76	519904759	674887600	688106098	532387711	253752	SRX8627946	SRS6916251	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94931	0.94824	0.16515	0.16656	0.74858	0.7497	0.57724	0.58102	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60034	60034	SRR12103774	SRX8627945	SRS6916250	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO3 IP	GSM4644244	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	DMSO3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644244	GSM4644244: DMSO3 IP; Danio rerio; RIP Seq	GSM4644244		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644244	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz	fastq fastq	2419255408.0	15916154.0	GSM4644244 r1	0:76 1:76	A:524637988;C:675158080;G:687344217;T:531861650;N:253473	76	76	524637988	675158080	687344217	531861650	253473	SRX8627945	SRS6916250	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93623	0.93621	0.18212	0.18165	0.74308	0.74426	0.60527	0.60757	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60035	60035	SRR12103773	SRX8627944	SRS6916249	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO2 IP	GSM4644243	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	DMSO2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644243	GSM4644243: DMSO2 IP; Danio rerio; RIP Seq	GSM4644243		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644243	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz	fastq fastq	2698406448.0	17752674.0	GSM4644243 r1	0:76 1:76	A:578126060;C:760791571;G:775423382;T:583783650;N:281785	76	76	578126060	760791571	775423382	583783650	281785	SRX8627944	SRS6916249	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9433	0.94318	0.17976	0.1816	0.74992	0.75215	0.58844	0.61497	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60036	60036	SRR12103772	SRX8627943	SRS6916248	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO1 IP	GSM4644242	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	DMSO1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644242	GSM4644242: DMSO1 IP; Danio rerio; RIP Seq	GSM4644242		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644242	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz	fastq fastq	2588221344.0	17027772.0	GSM4644242 r1	0:76 1:76	A:552076254;C:730948542;G:744135059;T:560788856;N:272633	76	76	552076254	730948542	744135059	560788856	272633	SRX8627943	SRS6916248	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93871	0.9398	0.17681	0.17588	0.74688	0.74915	0.59376	0.61045	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60037	60037	SRR12103771	SRX8627942	SRS6916247	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO4 Input	GSM4644241	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644241	GSM4644241: DMSO4 Input; Danio rerio; RIP Seq	GSM4644241		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644241	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz	fastq fastq	4085824752.0	26880426.0	GSM4644241 r1	0:76 1:76	A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588	76	76	734095239	1307425224	1339970208	703907493	426588	SRX8627942	SRS6916247	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94341	0.94693	0.21035	0.21294	0.86306	0.86571	0.66228	0.69648	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60038	60038	SRR12103770	SRX8627941	SRS6916246	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO3 Input	GSM4644240	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644240	GSM4644240: DMSO3 Input; Danio rerio; RIP Seq	GSM4644240		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644240	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz	fastq fastq	3627749800.0	23866775.0	GSM4644240 r1	0:76 1:76	A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850	76	76	677883991	1133504965	1166401920	649582074	376850	SRX8627941	SRS6916246	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92028	0.96282	0.2164	0.22913	0.86517	0.8661	0.73802	0.70578	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60039	60039	SRR12103769	SRX8627940	SRS6916245	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO2 Input	GSM4644239	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644239	GSM4644239: DMSO2 Input; Danio rerio; RIP Seq	GSM4644239		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644239	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz	fastq fastq	2991355592.0	19679971.0	GSM4644239 r1	0:76 1:76	A:555548434;C:937287598;G:965607991;T:532600162;N:311407	76	76	555548434	937287598	965607991	532600162	311407	SRX8627940	SRS6916245	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92966	0.96538	0.21752	0.22835	0.86137	0.86701	0.71065	0.70316	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60040	60040	SRR12103768	SRX8627939	SRS6916244	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …	pubmed:33064826	DMSO1 Input	GSM4644238	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644238	GSM4644238: DMSO1 Input; Danio rerio; RIP Seq	GSM4644238		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644238	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz	fastq fastq	3551567552.0	23365576.0	GSM4644238 r1	0:76 1:76	A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317	76	76	659305531	1112775748	1146213503	632894453	378317	SRX8627939	SRS6916244	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92942	0.96366	0.21295	0.2231	0.8574	0.85934	0.75989	0.75855	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
66086	66086	SRR15900240	SRX12190888	SRS10168725	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			EOM+CH 2	strain:AB\|isolate:CH2\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab CH2	tchenlab CH2	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	EOM_CH_5.8.IP_R1.fastq.gz EOM_CH_5.8.IP_R2.fastq.gz EOM_CH_5.8.Input_R1.fastq.gz EOM_CH_5.8.Input_R2.fastq.gz	fastq fastq fastq fastq	13391108400.0	44637028.0	EOM CH 5.8.IP R1.fastq.gz	0:150 1:150	A:2721241817;C:3886076819;G:4096587749;T:2611313908;N:75888107	150	150	2721241817	3886076819	4096587749	2611313908	75888107	SRX12190888	SRS10168725	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.8442	0.59467	0.17491	0.14724	0.86147	0.89112	0.7593	0.63363	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66087	66087	SRR15900241	SRX12190887	SRS10168724	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			EOM+CH 1	strain:AB\|isolate:CH1\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab CH1	tchenlab CH1	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	EOM_CH_4.16.IP_R1.fastq.gz EOM_CH_4.16.IP_R2.fastq.gz EOM_CH_4.16.Input_R1.fastq.gz EOM_CH_4.16.Input_R2.fastq.gz	fastq fastq fastq fastq	12428976000.0	41429920.0	EOM CH 4.16.IP R1.fastq.gz	0:150 1:150	A:2486344612;C:3648199763;G:3865825828;T:2365039093;N:63566704	150	150	2486344612	3648199763	3865825828	2365039093	63566704	SRX12190887	SRS10168724	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.91763	0.6223	0.18817	0.15102	0.84891	0.87957	0.74757	0.64429	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66088	66088	SRR15900242	SRX12190886	SRS10168723	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			EOM 3	strain:AB\|isolate:T3\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab T3	tchenlab T3	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	EOM_5.9.IP_R1.fastq.gz EOM_5.9.IP_R2.fastq.gz EOM_5.9.Input_R1.fastq.gz EOM_5.9.Input_R2.fastq.gz	fastq fastq fastq fastq	12301780200.0	41005934.0	EOM 5.9.IP R1.fastq.gz	0:150 1:150	A:2415542475;C:3651603114;G:3847935468;T:2318868176;N:67830967	150	150	2415542475	3651603114	3847935468	2318868176	67830967	SRX12190886	SRS10168723	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.87516	0.65874	0.18282	0.16547	0.85561	0.87657	0.72193	0.61862	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66089	66089	SRR15900243	SRX12190885	SRS10168722	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			EOM 2	strain:AB\|isolate:T2\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab T2	tchenlab T2	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	EOM_5.8.IP_R1.fastq.gz EOM_5.8.IP_R2.fastq.gz EOM_5.8.Input_R1.fastq.gz EOM_5.8.Input_R2.fastq.gz	fastq fastq fastq fastq	12373139700.0	41243799.0	EOM 5.8.IP R1.fastq.gz	0:150 1:150	A:2429212483;C:3679585650;G:3865741937;T:2330164654;N:68434976	150	150	2429212483	3679585650	3865741937	2330164654	68434976	SRX12190885	SRS10168722	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.88644	0.67829	0.18408	0.16867	0.84652	0.8704	0.76376	0.64158	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66090	66090	SRR15900244	SRX12190884	SRS10168721	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			EOM 1	strain:AB\|isolate:T1\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab T1	tchenlab T1	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	EOM_4.16.IP_R1.fastq.gz EOM_4.16.IP_R2.fastq.gz EOM_4.16.Input_R1.fastq.gz EOM_4.16.Input_R2.fastq.gz	fastq fastq fastq fastq	13638730800.0	45462436.0	EOM 4.16.IP R1.fastq.gz	0:150 1:150	A:2673949221;C:4057121296;G:4266457677;T:2562131972;N:79070634	150	150	2673949221	4057121296	4266457677	2562131972	79070634	SRX12190884	SRS10168721	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.87634	0.65649	0.18403	0.16375	0.85486	0.87913	0.69253	0.6405	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66091	66091	SRR15900245	SRX12190883	SRS10168720	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			DMSO 3	strain:AB\|isolate:C3\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab C3	tchenlab C3	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	DMSO_5.9.IP_R1.fastq.gz DMSO_5.9.IP_R2.fastq.gz DMSO_5.9.Input_R1.fastq.gz DMSO_5.9.Input_R2.fastq.gz	fastq fastq fastq fastq	12477964200.0	41593214.0	DMSO 5.9.IP R1.fastq.gz	0:150 1:150	A:2462053397;C:3697418372;G:3878832850;T:2368512335;N:71147246	150	150	2462053397	3697418372	3878832850	2368512335	71147246	SRX12190883	SRS10168720	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.94535	0.75289	0.20051	0.18779	0.84139	0.8646	0.74818	0.65269	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66092	66092	SRR15900246	SRX12190882	SRS10168719	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			DMSO 2	strain:AB\|isolate:C2\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab C2	tchenlab C2	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	DMSO_5.8.IP_R1.fastq.gz DMSO_5.8.IP_R2.fastq.gz DMSO_5.8.Input_R1.fastq.gz DMSO_5.8.Input_R2.fastq.gz	fastq fastq fastq fastq	12272849400.0	40909498.0	DMSO 5.8.IP R1.fastq.gz	0:150 1:150	A:2381041881;C:3673513092;G:3850518138;T:2295835815;N:71940474	150	150	2381041881	3673513092	3850518138	2295835815	71940474	SRX12190882	SRS10168719	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.88711	0.71046	0.18073	0.17436	0.84654	0.8674	0.76218	0.63257	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined
66093	66093	SRR15900247	SRX12190881	SRS10168718	SRP337081	PRJNA763243	m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos	PRJNA763243	Other	This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.			DMSO 1	strain:AB\|isolate:C1\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72 hpf organism or animal									RNA m6A methylation of zebrafish	tchenlab C1	tchenlab C1	M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.			RIP-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP337081	loader:fastq load.py	DMSO_4.16.IP_R1.fastq.gz DMSO_4.16.IP_R2.fastq.gz DMSO_4.16.Input_R1.fastq.gz DMSO_4.16.Input_R2.fastq.gz	fastq fastq fastq fastq	12900597000.0	43001990.0	DMSO 4.16.IP R1.fastq.gz	0:150 1:150	A:2517062962;C:3854768074;G:4032734290;T:2426295392;N:69736282	150	150	2517062962	3854768074	4032734290	2426295392	69736282	SRX12190881	SRS10168718	SRA1294636	Soochow University\|Department of Toxicology, School of Public Health	Soochow University	2	0.75605	0.5734	0.16268	0.14503	0.8714	0.89422	0.72976	0.64046	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	Unknown	2021-09-15	Larval	Larval	Undetermined	Undetermined

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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");;