metadata: run_metadata: 52 rows where experiment.library_strategy = "RIP-Seq" and tissue

52 rows where experiment.library_strategy = "RIP-Seq" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.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
41548	41548	SRR5017075	SRX2345570	SRS1796136	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input shield rep2	GSM2390028	tissue:Embryos\|developmental stage:Shield stage embryos\|strain:AB wild type	input shield rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:Shield stage embryos\|strain:AB wild type	GSM2390028	GSM2390028: input shield rep2; Danio rerio; RIP Seq	GSM2390028		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390028	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_shield_rep2.fastq.gz	fastq	6559838034.0	69785511.0	GSM2390028 r1	0:94	A:1785772532;C:1552902091;G:1571407685;T:1649464013;N:291713	94		1785772532	1552902091	1571407685	1649464013	291713	SRX2345570	SRS1796136	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03627		0.01		0.96676		0.66777		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41549	41549	SRR5017074	SRX2345569	SRS1796134	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input shield rep1	GSM2390027	tissue:Embryos\|developmental stage:Shield stage embryos\|strain:AB wild type	input shield rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:Shield stage embryos\|strain:AB wild type	GSM2390027	GSM2390027: input shield rep1; Danio rerio; RIP Seq	GSM2390027		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390027	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_shield_rep1.fastq.gz	fastq	3765873214.0	40062481.0	GSM2390027 r1	0:94	A:1002751444;C:902509483;G:908627718;T:951814220;N:170349	94		1002751444	902509483	908627718	951814220	170349	SRX2345569	SRS1796134	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03936		0.01095		0.96518		0.68725		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41550	41550	SRR5017073	SRX2345568	SRS1796132	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip shield rep2	GSM2390026	tissue:Embryos\|developmental stage:Shield stage embryos\|strain:AB wild type	ip shield rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:Shield stage embryos\|strain:AB wild type	GSM2390026	GSM2390026: ip shield rep2; Danio rerio; RIP Seq	GSM2390026		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390026	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_shield_rep2.fastq	fastq	3855863926.0	41019829.0	GSM2390026 r1	0:94	A:1044010018;C:931492803;G:952890289;T:926349254;N:1121562	94		1044010018	931492803	952890289	926349254	1121562	SRX2345568	SRS1796132	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03311		0.00481		0.96337		0.68612		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41551	41551	SRR5017072	SRX2345567	SRS1796131	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip shield rep1	GSM2390025	tissue:Embryos\|developmental stage:Shield stage embryos\|strain:AB wild type	ip shield rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:Shield stage embryos\|strain:AB wild type	GSM2390025	GSM2390025: ip shield rep1; Danio rerio; RIP Seq	GSM2390025		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390025	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_shield_rep1.fastq.gz	fastq	4107624502.0	43698133.0	GSM2390025 r1	0:94	A:1087077899;C:996101257;G:1020588721;T:1002667943;N:1188682	94		1087077899	996101257	1020588721	1002667943	1188682	SRX2345567	SRS1796131	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.01898		0.00264		0.97238		0.59809		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41552	41552	SRR5017071	SRX2345566	SRS1796152	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input sphere rep2	GSM2390024	tissue:Embryos\|developmental stage:sphere stage embryos\|strain:AB wild type	input sphere rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:sphere stage embryos\|strain:AB wild type	GSM2390024	GSM2390024: input sphere rep2; Danio rerio; RIP Seq	GSM2390024		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390024	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_sphere_rep2.fastq.gz	fastq	3684856024.0	39200596.0	GSM2390024 r1	0:94	A:991404019;C:883789087;G:892976599;T:916520929;N:165390	94		991404019	883789087	892976599	916520929	165390	SRX2345566	SRS1796152	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03619		0.00867		0.96051		0.63934		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41553	41553	SRR5017070	SRX2345565	SRS1796139	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input sphere rep1	GSM2390023	tissue:Embryos\|developmental stage:sphere stage embryos\|strain:AB wild type	input sphere rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:sphere stage embryos\|strain:AB wild type	GSM2390023	GSM2390023: input sphere rep1; Danio rerio; RIP Seq	GSM2390023		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390023	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_sphere_rep1.fastq.gz	fastq	3774515574.0	40154421.0	GSM2390023 r1	0:94	A:1014569244;C:912257296;G:925742711;T:921776107;N:170216	94		1014569244	912257296	925742711	921776107	170216	SRX2345565	SRS1796139	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04287		0.00892		0.95085		0.50435		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41554	41554	SRR5017069	SRX2345564	SRS1796133	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip sphere rep2	GSM2390022	tissue:Embryos\|developmental stage:sphere stage embryos\|strain:AB wild type	ip sphere rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:sphere stage embryos\|strain:AB wild type	GSM2390022	GSM2390022: ip sphere rep2; Danio rerio; RIP Seq	GSM2390022		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390022	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_sphere_rep2.fastq.gz	fastq	3926426624.0	41770496.0	GSM2390022 r1	0:94	A:1037910962;C:957162730;G:963824694;T:966381238;N:1147000	94		1037910962	957162730	963824694	966381238	1147000	SRX2345564	SRS1796133	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03492		0.00427		0.95026		0.60529		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41555	41555	SRR5017068	SRX2345563	SRS1796143	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip sphere rep1	GSM2390021	tissue:Embryos\|developmental stage:sphere stage embryos\|strain:AB wild type	ip sphere rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:sphere stage embryos\|strain:AB wild type	GSM2390021	GSM2390021: ip sphere rep1; Danio rerio; RIP Seq	GSM2390021		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390021	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_sphere_rep1.fastq.gz	fastq	4185867000.0	44530500.0	GSM2390021 r1	0:94	A:1114959829;C:1018236207;G:1019156922;T:1032304051;N:1209991	94		1114959829	1018236207	1019156922	1032304051	1209991	SRX2345563	SRS1796143	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03035		0.00288		0.94757		0.5787		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41556	41556	SRR5017067	SRX2345562	SRS1796129	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 64cell rep2	GSM2390020	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	input 64cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390020	GSM2390020: input 64cell rep2; Danio rerio; RIP Seq	GSM2390020		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390020	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_64cell_rep2.fastq.gz	fastq	3598782386.0	38284919.0	GSM2390020 r1	0:94	A:953869445;C:864903757;G:875832539;T:903947732;N:228913	94		953869445	864903757	875832539	903947732	228913	SRX2345562	SRS1796129	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04289		0.00757		0.9418		0.6078		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41557	41557	SRR5017066	SRX2345561	SRS1796141	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 64cell rep1	GSM2390019	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	input 64cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390019	GSM2390019: input 64cell rep1; Danio rerio; RIP Seq	GSM2390019		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390019	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_64cell_rep1.fastq.gz	fastq	3538898746.0	37647859.0	GSM2390019 r1	0:94	A:916878511;C:870431252;G:873611680;T:877750503;N:226800	94		916878511	870431252	873611680	877750503	226800	SRX2345561	SRS1796141	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03397		0.00616		0.95268		0.62545		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41558	41558	SRR5017065	SRX2345560	SRS1796153	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 64cell rep2	GSM2390018	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	ip 64cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390018	GSM2390018: ip 64cell rep2; Danio rerio; RIP Seq	GSM2390018		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390018	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_64cell_rep2.fastq.gz	fastq	3530677976.0	37560404.0	GSM2390018 r1	0:94	A:966880666;C:841411144;G:858285224;T:862983808;N:1117134	94		966880666	841411144	858285224	862983808	1117134	SRX2345560	SRS1796153	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04775		0.00421		0.92845		0.5748		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41559	41559	SRR5017064	SRX2345559	SRS1796135	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 64cell rep1	GSM2390017	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	ip 64cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390017	GSM2390017: ip 64cell rep1; Danio rerio; RIP Seq	GSM2390017		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390017	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_64cell_rep1.fastq.gz	fastq	3912003734.0	41617061.0	GSM2390017 r1	0:94	A:1040276279;C:945311584;G:953598043;T:971589029;N:1228799	94		1040276279	945311584	953598043	971589029	1228799	SRX2345559	SRS1796135	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03544		0.00268		0.93914		0.53712		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41560	41560	SRR5017063	SRX2345558	SRS1796155	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 1cell rep2	GSM2390016	tissue:Embryos\|developmental stage:1cell embryos\|strain:AB wild type	input 1cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:1cell embryos\|strain:AB wild type	GSM2390016	GSM2390016: input 1cell rep2; Danio rerio; RIP Seq	GSM2390016		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390016	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_1cell_rep2.fastq.gz	fastq	3379762010.0	35954915.0	GSM2390016 r1	0:94	A:898920912;C:816234808;G:823428476;T:840956466;N:221348	94		898920912	816234808	823428476	840956466	221348	SRX2345558	SRS1796155	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04513		0.00864		0.95085		0.51692		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Zygote	Embryo	Embryo Imprecise	All anatomical structures
41561	41561	SRR5017062	SRX2345557	SRS1796128	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 1cell rep1	GSM2390015	tissue:Embryos\|developmental stage:1cell embryos\|strain:AB wild type	input 1cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:1cell embryos\|strain:AB wild type	GSM2390015	GSM2390015: input 1cell rep1; Danio rerio; RIP Seq	GSM2390015		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390015	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_1cell_rep1.fastq.gz	fastq	3650321646.0	38833209.0	GSM2390015 r1	0:94	A:951411355;C:878458528;G:890250453;T:929968044;N:233266	94		951411355	878458528	890250453	929968044	233266	SRX2345557	SRS1796128	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03728		0.00668		0.94901		0.60038		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Zygote	Embryo	Embryo Imprecise	All anatomical structures
41562	41562	SRR5017061	SRX2345556	SRS1796127	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 1cell rep2	GSM2390014	tissue:Embryos\|developmental stage:1cell embryos\|strain:AB wild type	ip 1cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:1cell embryos\|strain:AB wild type	GSM2390014	GSM2390014: ip 1cell rep2; Danio rerio; RIP Seq	GSM2390014		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390014	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_1cell_rep2.fastq.gz	fastq	3485432580.0	37079070.0	GSM2390014 r1	0:94	A:953699047;C:835179152;G:846963064;T:848487912;N:1103405	94		953699047	835179152	846963064	848487912	1103405	SRX2345556	SRS1796127	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.02534		0.00219		0.95891		0.5975		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Zygote	Embryo	Embryo Imprecise	All anatomical structures
41563	41563	SRR5017060	SRX2345555	SRS1796130	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 1cell rep1	GSM2390013	tissue:Embryos\|developmental stage:1cell embryos\|strain:AB wild type	ip 1cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos		We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:1cell embryos\|strain:AB wild type	GSM2390013	GSM2390013: ip 1cell rep1; Danio rerio; RIP Seq	GSM2390013		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390013	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_1cell_rep1.fastq.gz	fastq	3610167102.0	38406033.0	GSM2390013 r1	0:94	A:961438376;C:875781200;G:891055201;T:880749228;N:1143097	94		961438376	875781200	891055201	880749228	1143097	SRX2345555	SRS1796130	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.01939		0.00159		0.96457		0.53652		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Zygote	Embryo	Embryo Imprecise	All anatomical structures
42000	42000	SRR5379364	SRX2674572	SRS2073700	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.		pubmed:29636379	ddx39a 24hpf RIPseq	GSM2550918	source name:embryos\|genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	ddx39a 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	GSM2550918	GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550918		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550918	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz	fastq fastq	3819239400.0	19096197.0	GSM2550918 r1	0:100 1:100	A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472	100	100	751858949	1169790479	1139713624	756987876	888472	SRX2674572	SRS2073700	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.98659	0.98572	0.28836	0.28975	0.89422	0.89558	0.75396	0.78553	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
42001	42001	SRR5379363	SRX2674571	SRS2073697	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.		pubmed:29636379	WT 24hpf RIPseq	GSM2550917	source name:embryos\|genotype:wild type\|tissue:embryo\|developmental stage:24hpf	WT 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:wild type\|tissue:embryo\|developmental stage:24hpf	GSM2550917	GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550917		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550917	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz	fastq fastq	3802882200.0	19014411.0	GSM2550917 r1	0:100 1:100	A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137	100	100	733911232	1178365174	1154031422	735690235	884137	SRX2674571	SRS2073697	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.9866	0.98469	0.30567	0.30486	0.90796	0.90928	0.82926	0.83029	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	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
54307	54307	SRR10129555	SRX6857975	SRS5395856	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.			Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo HA rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere HA	HA sphere	HA sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863		IP2_R1.fq.gz IP2_R2.fq.gz	fastq fastq	7528561800.0	25095206.0	IP2 R1.fq.gz	0:150 1:150	A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765	150	150	1638987252	1830922014	2628590112	1430016657	45765	SRX6857975	SRS5395856	SRA962995	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92316	0.96332	0.32571	0.34771	0.89173	0.88962	0.89557	0.89793	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	Embryo Imprecise	All anatomical structures
54308	54308	SRR10129346	SRX6857766	SRS5395649	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.			Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo IgG rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere IgG	IgG sphere	IgG sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863		IgG1_R1.fq.gz IgG1_R2.fq.gz	fastq fastq	2647374600.0	8824582.0	IgG1 R1.fq.gz	0:150 1:150	A:565620765;C:650153559;G:936592543;T:494992101;N:15632	150	150	565620765	650153559	936592543	494992101	15632	SRX6857766	SRS5395649	SRA962944	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.95349	0.96423	0.33504	0.34458	0.93748	0.93726	0.85176	0.91118	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	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
63731	63731	SRR13998081	SRX10375447	SRS8490053	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 4h WT rep1	GSM5179333	source name:control 4h RIP seq rep1\|tissue:zebrafish embryos\|genotype:wild type\|age:4 hpf	rip 4h WT rep1	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 4h RIP seq rep1		flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:4 hpf	GSM5179333	GSM5179333: rip 4h WT rep1; Danio rerio; RIP Seq	GSM5179333		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179333	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_4h_WT1.fq.gz	fastq	11966922300.0	79779482.0	GSM5179333 r1	0:150	A:3779410126;C:2709781787;G:3301583942;T:2175291644;N:854801	150		3779410126	2709781787	3301583942	2175291644	854801	SRX10375447	SRS8490053	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.30752		0.13393		0.90575		0.74028		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Blastula	Embryo	Embryo Imprecise	All anatomical structures
63732	63732	SRR13998080	SRX10375446	SRS8490052	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 2h WT rep2	GSM5179332	source name:control 2h RIP seq rep2\|tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	rip 2h WT rep2	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 2h RIP seq rep2		flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	GSM5179332	GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq	GSM5179332		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179332	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_2h_WT2.fq.gz	fastq	12320805000.0	82138700.0	GSM5179332 r1	0:150	A:3686415626;C:2826613772;G:3732955088;T:2073945227;N:875287	150		3686415626	2826613772	3732955088	2073945227	875287	SRX10375446	SRS8490052	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.1848		0.11194		0.9669		0.82171		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
63733	63733	SRR13998079	SRX10375445	SRS8490051	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 2h WT rep1	GSM5179331	source name:control 2h RIP seq rep1\|tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	rip 2h WT rep1	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 2h RIP seq rep1		flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	GSM5179331	GSM5179331: rip 2h WT rep1; Danio rerio; RIP Seq	GSM5179331		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179331	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_2h_WT1.fq.gz	fastq	8787958800.0	58586392.0	GSM5179331 r1	0:150	A:2671043775;C:2046825976;G:2545406298;T:1524056303;N:626448	150		2671043775	2046825976	2545406298	1524056303	626448	SRX10375445	SRS8490051	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.30731		0.17665		0.94117		0.79653		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
63734	63734	SRR13998082	SRX10375444	SRS8490050	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 4h WT rep2	GSM5179334	source name:control 4h RIP seq rep2\|tissue:zebrafish embryos\|genotype:wild type\|age:4 hpf	rip 4h WT rep2	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 4h RIP seq rep2		flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:4 hpf	GSM5179334	GSM5179334: rip 4h WT rep2; Danio rerio; RIP Seq	GSM5179334		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179334	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_4h_WT2.fq.gz	fastq	13945270350.0	92968469.0	GSM5179334 r1	0:150	A:4325573323;C:3059456045;G:4094407908;T:2464843410;N:989664	150		4325573323	3059456045	4094407908	2464843410	989664	SRX10375444	SRS8490050	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.19992		0.08953		0.93046		0.71052		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Blastula	Embryo	Embryo Imprecise	All anatomical structures
70712	70712	SRR20077343	SRX16115141	SRS13777745	SRP385866	PRJNA857663	RIP seq for Cpeb1b in zebrafish embryos	GSE207904	Transcriptome Analysis	Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates	parent bioproject:PRJNA857656		Flag Cpeb1b replicate 2	GSM6322839	source name:Flag Cpeb1b replicate 2\|tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	Flag Cpeb1b replicate 2	The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples	Flag Cpeb1b replicate 2		Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	GSM6322839	GSM6322839: Flag Cpeb1b replicate 2; Danio rerio; RIP Seq	GSM6322839 r1	GSM6322839	1	Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385866	loader:fastq load.py	Flag_Cpeb1b_replicate_2.R1.fq.gz Flag_Cpeb1b_replicate_2.R2.fq.gz	fastq fastq	14733801000.0	49112670.0	GSM6322839 r1	0:150 1:150	A:4141614412;C:3363207101;G:3881752054;T:3344596903;N:2630530	150	150	4141614412	3363207101	3881752054	3344596903	2630530	SRX16115141	SRS13777745	SRA1452503	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.05175	0.02071	0.01394	0.00703	0.99383	0.99758	0.80854	0.85616	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2022-07-11	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
70713	70713	SRR20077344	SRX16115140	SRS13777744	SRP385866	PRJNA857663	RIP seq for Cpeb1b in zebrafish embryos	GSE207904	Transcriptome Analysis	Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates	parent bioproject:PRJNA857656		Flag Cpeb1b replicate 1	GSM6322838	source name:Flag Cpeb1b replicate 1\|tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	Flag Cpeb1b replicate 1	The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples	Flag Cpeb1b replicate 1		Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	GSM6322838	GSM6322838: Flag Cpeb1b replicate 1; Danio rerio; RIP Seq	GSM6322838 r1	GSM6322838	1	Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385866	loader:fastq load.py	Flag_Cpeb1b_replicate_1.R1.fq.gz Flag_Cpeb1b_replicate_1.R2.fq.gz	fastq fastq	15482669700.0	51608899.0	GSM6322838 r1	0:150 1:150	A:4303443264;C:3570990345;G:4030059369;T:3575508224;N:2668498	150	150	4303443264	3570990345	4030059369	3575508224	2668498	SRX16115140	SRS13777744	SRA1452503	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.03751	0.01773	0.01056	0.00621	0.99346	0.99736	0.89693	0.8036	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2022-07-11	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
75639	75639	SRR24746222	SRX20523357	SRS17832947	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c RIP biol rep 2	GSM7430662	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c RIP biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP		RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430662	GSM7430662: eIF4E1c RIP biol rep 2; Danio rerio; RIP Seq	GSM7430662 r1	GSM7430662	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_3_1.fastq.gz e1c-RIP_3_2.fastq.gz	fastq fastq	3658509264.0	18111432.0	GSM7430662 r1	0:101 1:101	A:1021449118;C:787165883;G:803394137;T:1046320964;N:179162	101	101	1021449118	787165883	803394137	1046320964	179162	SRX20523357	SRS17832947	SRA1645065	IMP	IMP	2	0.89621	0.89533	0.04125	0.04128	0.7722	0.77244	0.5895	0.5976	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75640	75640	SRR24746223	SRX20523356	SRS17832945	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c RIP biol rep 1	GSM7430661	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c RIP biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP		RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430661	GSM7430661: eIF4E1c RIP biol rep 1; Danio rerio; RIP Seq	GSM7430661 r1	GSM7430661	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_1_1.fastq.gz e1c-RIP_1_2.fastq.gz	fastq fastq	3661517448.0	18126324.0	GSM7430661 r1	0:101 1:101	A:1033737040;C:769143038;G:789231169;T:1069383557;N:22644	101	101	1033737040	769143038	789231169	1069383557	22644	SRX20523356	SRS17832945	SRA1645065	IMP	IMP	2	0.63898	0.63654	0.0292	0.02977	0.8202	0.8216	0.63773	0.65353	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75641	75641	SRR24746224	SRX20523355	SRS17832943	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 3	GSM7430660	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 3	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP		RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430660	GSM7430660: eIF4E1b RIP biol rep 3; Danio rerio; RIP Seq	GSM7430660 r1	GSM7430660	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_3_1.fastq.gz e1b-RIP_3_2.fastq.gz	fastq fastq	3668401608.0	18160404.0	GSM7430660 r1	0:101 1:101	A:994142435;C:809751406;G:823521552;T:1040962762;N:23453	101	101	994142435	809751406	823521552	1040962762	23453	SRX20523355	SRS17832943	SRA1645065	IMP	IMP	2	0.89614	0.8938	0.02204	0.02191	0.77968	0.77938	0.46572	0.46433	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75642	75642	SRR24746225	SRX20523354	SRS17832942	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 2	GSM7430659	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP		RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430659	GSM7430659: eIF4E1b RIP biol rep 2; Danio rerio; RIP Seq	GSM7430659 r1	GSM7430659	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_2_1.fastq.gz e1b-RIP_2_2.fastq.gz	fastq fastq	3659386752.0	18115776.0	GSM7430659 r1	0:101 1:101	A:989766620;C:801915789;G:824369857;T:1043313396;N:21090	101	101	989766620	801915789	824369857	1043313396	21090	SRX20523354	SRS17832942	SRA1645065	IMP	IMP	2	0.89181	0.89107	0.0234	0.02432	0.77254	0.77341	0.4984	0.49917	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75643	75643	SRR24746226	SRX20523353	SRS17832941	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 1	GSM7430658	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP		RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430658	GSM7430658: eIF4E1b RIP biol rep 1; Danio rerio; RIP Seq	GSM7430658 r1	GSM7430658	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_1_1.fastq.gz e1b-RIP_1_2.fastq.gz	fastq fastq	3664341206.0	18140303.0	GSM7430658 r1	0:101 1:101	A:1002079901;C:797505762;G:819102400;T:1045629643;N:23500	101	101	1002079901	797505762	819102400	1045629643	23500	SRX20523353	SRS17832941	SRA1645065	IMP	IMP	2	0.89693	0.89111	0.03355	0.03395	0.77009	0.77157	0.48797	0.48637	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75646	75646	SRR24754508	SRX20530612	SRS17839502	SRP439912	PRJNA976946	MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976946	Other	MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			m6A Embryos 5hpf	m6A Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal									MeRIP Seq of Embryo 5hpf Gentanicin	2	2	Embryo 5hpf Gentanicin			RIP-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP439912		QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz	fastq fastq fastq fastq	16015155900.0	53383853.0	QingdaIP 1.fq.gz	0:150 1:150	A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972	150	150	3341079522	3427050846	6045646273	3201293287	85972	SRX20530612	SRS17839502	SRA1645459	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.75159	0.73659	0.1359	0.13542	0.8117	0.81172	0.51543	0.51251	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures
75647	75647	SRR24754509	SRX20530611	SRS17839502	SRP439912	PRJNA976946	MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976946	Other	MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			m6A Embryos 5hpf	m6A Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal									MeRIP Seq of WT Embryo 5hpf	1	1	WT Embryo 5hpf			RIP-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP439912		WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz	fastq fastq fastq fastq	15326922600.0	51089742.0	WT blankIP 1.fq.gz	0:150 1:150	A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844	150	150	3289509867	3239692571	5510216977	3287142341	360844	SRX20530611	SRS17839502	SRA1645459	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.71182	0.69789	0.02169	0.02058	0.80409	0.80395	0.47813	0.48125	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures

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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");;