metadata: run_metadata: 49 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and experiment.library

49 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and experiment.library_strategy = "RIP-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.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.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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
40576	40576	SRR3228716	SRX1634616	SRS1345843	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 8	GSM2088181	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088181	GSM2088181: m6A CLIP 8; Danio rerio; RIP Seq	GSM2088181	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088181	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_8h-IP.fastq.gz	fastq	921977050.0	18439541.0	GSM2088181 r1	0:50	A:233396466;C:263744643;G:252737160;T:172064890;N:33891	50	233396466	263744643	252737160	172064890	33891	SRX1634616	SRS1345843	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.61408	0.1783	0.88032	0.72361	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40577	40577	SRR3228715	SRX1634615	SRS1345844	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 6	GSM2088180	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088180	GSM2088180: m6A CLIP 6; Danio rerio; RIP Seq	GSM2088180	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088180	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_6h-IP.fastq.gz	fastq	811777600.0	16235552.0	GSM2088180 r1	0:50	A:214241727;C:241830821;G:208608337;T:147066789;N:29926	50	214241727	241830821	208608337	147066789	29926	SRX1634615	SRS1345844	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.68946	0.17622	0.9194	0.62968	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40578	40578	SRR3228714	SRX1634614	SRS1345845	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 4	GSM2088179	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088179	GSM2088179: m6A CLIP 4; Danio rerio; RIP Seq	GSM2088179	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088179	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_4h-IP.fastq.gz	fastq	746223800.0	14924476.0	GSM2088179 r1	0:50	A:185147085;C:236139555;G:187875436;T:137034934;N:26790	50	185147085	236139555	187875436	137034934	26790	SRX1634614	SRS1345845	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.80174	0.17015	0.86164	0.77262	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40579	40579	SRR3228713	SRX1634613	SRS1345846	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 2	GSM2088178	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088178	GSM2088178: m6A CLIP 2; Danio rerio; RIP Seq	GSM2088178	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088178	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_2h-IP.fastq.gz	fastq	937426800.0	18748536.0	GSM2088178 r1	0:50	A:263526034;C:262864870;G:241415141;T:169586820;N:33935	50	263526034	262864870	241415141	169586820	33935	SRX1634613	SRS1345846	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.75612	0.2242	0.87823	0.61308	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40580	40580	SRR3228712	SRX1634612	SRS1345847	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 0	GSM2088177	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088177	GSM2088177: m6A CLIP 0; Danio rerio; RIP Seq	GSM2088177	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088177	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_0h-IP.fastq.gz	fastq	1320186200.0	26403724.0	GSM2088177 r1	0:50	A:362282258;C:387362464;G:326692598;T:243799324;N:49556	50	362282258	387362464	326692598	243799324	49556	SRX1634612	SRS1345847	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.50689	0.10395	0.89755	0.72663	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40581	40581	SRR3228711	SRX1634611	SRS1345848	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 8	GSM2088176	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088176	GSM2088176: input CLIP 8; Danio rerio; RIP Seq	GSM2088176	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088176	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_8h-input.fastq.gz	fastq	1971263900.0	39425278.0	GSM2088176 r1	0:50	A:530986171;C:559974651;G:547087685;T:333110850;N:104543	50	530986171	559974651	547087685	333110850	104543	SRX1634611	SRS1345848	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.64576	0.23563	0.91618	0.71461	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40582	40582	SRR3228710	SRX1634610	SRS1345849	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 6	GSM2088175	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088175	GSM2088175: input CLIP 6; Danio rerio; RIP Seq	GSM2088175	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088175	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_6h-input.fastq.gz	fastq	2424925650.0	48498513.0	GSM2088175 r1	0:50	A:622469966;C:699224547;G:701719139;T:401382845;N:129153	50	622469966	699224547	701719139	401382845	129153	SRX1634610	SRS1345849	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.68121	0.23857	0.93123	0.73919	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40583	40583	SRR3228709	SRX1634609	SRS1345850	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 4	GSM2088174	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088174	GSM2088174: input CLIP 4; Danio rerio; RIP Seq	GSM2088174	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088174	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_4h-input.fastq.gz	fastq	1996829250.0	39936585.0	GSM2088174 r1	0:50	A:527211013;C:600800804;G:528828160;T:339883128;N:106145	50	527211013	600800804	528828160	339883128	106145	SRX1634609	SRS1345850	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.60745	0.19305	0.92537	0.74508	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40584	40584	SRR3228708	SRX1634608	SRS1345851	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 2	GSM2088173	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088173	GSM2088173: input CLIP 2; Danio rerio; RIP Seq	GSM2088173	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088173	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_2h-input.fastq.gz	fastq	2119606350.0	42392127.0	GSM2088173 r1	0:50	A:555894042;C:598667411;G:609233481;T:355698501;N:112915	50	555894042	598667411	609233481	355698501	112915	SRX1634608	SRS1345851	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.65392	0.2263	0.9049	0.72736	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40585	40585	SRR3228707	SRX1634607	SRS1345852	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 0	GSM2088172	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088172	GSM2088172: input CLIP 0; Danio rerio; RIP Seq	GSM2088172	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088172	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_0h-input.fastq.gz	fastq	2150269400.0	43005388.0	GSM2088172 r1									SRX1634607	SRS1345852	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.57233	0.18947	0.91323	0.75741	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40586	40586	SRR3228706	SRX1634606	SRS1345853	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 8	GSM2088171	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088171	GSM2088171: m6A IP 8; Danio rerio; RIP Seq	GSM2088171	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088171	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_8h.IP.fastq.gz	fastq	527347000.0	10546940.0	GSM2088171 r1	0:50	A:90387238;C:157767772;G:129133581;T:150048442;N:9967	50	90387238	157767772	129133581	150048442	9967	SRX1634606	SRS1345853	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.90207	0.11796	0.80208	0.51587	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40587	40587	SRR3228705	SRX1634605	SRS1345854	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 6	GSM2088170	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088170	GSM2088170: m6A IP 6; Danio rerio; RIP Seq	GSM2088170	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088170	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_6h.IP.fastq.gz	fastq	606551300.0	12131026.0	GSM2088170 r1	0:50	A:100429722;C:200919401;G:156361859;T:148828837;N:11481	50	100429722	200919401	156361859	148828837	11481	SRX1634605	SRS1345854	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.94517	0.23269	0.84571	0.73203	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40588	40588	SRR3228704	SRX1634604	SRS1345855	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 4	GSM2088169	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088169	GSM2088169: m6A IP 4; Danio rerio; RIP Seq	GSM2088169	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088169	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_4h.IP.fastq.gz	fastq	616373350.0	12327467.0	GSM2088169 r1	0:50	A:103511937;C:199101152;G:159952372;T:153796186;N:11703	50	103511937	199101152	159952372	153796186	11703	SRX1634604	SRS1345855	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.9484	0.20806	0.81349	0.68893	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40589	40589	SRR3228703	SRX1634603	SRS1345856	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 2	GSM2088168	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088168	GSM2088168: m6A IP 2; Danio rerio; RIP Seq	GSM2088168	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088168	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_2h.IP.fastq.gz	fastq	560037350.0	11200747.0	GSM2088168 r1	0:50	A:90079119;C:192220024;G:154098019;T:123629702;N:10486	50	90079119	192220024	154098019	123629702	10486	SRX1634603	SRS1345856	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.95056	0.25053	0.87322	0.82008	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40590	40590	SRR3228702	SRX1634602	SRS1345857	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 0	GSM2088167	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088167	GSM2088167: m6A IP 0; Danio rerio; RIP Seq	GSM2088167	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088167	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_0h.IP.fastq.gz	fastq	458827450.0	9176549.0	GSM2088167 r1	0:50	A:74889651;C:150121353;G:121032505;T:112775237;N:8704	50	74889651	150121353	121032505	112775237	8704	SRX1634602	SRS1345857	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.96567	0.22221	0.84471	0.70341	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40591	40591	SRR3228701	SRX1634601	SRS1345858	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 8	GSM2088166	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088166	GSM2088166: input 8; Danio rerio; RIP Seq	GSM2088166	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088166	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_8h.input.fastq.gz	fastq	575536100.0	11510722.0	GSM2088166 r1	0:50	A:111158012;C:168916114;G:151564939;T:143886262;N:10773	50	111158012	168916114	151564939	143886262	10773	SRX1634601	SRS1345858	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.95515	0.19883	0.79245	0.6247	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40592	40592	SRR3228700	SRX1634600	SRS1345859	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 6	GSM2088165	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088165	GSM2088165: input 6; Danio rerio; RIP Seq	GSM2088165	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088165	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_6h.input.fastq.gz	fastq	613333150.0	12266663.0	GSM2088165 r1	0:50	A:113451661;C:194144306;G:164598114;T:141127589;N:11480	50	113451661	194144306	164598114	141127589	11480	SRX1634600	SRS1345859	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.97989	0.33526	0.84798	0.72512	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40593	40593	SRR3228699	SRX1634599	SRS1345860	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 4	GSM2088164	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088164	GSM2088164: input 4; Danio rerio; RIP Seq	GSM2088164	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088164	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_4h.input.fastq.gz	fastq	576058200.0	11521164.0	GSM2088164 r1	0:50	A:108062480;C:178888385;G:153976688;T:135119699;N:10948	50	108062480	178888385	153976688	135119699	10948	SRX1634599	SRS1345860	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.97495	0.29544	0.81162	0.71268	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40594	40594	SRR3228698	SRX1634598	SRS1345861	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 2	GSM2088163	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088163	GSM2088163: input 2; Danio rerio; RIP Seq	GSM2088163	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088163	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_2h.input.fastq.gz	fastq	703375200.0	14067504.0	GSM2088163 r1	0:50	A:125686246;C:228251341;G:193846290;T:155577830;N:13493	50	125686246	228251341	193846290	155577830	13493	SRX1634598	SRS1345861	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.98596	0.35619	0.88521	0.80927	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40595	40595	SRR3228697	SRX1634597	SRS1345862	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 0	GSM2088162	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088162	GSM2088162: input 0; Danio rerio; RIP Seq	GSM2088162	1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088162	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_0h.input.fastq.gz	fastq	650787500.0	13015750.0	GSM2088162 r1	0:50	A:117902403;C:207274717;G:177773347;T:147824646;N:12387	50	117902403	207274717	177773347	147824646	12387	SRX1634597	SRS1345862	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.98268	0.32108	0.85669	0.76239	50	B	usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40701	40701	SRR3231363	SRX1637111	SRS1342926	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 3	GSM2087141	tissue:Zebrafish Zygotes\|fraction:Input	Input 3	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087141	GSM2087141: Input 3; Danio rerio; RIP Seq	GSM2087141	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087141	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Input_3.fastq.gz	fastq	1902296226.0	37299926.0	GSM2087141 r1	0:51	A:466290166;C:465344039;G:486942278;T:483240280;N:479463	51	466290166	465344039	486942278	483240280	479463	SRX1637111	SRS1342926	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.85793	0.14814	0.79941	0.55214	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40702	40702	SRR3231362	SRX1637110	SRS1342927	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 2	GSM2087140	tissue:Zebrafish Zygotes\|fraction:Input	Input 2	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087140	GSM2087140: Input 2; Danio rerio; RIP Seq	GSM2087140	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087140	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Input_2.fastq.gz	fastq	1540737999.0	30210549.0	GSM2087140 r1	0:51	A:380481772;C:379741192;G:395453141;T:384675313;N:386581	51	380481772	379741192	395453141	384675313	386581	SRX1637110	SRS1342927	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.8787	0.14935	0.79202	0.54381	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40703	40703	SRR3231361	SRX1637109	SRS1342928	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Input 1	GSM2087139	tissue:Zebrafish Zygotes\|fraction:Input	Input 1	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Input	GSM2087139	GSM2087139: Input 1; Danio rerio; RIP Seq	GSM2087139	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087139	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Input_1.fastq.gz	fastq	1109818905.0	21761155.0	GSM2087139 r1									SRX1637109	SRS1342928	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.87467	0.18794	0.79411	0.63378	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40704	40704	SRR3231360	SRX1637108	SRS1342929	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 3	GSM2087138	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 3	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087138	GSM2087138: Tdrd6a IP 3; Danio rerio; RIP Seq	GSM2087138	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087138	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Tdrd6a_IP_3.fastq.gz	fastq	843641439.0	16541989.0	GSM2087138 r1	0:51	A:216465581;C:196892096;G:207722567;T:222361382;N:199813	51	216465581	196892096	207722567	222361382	199813	SRX1637108	SRS1342929	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.84615	0.08957	0.78768	0.50612	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40705	40705	SRR3231359	SRX1637107	SRS1342930	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 2	GSM2087137	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 2	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087137	GSM2087137: Tdrd6a IP 2; Danio rerio; RIP Seq	GSM2087137	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087137	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Tdrd6a_IP_2.fastq.gz	fastq	391198050.0	7670550.0	GSM2087137 r1	0:51	A:99015594;C:91525929;G:97155710;T:103371571;N:129246	51	99015594	91525929	97155710	103371571	129246	SRX1637107	SRS1342930	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.85778	0.12015	0.80515	0.47541	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
40706	40706	SRR3231358	SRX1637106	SRS1342931	SRP071849	PRJNA315400	Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]	GSE79161	Transcriptome Analysis	Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.	parent bioproject:PRJNA315403	pubmed:30086300	Tdrd6a IP 1	GSM2087136	tissue:Zebrafish Zygotes\|fraction:Tdrd6a IP	Tdrd6a IP 1	Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.	Zebrafish Zygotes		mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	Zebrafish were maintained under standard conditions.	fraction:Tdrd6a IP	GSM2087136	GSM2087136: Tdrd6a IP 1; Danio rerio; RIP Seq	GSM2087136	1	mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.	GEO Accession:GSM2087136	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP071849		WT_Tdrd6a_IP_1.fastq.gz	fastq	1927415052.0	37792452.0	GSM2087136 r1	0:51	A:498125298;C:444860381;G:468826607;T:515142356;N:460410	51	498125298	444860381	468826607	515142356	460410	SRX1637106	SRS1342931	SRA385813	GEO	Rene Ketting, RNA silencing, IMB	1	0.86194	0.09753	0.80146	0.47808	51	B	usable mapping rate	illumina	hiseq_era	unknown	other	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2016-03-13	Zygote	Embryo	Oocyte	Reproductive System
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
53427	53427	SRR9854014	SRX6608456	SRS5172704	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep3	GSM3983830	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep3	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983830	GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq	GSM3983830	1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983830	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB3.fastq.gz	fastq	1174462616.0	32753220.0	GSM3983830 r1	0:35.86	A:277856243;C:303697175;G:340240303;T:252574884;N:94011	35	277856243	303697175	340240303	252574884	94011	SRX6608456	SRS5172704	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.90426	0.1746	0.77341	0.57553	35	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53428	53428	SRR9854013	SRX6608455	SRS5172702	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep2	GSM3983829	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep2	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983829	GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq	GSM3983829	1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983829	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB2.fastq.gz	fastq	65641776.0	2466295.0	GSM3983829 r1	0:26.62	A:18933213;C:16060113;G:13492679;T:17151951;N:3820	26	18933213	16060113	13492679	17151951	3820	SRX6608455	SRS5172702	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.17621	0.02351	0.88069	0.60622	15	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53429	53429	SRR9854012	SRX6608454	SRS5172701	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep1	GSM3983828	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep1	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983828	GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq	GSM3983828	1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983828	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB1.fastq.gz	fastq	403183413.0	11908151.0	GSM3983828 r1	0:33.86	A:80085450;C:111343041;G:140916198;T:70619085;N:219639	33	80085450	111343041	140916198	70619085	219639	SRX6608454	SRS5172701	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.862	0.1026	0.95359	0.79372	33	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	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

Advanced export

JSON shape: default, array, newline-delimited

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");;