metadata: run_metadata: 33 rows where devstage_curation = "Undetermined" and experiment.library

33 rows where devstage_curation = "Undetermined" 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.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33123	33123	SRR29672615	SRX25176099	SRS21866000	SRP517393	PRJNA1130538	ac4C transcriptomes of Zebrafish and Worm	GSE271258	Other	ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.			Zebrafish ac4C	GSM8372406	tissue:Animal organ cells\|cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215\|geo loc name:missing\|collection date:missing	Zebrafish ac4C	The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene.	Animal organ cells	Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched		cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215	GSM8372406	GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq	GSM8372406 r1	GSM8372406	1	Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP517393		Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz	fastq fastq	816231517.0	3830403.0	GSM8372406 r1	0:102.34 1:110.76	A:199381841;C:207571478;G:205740791;T:203535549;N:1858	102	110	199381841	207571478	205740791	203535549	1858	SRX25176099	SRS21866000	SRA1914369	Fujian Medical University	Fujian Medical University	2	0.60415	0.60545	0.08824	0.08794	0.78796	0.78733	0.43432	0.43842	126	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-07-01	Undetermined	Undetermined	Undetermined	Undetermined
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
60021	60021	SRR12103084	SRX8627422	SRS6915731	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				SCI IP	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:SCI IP\|BioSampleModel:Model organism or animal								IP library sequencing data of treated sample	SCIIP BKDL192540807 1a	SCIIP BKDL192540807 1a	IP library sequencing data of treated sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz	fastq fastq	7110503700.0	23701679.0	SCIIP BKDL192540807 1a 1.fq.gz	0:150 1:150	A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903	150	150	1520693228	1953670419	2215620460	1420407690	111903	SRX8627422	SRS6915731	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.9115	0.9147	0.19936	0.2033	0.81864	0.81919	0.66838	0.6677	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60022	60022	SRR12103085	SRX8627421	SRS6915730	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				SCI Input	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:SCI Input\|BioSampleModel:Model organism or animal								Input library sequencing data of treated sample	SCIIN BKDL192540809 1a	SCIIN BKDL192540809 1a	Input library sequencing data of treated sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz	fastq fastq	7774587300.0	25915291.0	SCIIN BKDL192540809 1a 1.fq.gz	0:150 1:150	A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571	150	150	1595151855	2243828590	2397611978	1537918306	76571	SRX8627421	SRS6915730	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.96018	0.96291	0.23754	0.23744	0.84904	0.85245	0.74661	0.74738	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60023	60023	SRR12103086	SRX8627420	SRS6915729	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				Control IP	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:Control IP\|BioSampleModel:Model organism or animal								IP library sequencing data of control sample	controlIP BKDL192540808 1a	controlIP BKDL192540808 1a	IP library sequencing data of control sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz	fastq fastq	7359972600.0	24533242.0	controlIP BKDL192540808 1a 1.fq.gz	0:150 1:150	A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639	150	150	1569051886	2002692591	2333418000	1454676484	133639	SRX8627420	SRS6915729	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.92004	0.92293	0.20272	0.20739	0.83254	0.83291	0.68471	0.65224	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60024	60024	SRR12103087	SRX8627419	SRS6915728	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				Control Input	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:Control Input\|BioSampleModel:Model organism or animal								Input library sequencing data of control sample	controlIN BKDL192540810 1a	controlIN BKDL192540810 1a	Input library sequencing data of control sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz	fastq fastq	7830123600.0	26100412.0	controlIN BKDL192540810 1a 1.fq.gz	0:150 1:150	A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635	150	150	1589371287	2296547915	2409439612	1534684151	80635	SRX8627419	SRS6915728	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.97501	0.97626	0.23177	0.23578	0.89497	0.8971	0.78501	0.77674	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
74097	74097	SRR23433707	SRX19347585	SRS16745103	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt input rep2	GSM7039976	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1\|geo loc name:missing\|collection date:missing	mt input rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1	GSM7039976	GSM7039976: mt input rep2; Danio rerio; RIP Seq	GSM7039976 r1	GSM7039976	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz	fastq fastq	11987520719.0	46102921.0	GSM7039976 r1	0:129.98 1:130.04	A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407	129	130	2818961833	3185310727	3125514774	2857679978	53407	SRX19347585	SRS16745103	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.92498	0.92723	0.26901	0.26318	0.72691	0.72646	0.55297	0.56674	103	103	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74098	74098	SRR23433708	SRX19347584	SRS16745102	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt IP rep2	GSM7039975	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	mt IP rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A	GSM7039975	GSM7039975: mt IP rep2; Danio rerio; RIP Seq	GSM7039975 r1	GSM7039975	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz	fastq fastq	10153956215.0	38248544.0	GSM7039975 r1	0:132.74 1:132.73	A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740	132	132	2745473943	2337991849	2337827470	2732618213	44740	SRX19347584	SRS16745102	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.91716	0.92124	0.17169	0.17213	0.69057	0.69092	0.45478	0.4582	133	133	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74099	74099	SRR23433709	SRX19347583	SRS16745101	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt input rep1	GSM7039974	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1\|geo loc name:missing\|collection date:missing	mt input rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1	GSM7039974	GSM7039974: mt input rep1; Danio rerio; RIP Seq	GSM7039974 r1	GSM7039974	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz	fastq fastq	11979139891.0	42665152.0	GSM7039974 r1	0:140.37 1:140.40	A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416	140	140	3143624979	2854874515	2775482425	3204809556	348416	SRX19347583	SRS16745101	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.89189	0.90001	0.35263	0.34917	0.71058	0.70907	0.54777	0.55293	125	125	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74100	74100	SRR23433710	SRX19347582	SRS16745100	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt IP rep1	GSM7039973	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	mt IP rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A	GSM7039973	GSM7039973: mt IP rep1; Danio rerio; RIP Seq	GSM7039973 r1	GSM7039973	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz	fastq fastq	12145897814.0	43352862.0	GSM7039973 r1	0:140.09 1:140.07	A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089	140	140	3459248498	2615706052	2628261332	3442334843	347089	SRX19347582	SRS16745100	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.86681	0.87664	0.304	0.305	0.68012	0.67831	0.44055	0.4418	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74101	74101	SRR23433711	SRX19347581	SRS16745099	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling input rep2	GSM7039972	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1\|geo loc name:missing\|collection date:missing	sibling input rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1	GSM7039972	GSM7039972: sibling input rep2; Danio rerio; RIP Seq	GSM7039972 r1	GSM7039972	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz	fastq fastq	12272791017.0	47579480.0	GSM7039972 r1	0:128.94 1:129.00	A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414	128	129	2905993856	3237323144	3186607999	2942811604	54414	SRX19347581	SRS16745099	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.92733	0.92947	0.27234	0.26711	0.72391	0.72409	0.52625	0.55052	126	126	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74102	74102	SRR23433712	SRX19347580	SRS16745098	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling IP rep2	GSM7039971	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	sibling IP rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A	GSM7039971	GSM7039971: sibling IP rep2; Danio rerio; RIP Seq	GSM7039971 r1	GSM7039971	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz	fastq fastq	10402768351.0	39113148.0	GSM7039971 r1	0:132.99 1:132.98	A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607	132	132	2806053427	2400476074	2403977422	2792214821	46607	SRX19347580	SRS16745098	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.90198	0.9063	0.18008	0.18091	0.69428	0.69396	0.44811	0.42925	147	147	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74103	74103	SRR23433713	SRX19347579	SRS16745097	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling input rep1	GSM7039970	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1\|geo loc name:missing\|collection date:missing	sibling input rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1	GSM7039970	GSM7039970: sibling input rep1; Danio rerio; RIP Seq	GSM7039970 r1	GSM7039970	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz	fastq fastq	13094981449.0	46647417.0	GSM7039970 r1	0:140.35 1:140.37	A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966	140	140	3434495131	3120669719	3036482303	3502963330	370966	SRX19347579	SRS16745097	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.89276	0.90193	0.352	0.3489	0.70905	0.70719	0.52165	0.52427	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74104	74104	SRR23433714	SRX19347578	SRS16745096	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling IP rep1	GSM7039969	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	sibling IP rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A	GSM7039969	GSM7039969: sibling IP rep1; Danio rerio; RIP Seq	GSM7039969 r1	GSM7039969	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz	fastq fastq	12317957591.0	43954374.0	GSM7039969 r1	0:140.17 1:140.08	A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720	140	140	3509912915	2650796924	2663699373	3493137659	410720	SRX19347578	SRS16745096	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.87054	0.88058	0.30375	0.30421	0.67783	0.67584	0.44329	0.44327	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure

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