run_metadata: 40592

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	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.r3_length	run.r4_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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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 were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.	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