run_metadata: 49535

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
49535	SRR7942606	SRX4776871	SRS3857410	SRP162874	PRJNA493827	Transcriptomics analysis of gene expression in wide type ybx1 MO pabpc1a MO zebrafish embryo sample.	GSE120643	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of [1] gene expressive levels in wide type and ybx1 MO zebrafish embryo [2] gene expressive levels in pabpc1a MO zebrafish embryo [3] mRNA lifetime in wide type zebrafish embryo. Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol Reagent Ambion. mRNA was extracted with using Dynabeads mRNA Purification Kit Ambion and subjected to TURBO DNase Invitrogen treatment at 37C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. Synchronously developing embryos were treated with 0.2 ng of Pol II inhibition alpha amanitin Sigma at one cell stage and were collected at indicated time points. 100 embryos were collected for each time point in duplicates. The total RNA was extracted by Trizol Invitrogen and used for RNA Seq. An equal amount of external RNA control consortium ERCC RNA spike in control Thermo Fisher was added to the total RNA samples as internal controls. The RNA was subjected to ribosomal RNA depletion with Ribo Zero rRNA Removal Kit Illumina followed by library construction using NEB Next® Ultra? RNA library Prep Kit NEB. RNA stability profiling was generated from two biological replicates.	parent bioproject:PRJNA534030			WT 0hpf rep2	GSM3406870		source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	WT 0hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1 The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0 Genome build: zv9 Supplementary files format and content: Reads count for each gene in wild type ybx1 MO and pabpc1a MO sample	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.		strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	GSM3406870	GSM3406870: WT 0hpf rep2; Danio rerio; RNA Seq	GSM3406870		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.	GEO Accession:GSM3406870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162874		loader:latf load	WT_0hpf_rep2_R1.fastq.gz WT_0hpf_rep2_R2.fastq.gz	fastq fastq	9235008100.0	34013490.0	GSM3406870 r1	0:135.76 1:135.76	A:2585376157;C:2035534424;G:2087400121;T:2523389569;N:3307829	135	135			2585376157	2035534424	2087400121	2523389569	3307829	SRX4776871	SRS3857410	SRA786936	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.95881	0.96263	0.02093	0.01978	0.79121	0.79446	0.71203	0.33092	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	bulk	unknown	unknown		China	2018-09-28	Zygote	Embryo	Whole Organism	All anatomical structures