run_metadata: 41861

This data as json

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41861	SRR6384888	SRX3478478	SRS2764467	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Zfpm1 21dpf heart rep1	GSM2892213		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	Zfpm1 21dpf heart rep1	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	GSM2892213	GSM2892213: Zfpm1 21dpf heart rep1; Danio rerio; RNA Seq	GSM2892213		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP100425			Zfpm1_heart_RNAseq_rep1_1.fq.gz Zfpm1_heart_RNAseq_rep1_2.fq.gz	fastq fastq	5936614800.0	19788716.0	GSM2892213 r1	0:150 1:150	A:1616123286;C:1354032331;G:1348383945;T:1617882201;N:193037	150	150			1616123286	1354032331	1348383945	1617882201	193037	SRX3478478	SRS2764467	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.93121	0.93134	0.08641	0.08612	0.69501	0.69751	0.51182	0.50932	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		China	2017-12-18	Larval	Larval	Heart	Cardiovascular System