run_metadata: 58411

This data as json

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58411	SRR11309038	SRX7913587	SRS6320429	SRP252869	PRJNA612697	RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish	GSE146995	Transcriptome Analysis	The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.		pubmed:33651979		cd41gfp mut2	GSM4411866		tissue:hematopoietic stem and progenitor cells\|develpmental stage:40 hpf mutant	cd41gfp mut2	basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample	hematopoietic stem and progenitor cells		cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.		develpmental stage:40 hpf mutant	GSM4411866	GSM4411866: cd41gfp mut2; Danio rerio; RNA Seq	GSM4411866		1	cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.	GEO Accession:GSM4411866	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP252869			cd41gfp_mut2_1.fq.gz cd41gfp_mut2_2.fq.gz	fastq fastq	10547871900.0	35159573.0	GSM4411866 r1	0:150 1:150	A:2823130170;C:2469329724;G:2474038085;T:2781202013;N:171908	150	150			2823130170	2469329724	2474038085	2781202013	171908	SRX7913587	SRS6320429	SRA1055135	GEO	Albert Einstein College of Medicine	2	0.77081	0.76762	0.19951	0.20063	0.78518	0.7905	0.62792	0.62645	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2020-03-15	Pharyngula	Embryo	Blood	Hematopoietic System