run_metadata: 74635

This data as json

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74635	SRR23908128	SRX19719610	SRS17086727	SRP428084	PRJNA946304	Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf	GSE227668	Transcriptome Analysis	To investigate the underlying mechanisms of sirt6 in the regulation of HSCs and neutrophils lineage expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods				tail WT 3	GSM7104974		source name:tail\|tissue:tail\|genotype:WT\|developmental stage:larvae at 3 dpf\|geo loc name:missing\|collection date:missing	tail WT 3	The generated fastq files were subjected to FastQC to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt	tail		Larvae were collected at 3 dpf then grouped into sirt6 mutant and WT groups through genotyping total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.		tissue:tail\|genotype:WT\|developmental stage:larvae at 3 dpf	GSM7104974	GSM7104974: tail WT 3; Danio rerio; RNA Seq	GSM7104974 r1	GSM7104974	1	Larvae were collected at 3 dpf then grouped into sirt6 mutant and WT groups through genotyping total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP428084		loader:fastq load.py	WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	6599139300.0	21997131.0	GSM7104974 r1	0:150 1:150	A:1862099481;C:1460254817;G:1446030038;T:1828044493;N:2710471	150	150			1862099481	1460254817	1446030038	1828044493	2710471	SRX19719610	SRS17086727	SRA1606833	South China University of Technology	South China University of Technology	2	0.93499	0.93641	0.11822	0.11847	0.66561	0.66636	0.47204	0.47094	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		China	2023-03-19	Larval	Larval	Tail	Multi-system