run_metadata: 74889

This data as json

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74889	SRR24100386	SRX19900535	SRS17254309	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019		Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5	GSM7156163		source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156163	GSM7156163: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5; Danio rerio; RNA Seq	GSM7156163 r1	GSM7156163	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400		SRP431420			V300083329_L01_10_1.fq.gz V300083329_L01_10_2.fq.gz	fastq fastq	5909038000.0	29545190.0	GSM7156163 r1	0:100 1:100	A:1623230733;C:1331545315;G:1343152861;T:1610987311;N:121780	100	100			1623230733	1331545315	1343152861	1610987311	121780	SRX19900535	SRS17254309	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91221	0.92929	0.10504	0.10961	0.72078	0.71875	0.49598	0.49947	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures