run_metadata: 74890
This data as json
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| 74890 | SRR24100387 | SRX19900534 | SRS17254308 | 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 4 | GSM7156162 | 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 4 | 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 | GSM7156162 | GSM7156162: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 4; Danio rerio; RNA Seq | GSM7156162 r1 | GSM7156162 | 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_9_1.fq.gz V300083329_L01_9_2.fq.gz | fastq fastq | 7158980600.0 | 35794903.0 | GSM7156162 r1 | 0:100 1:100 | A:1968354520;C:1609788228;G:1624681203;T:1956008153;N:148496 | 100 | 100 | 1968354520 | 1609788228 | 1624681203 | 1956008153 | 148496 | SRX19900534 | SRS17254308 | 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 | 0.91862 | 0.93327 | 0.10568 | 0.10926 | 0.72011 | 0.7178 | 0.49831 | 0.49497 | 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 |