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Sample GSM7730279 Query DataSets for GSM7730279
Status Public on Oct 03, 2023
Title Gonad WT 3
Sample type SRA
Source name Ovary
Organism Danio rerio
Characteristics tissue: Ovary
Sex: female
cell type: Gonad
genotype: tg(ziwi:GFP), eif4e1b +/+
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (Qiagen)
SMARTerStrandedRNA library (Ribo-Zero)
Library strategy ssRNA-seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing RNA-seq reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences (Dr mitochondrial chromosome, SILVA Dr ribosomal RNA, phiX174 genome) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2).
Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files with per gene read counts
Submission date Aug 23, 2023
Last update date Oct 03, 2023
Contact name Marcus Strobl
Organization name IMP
Street address Campus Vienna Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
Platform ID GPL24995
Series (1)
GSE241537 RNA-seq of female gonads isolated from juvenile eif4e1b mutant and wild-type zebrafish
BioSample SAMN37124332
SRA SRX21467659

Supplementary file Size Download File type/resource
GSM7730279_Ovary_WT3_counts.tsv.gz 131.3 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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