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| Status |
Public on Oct 03, 2023 |
| Title |
Gonad WT 3 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Danio rerio |
| Characteristics |
tissue: Ovary
Sex: female
cell type: Gonad
genotype: tg(ziwi:GFP), eif4e1b +/+
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen)
SMARTerStrandedRNA library (Ribo-Zero)
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| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Aug 23, 2023 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Marcus Strobl |
| Organization name |
IMP
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| Street address |
Campus Vienna Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL24995 |
| Series (1) |
| GSE241537 |
RNA-seq of female gonads isolated from juvenile eif4e1b mutant and wild-type zebrafish |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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