|
| Status |
Public on Apr 15, 2024 |
| Title |
male_3d_2 (GRZ_GONAD_8b) |
| Sample type |
SRA |
| |
|
| Source name |
trunk
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: trunk
Sex: male
age: 3 dph
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen) according to Baumgart et al., 2012 (PMID: 22487494)
Libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HiSeq 2500 was run in Rapid mode
GRZ_GONAD_8b
|
| Data processing |
Reads were extracted as FastQ sequences using bcl2fastq v1.8.4 (provided by Illumina).
The reads were filtered with sga (parameters: preprocess -q 30 -m 50 --dust; https://github.com/jts/sga).
Quality-passed reads were mapped to the N. furzeri reference genome (assembly version Nfu_20150522, gene annotation version 150922) using STAR (parameters: --alignIntronMax 100000) (PMID: 23104886)
Counts per sample and gene were obtained with the summarizeOverlaps function of the R package GenomicAlignments (PMID: 23950696)
Assembly: Genome Nfu_20150522 and annotation 20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (https://nfingb.leibniz-fli.de) (PMID: 26638077)
Supplementary files format and content: csv file containing raw read counts per gene over all samples
|
| |
|
| Submission date |
Apr 10, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Philipp Koch |
| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute
|
| Department |
Core Facility Life Science Computing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19871 |
| Series (1) |
| GSE263626 |
RNA sequencing of gonad tissue of Nothobranchius furzeri at different age in males and females |
|
| Relations |
| SRA |
ERX958447 |
| BioSample |
SAMEA3388817 |
