 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 05, 2023 |
| Title |
Abca1cKO_biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Adrenal gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Adrenal gland
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from whole adrenals cleaned of the adherent fat and homogenized in TRI Reagent (Sigma) using the Direct-zol miniprep RNA kit (Zymo Research)
Illumina Stranded mRNA Prep Preparation including polyA enrichment was used according to manufacturer’s recommendations to construct libraries from total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The produced paired-end reads which passed Illumina’s chastity filter were demultiplexed using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection).
Illumina adapter residuals were trimmed using cutadapt (v4.0 with Python 3.9.16).
Quality of the reads in fastq format was checked with the software FastQC (version 0.11.9). Raw reads shorter than 10 bp, having average Q-values below 24 or incorporating uncalled ‘N’ bases were filtered out using the BBTools software suite (version 38.86).
The splice aware RNA mapping software STAR (version 2.7.10a) was used to map the remaining reads.
To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.13.5) was used. Normalization of the raw counts and differential gene expression analysis was carried out with the R software package DESeq2 (version 1.38.3)
Assembly: mm10 reference genome provided by IGenomes (archive-2015-07-17-14-33-26).
Supplementary files format and content: The processed data file submitted containes normalized expression values for Abca1cKO+Cre controls, and Abcg1cKO values, their respective averages, log2fold, IfcSE, p value and p adjusted value for the comparison.
|
| |
|
| Submission date |
Aug 31, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Emanuele Pignatti |
| Organization name |
University of bern
|
| Street address |
Freiburgstrasse 15
|
| City |
Bern |
| ZIP/Postal code |
3010 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE242081 |
Adrenal Abcg1 controls cholesterol flux and steroidogenesis |
|
| Relations |
| BioSample |
SAMN37217125 |
| SRA |
SRX21562881 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
