|
| Status |
Public on Mar 28, 2022 |
| Title |
Sample_acute_L14A_CORT |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B6/J
tissue: liver
treatment: Corticosterone
duration: acute
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rnease kit (Qiagen)
Total RNA was isolated from the snap-frozen liver samples.
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
L14A
|
| Data processing |
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using STAR aligner (version 2.7.3a) settings: --runThreadN' '4' '--outSAMunmapped' 'Within KeepPairs' '--twopassMode' 'Basic’
Gene-read quantification was perfromed using HTSeq-count (version 0.12.4) settings: --format' 'bam' '--order' 'pos' '--stranded' 'reverse'
HTSeq-count output files were merged into the raw_gene_count_matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature according to Ensembl97 for each sample.
|
| |
|
| Submission date |
Jul 20, 2021 |
| Last update date |
Mar 28, 2022 |
| Contact name |
Jacobus Cornelis Buurstede |
| E-mail(s) |
j.c.buurstede@lumc.nl
|
| Organization name |
Leiden University Medical Center
|
| Department |
Endocrinology
|
| Lab |
Meijer lab
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE180445 |
Hepatic transcriptome analysis after acute and chronic glucocorticoid exposure combined with androgen receptor antagonism. |
|
| Relations |
| BioSample |
SAMN20325825 |
| SRA |
SRX11504240 |
