|
| Status |
Public on Dec 07, 2020 |
| Title |
WT + Dox_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT + Dox_rep1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MEFs
genotype: WT
treatment: Dox
|
| Treatment protocol |
For doxycycline (Dox) treatment, MEFs were treated with 30 μg/ml doxycycline (Cat. D9891, Sigma) for 24 hours and without any other antibiotics.
|
| Growth protocol |
Mouse embryonic fibroblasts (MEFs) were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS. CBP/p300 depletion was achieved by treat the Immortalized Crebbpfl/fl; Ep300fl/fl MEFs stably expressing Cre-ERT2 with 4-OHT as described previously (Weinert, B. T. et al. Cell 174, 231-244, 2018).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
G1
|
| Data processing |
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: xlsx file with counts per gene per sample
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Terytty Yang Li |
| E-mail(s) |
[email protected]
|
| Organization name |
EPFL
|
| Street address |
EPFL SV IBI-SV LISP AI 1145
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE131613 |
The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [Mus musculus] |
| GSE131616 |
The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress |
|
| Relations |
| BioSample |
SAMN11821621 |
| SRA |
SRX5882480 |
