|
Status |
Public on Jun 19, 2023 |
Title |
WT + ConA + AntiA_rep1 |
Sample type |
SRA |
|
|
Source name |
MEFs
|
Organism |
Mus musculus |
Characteristics |
cell type: MEFs genotype: WT treatment: ConA and AntiA
|
Treatment protocol |
mouse embryonic fibroblasts (MEFs) pretreated with DMSO control or v-ATPase inhibitor Concanamycin A (ConA) (200 nM) for 1 h, and then co-treated with or without Dox (30 μg/ml), AntiA (2 μM) or FCCP (2 μM) for 24 h
|
Growth protocol |
Mouse embryonic fibroblasts (MEFs) were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS.
|
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
|
|
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 Assembly: Mus_musculus.GRCm38.95 Supplementary files format and content: xlsx file with counts per gene per sample
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|
|
Submission date |
Oct 17, 2022 |
Last update date |
Jun 19, 2023 |
Contact name |
Terytty Yang Li |
E-mail(s) |
teryttyliyang@fudan.edu.cn
|
Organization name |
EPFL
|
Street address |
EPFL SV IBI-SV LISP AI 1145
|
City |
Lausanne |
ZIP/Postal code |
1015 |
Country |
Switzerland |
|
|
Platform ID |
GPL23479 |
Series (1) |
GSE179510 |
Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation |
|
Relations |
BioSample |
SAMN31323851 |
SRA |
SRX17920753 |