NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6650176 Query DataSets for GSM6650176
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
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap