NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6833408 Query DataSets for GSM6833408
Status Public on Mar 04, 2024
Title Clone43
Sample type SRA
 
Source name mESC clones
Organism Mus musculus
Characteristics cell line: mESC clones
cell type: mouse embryonic stem cells
genotype: Brca2ko/ko-r
treatment: Mirin Pretreatment
time: Passage 1
Treatment protocol Mirin Pretreatment was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
Growth protocol mESC clones mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol Cells were resuspended with QIAzol (QIAGEN, Hilden, Germany) and RNA was extracted (Zymo Direct-zol RNA miniprep kit).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA library protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Trimmomatic v0.36 software
Genome mapping and transcript annotation were using STAR v2.5.1 with mouse reference genome mm10
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RSEM raw count values for each Sample
 
Submission date Dec 14, 2022
Last update date Mar 04, 2024
Contact name Yongmei Zhao
E-mail(s) zhaoyong@mail.nih.gov
Organization name Frederick National Labroatory for Cancer Research
Department Biomedical Informatics and Data Science (BIDS) Directorate
Street address Post Office Box B
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL21103
Series (1)
GSE220973 Mismatch repair protein MLH1 suppresses replicative stress in BRCA2 deficient breast tumors
Relations
BioSample SAMN32232757
SRA SRX18700734

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