|
| Status |
Public on Mar 04, 2024 |
| Title |
Clone54 |
| 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 |
SAMN32232754 |
| SRA |
SRX18700737 |
