|
| Status |
Public on Jun 21, 2022 |
| Title |
BT549/control for shIRF1, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
BT549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT549
disease state: Breast Cancer
resistance: puromycin resistance
phenotype: TNBCÂ
shRNA: control shRNA (stable)
|
| Treatment protocol |
Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline for inducible model.
|
| Growth protocol |
MDAMB436 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS. BT549cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 10ug/ml Insulin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BT549 shIRF1_Gene_TPM.csv
BT549_shIRF1vControl.deseq.csv
|
| Data processing |
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: GRCh38.74
Supplementary files format and content: Gene_TPM, log2FoldChange
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Nami Yamashita |
| E-mail(s) |
namanaminy0117@gmail.com
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Kufe Lab
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE206212 |
Muc1-C Induces Pbrm1-Mediated Chromatin Remodeling in Driving Chronic Inflammation and DNA Damage Resistance in Triple-Negative Breast Cancer |
|
| Relations |
| BioSample |
SAMN29100476 |
| SRA |
SRX15714110 |
