|
| Status |
Public on Jul 18, 2017 |
| Title |
MDA-MB-231_shSETD1A_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231 shSETD1A
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Breast cancer cell line MDA-MB-231
genotype/variation: SETD1A depletion
|
| Treatment protocol |
Lentiviral shRNA constructs were obtained from the RNAi Consortium shRNA Library at the Broad Institute. Conditioned medium containing infective lentiviral particles was generated by cotransfecting 3µg of each lentiviral vector, 3µg of pCMV d8.91 and 1µg pHCMV-G into 1×10*6 293T human embryonic kidney cells using FuGENE 6 transfection reagent (Roche Applied Science). Supernatants were collected 48 hr after transfection and filtered through a 0.45 µM membrane (Millipore). Cells were infected with each supernatants using 8µg/mL polybrene and selected with 2µg/mL puromycin. RNA was isolated 72 hr after lentiviral shRNA infection.
|
| Growth protocol |
Human breast (MDA-MB-231) and lung (A549) cancer cell lines (American Type Culture Collection, Manassas, VA, USA) were grown in Dulbeccco’s modified medium, which supplemented with 10% fetal bovine serum and penicillin/streptomycin (Pen/Strep). Both cell lines were maintained in 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was isolated 72 hr after lentiviral shRNA infection.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Arrays were scanned on Nimblegen MS200 at 2um resolution
|
| Description |
This sample is of shSETD1A in MDA-MB-231 cells replicates 2.
|
| Data processing |
Array data was background corrected and normalized as suggested using the Roche NimbleScan 2.6 software
|
| |
|
| Submission date |
Jul 29, 2015 |
| Last update date |
Jul 19, 2017 |
| Contact name |
Robert Morris |
| E-mail(s) |
morris.robert@mgh.harvard.edu
|
| Phone |
617-724-6552
|
| Organization name |
Mass. General Hospital Cancer Center
|
| Street address |
149 13th Street
|
| City |
Charlestown |
| State/province |
Massachusetts |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL18734 |
| Series (1) |
| GSE71498 |
Arrayed gene expression analysis of the SETD1A depleted cancer cells |
|
