|
| Status |
Public on Sep 30, 2013 |
| Title |
MCF7_PALB2_unstimulated rep3 |
| Sample type |
RNA |
| |
|
| Source name |
MCF7_PALB2_unstimulated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast adenocarcinoma cells
infected with: PALB2 shRNAs
cell subtype: PALB2 depleted cells
stimulated with: none (unstimulated)
|
| Treatment protocol |
cells were treated with 10 ng/ml of TNF-alpha for 1h
|
| Growth protocol |
MCF7 cells were infected with sh vectors and selected in puromycin for 3 days, medium was DMEM + 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were harvested and lysed in RLT buffer (Qiagen), total RNA was extracted with Rneasy mini kit
|
| Label |
biotin
|
| Label protocol |
samples were biotin-labeled using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)
|
| |
|
| Hybridization protocol |
Biotin labeled aRNA at 750ng was hybridized to Illumina HumanHT-12V4 expression Beadchip with Illumina HumanHT-12 v4 Expression BeadChip Kit (cat# BD-103-0204 ) Subsequent steps include washing, blocking, and streptavadin-Cy3 staining of the beadchip.
|
| Scan protocol |
Fluorescence emission by Cy3 is quantitatively detected with Illumina BeadArray Reader (scan software : Illumina BeadSacn) and GenomeStudio software provides results in standard file format
|
| Description |
PALB2 0h_rep3
|
| Data processing |
Intensity raw data were log2 transformed and normalized by quantile normalization using BeadArray package (version 2.8.1) on R.
|
| |
|
| Submission date |
Apr 02, 2013 |
| Last update date |
Sep 30, 2013 |
| Contact name |
Alessandro Gardini |
| E-mail(s) |
agardini@wistar.org
|
| Phone |
305-243-7394
|
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Lab |
Ramin Shiekhattar
|
| Street address |
1501 NW 10 Avenue
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE45713 |
Genome-wide analysis of BRCA1 and PALB2 [TNF-alpha stimulation] |
| GSE45715 |
Genome-wide analysis of BRCA1 and PALB2 |
|
