|
| Status |
Public on Jul 16, 2012 |
| Title |
control 1 |
| Sample type |
RNA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
knockdown: lentiviral construct shRNA SHC002
expression: H2A.Bbd-FLAG histone
|
| Treatment protocol |
Cells were transduced with a pLKO.1 lentivirus expressing a non-mammalian shRNA (SigmaAldrich SHC002V and selected with puromycin for 9 days.
|
| Growth protocol |
HeLa cells were grown in DMEM with 10% calf serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated by Trizol and sent to NimbleGen Systems Inc., Madison, WI USA for library constrcution and hybridization to the 4plex human gene expression array
|
| 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 |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
replicate 1
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jun 22, 2012 |
| Last update date |
Jul 19, 2013 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL8971 |
| Series (2) |
| GSE38771 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells |
| GSE38890 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA] |
|
