|
| Status |
Public on Jul 24, 2010 |
| Title |
L-UHO-1 siSCR rep3 |
| Sample type |
RNA |
| |
|
| Source name |
siSCR UHO-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UHO-1
sirna: siSCR
|
| Treatment protocol |
U-HO1 and L-1236 cells were transduced with shRNAs against GATA-3 or non-functional control shRNAs, cultured for three days, and sorted according to their GFP positivity.
|
| Growth protocol |
Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).UHO-1 cells were cultured as above but in IMDM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from 25,000 GFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT expression Kit (Ambion, Austin, USA)
|
| Label |
biotin
|
| Label protocol |
Samples were labelled with WT target labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
25,000 GFP-positive cells
|
| Data processing |
Statistical analysis was done with the statistical computing environment R (version 2.8.1). Additional software packages (affy_1.20.2, vsn_3.8.0, geneplotter_1.20.0, multtest_1.23.3) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)
|
| |
|
| Submission date |
Jun 24, 2010 |
| Last update date |
Jun 25, 2010 |
| Contact name |
Claudia Döring |
| E-mail(s) |
C.Doering@em.uni-frankfurt.de
|
| Organization name |
Johann Wolfgang-Goethe University Frankfurt a.M.
|
| Department |
Medical School, Institite of Pathology
|
| Street address |
Theodor Stern Kai 7
|
| City |
Frankfurt |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE22550 |
Expression data from Hodgkin lymphoma cell lines UHO-1 and L-1236 transduced with shRNAs against GATA-3 or non-functional control shRNAs |
|
