|
| Status |
Public on Dec 01, 2010 |
| Title |
Untreated TG2 knockout NB4, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
NB4 cell line, TG2 knockout, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NB4
genotype: TG2 knockout
treatment: untreated
biological replicate: 2
|
| Treatment protocol |
Differentiation of NB4 cells was induced at 1 x 100,000 cells/mL by administration of 1 µM ATRA (Sigma) for 0, 48 or 72 hours.
|
| Growth protocol |
The NB4 cell line (purchased from DSMZ GmbH) was cultured in RPMI 1640 Medium (Sigma) supplemented with (10% v/v) fetal bovine serum (FBS) (Sigma), 2 mM glutamine (Sigma), 100 U/mL penicillin and 100 µg/mL streptomycin solution (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).
|
| Label |
biotin
|
| Label protocol |
Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using the WT Expression kit (Ambion).
|
| |
|
| Hybridization protocol |
10 ug of ss cDNA was fragmented and labeled with biotin, and hybridized for 16 hr at 45C on the GeneChip 1.0 ST Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Description |
0KD2
Gene expression data from undifferentiated TG2 knockout NB4.
|
| Data processing |
Affymetrix CEL files were imported into GeneSpring GX11 Software (Agilent). The RMA16 algorithm was used for probe summarization and then median normalization was performed.
|
| |
|
| Submission date |
Sep 14, 2010 |
| Last update date |
Sep 14, 2010 |
| Contact name |
Krisztian Csomos |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Debrecen
|
| Street address |
Egyetem ter 1.
|
| City |
Debrecen |
| ZIP/Postal code |
4012 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE23702 |
Gene expression profiling of ATRA-differentiated wild-type and TG2 knockout NB4 cells |
|
