|
| Status |
Public on Apr 28, 2011 |
| Title |
csh2 No 4-OHT rep2 |
| Sample type |
RNA |
| |
|
| Source name |
csh2 cell line, MLL wild type
|
| Organism |
Mus musculus |
| Characteristics |
mll fusion: MLL wild type
cell line: csh2
|
| Growth protocol |
MLL-ENL inducible cell line (csh2) was obtained from Dr. Robert Slany (University Erlangen, Germany). Cells grow in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), with 5ng/ml IL-3, IL-6, GM-CSF 50ng/ml SCF, and 100nM 4-Hydroxy-tamoxifen (4-OHT)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample under the two experimental conditions, 4-OHT and No 4-OHT, each with one replicate, 20 ng of high-quality total RNAs were amplified.
|
| Label |
biotin
|
| Label protocol |
Labeled according to the Affymetrix’s specifications
|
| |
|
| Hybridization protocol |
Hybridized according to the Affymetrix’s specifications
|
| Scan protocol |
Scanned according to the Affymetrix’s specifications
|
| Description |
csh2 cell line 4-OHT withdrawal, MLL wild type
|
| Data processing |
We used GeneBASE to estimate gene expression from the Affymetrix exon arrays (Kapur et al. 2007; Kapur et al. 2008). Specifically, probes were scalar normalized and then corrected for background using the MAT method (Johnson et al. 2006). For probes with high correlation with matching off-target transcripts, expression patterns were excluded. Among the remaining set of probes, we selected for probes with highly correlated intensities across different samples to be included in the gene-level estimates.
|
| |
|
| Submission date |
Oct 19, 2010 |
| Last update date |
Apr 28, 2011 |
| Contact name |
Jun Wu |
| E-mail(s) |
wuj@big.ac.cn
|
| Organization name |
Beijing Institue of Genomics, Chinese Academy of Science
|
| Street address |
No.7 Beitucheng West Road
|
| City |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
| |
|
| Platform ID |
GPL6096 |
| Series (1) |
| GSE24794 |
MLL Fusion Proteins Preferentially Regulate a Small Set of Wild Type MLL Target Genes in the Leukemic Genome |
|
