|
| Status |
Public on Sep 08, 2014 |
| Title |
LSK-Control-K1603 |
| Sample type |
RNA |
| |
|
| Source name |
Wild type LSKs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57/BL6
genotype/variation: Dot1 wt/wt x Mx-Cre; wild type
cell type: Sorted BM cells
cell subtype: Lineage negative Sca-1 positive Kit positive (LSK) cells
|
| Treatment protocol |
Cells were sorted on the basis of surface markers for LSKs and GMPs using standard protocols prior to RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
According to manufacturer's instructions (Affymetrix)
|
| Scan protocol |
According to manufacturer's instructions (Affymetrix)
|
| Description |
Wild type LSKs
|
| Data processing |
RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).
|
| |
|
| Submission date |
Jan 29, 2014 |
| Last update date |
Sep 08, 2014 |
| Contact name |
Scott Armstrong |
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Street address |
1275 York Avenue
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE54498 |
Effect of Dot1l deletion on LSKs and GMPs |
| GSE54500 |
Role of H3K79 methylation states in HOX gene expression and leukemogenesis |
|
