|
| Status |
Public on Nov 04, 2008 |
| Title |
ALL#153 |
| Sample type |
RNA |
| |
|
| Source name |
B220+ CD43- IgM- IgD-
|
| Organism |
Mus musculus |
| Characteristics |
cell type: leukemic preB
Mll-AF4stop knock-in mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction following manufacturer's protocol.
|
| Label |
Biotin
|
| Label protocol |
20 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using the NuGen Ovation Biotin labeling system.
|
| |
|
| Hybridization protocol |
3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.
|
| Scan protocol |
Standard Affymetrix protocol
|
| Description |
purified pre B-lymphocytes (B220+ CD43- IgM- IgD-) from bone marrow of a leukemic mouse
|
| 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 |
Jul 31, 2008 |
| Last update date |
Mar 18, 2009 |
| Contact name |
Madeleine E. Lemieux |
| E-mail(s) |
[email protected]
|
| Phone |
617-595-6695
|
| URL |
http://www.bioinfo.ca
|
| Organization name |
Bioinfo
|
| Street address |
275 Main St., Suite 252
|
| City |
Plantagenet |
| State/province |
ON |
| ZIP/Postal code |
K0B 1L0 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8321 |
| Series (2) |
| GSE12310 |
Expression profiling of normal murine lymphoid progenitors and MLL-AF4 leukemic lymphoblasts |
| GSE12363 |
H3K79 methylation profiles define murine and human MLL-AF4 leukemias |
|
