|
| Status |
Public on Feb 22, 2012 |
| Title |
WT MLL-AF9 BM-cells, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted GFP+/YFP+ bone marrow cells, WT
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: WT
cell type: sorted GFP+/YFP+ bone marrow cells
|
| Treatment protocol |
Bone marrow cells from leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
|
| Growth protocol |
Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
|
| Label |
biotin
|
| Label protocol |
Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
|
| |
|
| Hybridization protocol |
5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
|
| Scan protocol |
GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
|
| Description |
CTL-2
|
| Data processing |
RMA background correction and quantile normalization was 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 09, 2012 |
| Last update date |
Feb 22, 2012 |
| Contact name |
Amit Sinha |
| E-mail(s) |
amit.sinha@childrens.harvard.edu
|
| Phone |
617-582-7579
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Armstrong Lab
|
| Street address |
44 Binney St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02135 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE34959 |
Expression profiling of primary wild type (WT), Ezh2-null and Eed-null murine MLL-AF9 AML |
| GSE34963 |
The Polycomb Repressive Complex 2 Is Required For MLL-AF9 Leukemia |
|
