|
| Status |
Public on Jun 27, 2011 |
| Title |
HSC 2 |
| Sample type |
RNA |
| |
|
| Source name |
Murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: hematopoietic stem cells (HSC)
transduction protocol: untransduced
|
| Extracted molecule |
total RNA |
| Extraction protocol |
36 hours after spininoculation of oncogene or empty-vector transduced GMP, GFP positive cells were homogenized with TRIzol® Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. RNA isolated from the above populations along with sorted normal LSK, GMP, and MOZ-TIF2 leukemic GMP were quantitated with the Quant-iT™ RiboGreen® RNA Reagent and Kit (Invitrogen) according to manufacturer’s specifications, and used for RNA amplification and hybridization as previously published.
|
| Label |
biotin
|
| Label protocol |
As per the manufacturer's instructions and as previously published, with one modification: biotinylated CTP and UTP (Enzo Diagnostics, Farmingdale, NY) in a 2.5:1 proportion to non-biotinylated CTP and UTP. All RNA populations were simultaneously amplified.
|
| |
|
| Hybridization protocol |
Gene expression levels were measured using Affymetrix (Santa Clara, CA) GeneChip Mouse Genome 430A 2.0 arrays (22,690 probesets) with hybridisation and washes as per the manufacturers specifications.
|
| Scan protocol |
As per Affymetrix specifications.
|
| Description |
Gene expression data from murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced
B_HSC 2_020407.CEL
|
| Data processing |
The starting point for all analyses was the ''.CEL'' files from the MAS5 software. Data was analyzed using the R statistical package bioconductor. Data quality was assessed using functions in the affy and affyPLM packages and outlier arrays were removed from subsequent analysis.
The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates.
|
| |
|
| Submission date |
Oct 19, 2010 |
| Last update date |
Jun 27, 2011 |
| Contact name |
Brian J.P. Huntly |
| E-mail(s) |
[email protected]
|
| URL |
http://www.cam.ac.uk/
|
| Organization name |
University of Cambridge
|
| Department |
Cambridge Institute for Medical Research
|
| Lab |
Department of Haematology
|
| Street address |
Wellcome Trust/MRC Building, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE24797 |
Common and overlapping oncogenic pathways contribute to the evolution of acute myeloid leukemias |
|
