normalization data transformation protocol
CEL files were read into the R software environment http://www.cran.r-project.org/ and normalized with RMA. Normalized data were fit with a linear model using the limma package, default methods. These are in Normalized.txt. Linear model coefficients (average normalized expression) and standard deviations were extracted, these are in Coefficients.txt.
nucleic acid labeling protocol
Affymetrix default protocol.
nucleic acid extraction protocol
RNA was extracted by conventional trizol method from sorted LT-HSCs, ST-HSCs and MPPs (10,000 cells each).
LSK cells were isolated from whole bone marrow by FACS, selecting for Lineage- Sca-1+ cKit+. Cells were further sorted into LT-HSC (Flk2- CD34-), ST-HSC (Flk2- CD34-), and MPP (Flk2+ CD34+) populations.
All mice used in this study were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institutes of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR