cell type: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90- cells disease status: healthy
Treatment protocol
No treatment.
Growth protocol
Uncultured primary cells.
Extracted molecule
total RNA
Extraction protocol
Cells were sorted into RLT buffer (Qiagen, Valencia, CA), homogenized by passing five times through a needle. Simultaneous harvest of RNA and genomic DNA was achieved with the AllPrep kit (Qiagen, Valencia, CA) following the instructions of the manufacturer. Total RNA was linearly amplified and transcribed with the MessageAmp Kit AM1751 (Ambion/ Life Technologies, Carlsbad, CA) prior to microarray gene expression analysis following the NimbleGen Arrays User's Guide (NimbleGen, Madison, WI). Integrity of RNA and cDNA was verified at each step of amplification using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
Label
Cy5
Label protocol
See manufacturer's web site (www.nimblegen.com).
Hybridization protocol
Labeling and hybridization onto the NimbleGen Homo sapiens HG18 60mer expr (385k) was carried out by Roche/NimblGen (Madison, WI) according to the manufacturer's protocols (see manufacturer's website (www.nimblegen.com)).
Scan protocol
See manufacturer's web site (www.nimblegen.com).
Description
0100STHSC
Data processing
Gene expression profiling was performed on NimbleGen HG18 arrays (design name 2006-08-03_HG18_60mer_expr, Roche-NimbleGen Inc., Madison, WI). The raw data (.pair file) was analyzed by the NimbleScan software package (Roche NimbleGen, Inc.). The data was normalized using the RMA algorithm.
