|
| Status |
Public on Oct 01, 2007 |
| Title |
NA19192_across_population_normalised |
| Sample type |
RNA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
HapMap YRI_parent, Male
|
| Biomaterial provider |
Coriell http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19192
|
| Growth protocol |
RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80 Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen).
|
| Label |
biotin
|
| Label protocol |
One-quarter scale Message Amp II reactions (Ambion) were performed for each RNA extraction using 200 ng of total RNA. Biotin-16-UTP (Perkin Elmer) made up half of the UTP used in the in vitro transcription (IVT) reaction (37 Celsius for 18 hours).
|
| |
|
| Hybridization protocol |
1.5ug cRNA as per Gene expression on Sentrix Arrays direct hybridization system manual (Illumina Doc. #11161707, Rev. B). Arrays were hybridized for 18 hours and stained with Cy3-Streptavidin.
|
| Scan protocol |
Standard Illumina protocol, PMT 638
|
| Description |
HapMap YRI_parent Male
|
| Data processing |
background-corrected values for each single bead type (raw data) were normalized on a log scale using a quantile normalization method (Bolstad et al. Bioinformatics, 2003. 19(2): p. 185-93) across replicates of a single individual, followed by a median normalisation across all 270 individuals of the 4 populations.
|
| |
|
| Submission date |
Sep 28, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Emmanouil T Dermitzakis |
| E-mail(s) |
emmanouil.dermitzakis@unige.ch
|
| Phone |
+41 (0) 22 379 5483
|
| Organization name |
University of Geneva Medical School
|
| Department |
Department of Genetic Medicine and Development
|
| Lab |
Population and comparative genomics
|
| Street address |
1 Rue Michel-Servet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL2507 |
| Series (1) |
| GSE6536 |
Whole-genome gene expression variation in 210 unrelated HapMap individuals |
|
