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Sample GSM159654 Query DataSets for GSM159654
Status Public on Feb 09, 2007
Title NA18994
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics HapMap JPT, Male
Biomaterial provider Coriell http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18994
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°C.
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 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 JPT Male
Data processing background-corrected values for each single bead type (raw data) were normalised 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 individuals of a single population.
 
Submission date Jan 31, 2007
Last update date Oct 01, 2007
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

Data table header descriptions
ID_REF
VALUE log quantile + median normalised data

Data table
ID_REF VALUE
GI_10047089-S 5.922236
GI_10047091-S 6.363359
GI_10047093-S 9.863295
GI_10047099-S 7.862148
GI_10047103-S 12.262323
GI_10047105-S 6.889602
GI_10047121-S 6.063625
GI_10047123-S 9.520123
GI_10047133-A 5.972701
GI_10047133-I 6.399583
GI_10092578-S 6.082507
GI_10092585-S 7.104882
GI_10092596-S 7.250823
GI_10092600-S 8.791589
GI_10092602-S 5.963004
GI_10092603-S 5.930856
GI_10092611-A 7.793699
GI_10092616-S 7.389136
GI_10092618-S 13.433572
GI_10092638-S 6.594262

Total number of rows: 47293

Table truncated, full table size 1009 Kbytes.




Supplementary file Size Download File type/resource
GSM159654_NA18994_1_1.txt.gz 253.2 Kb (ftp)(http) TXT
GSM159654_NA18994_1_2.txt.gz 250.7 Kb (ftp)(http) TXT
GSM159654_NA18994_2_1.txt.gz 247.8 Kb (ftp)(http) TXT
GSM159654_NA18994_2_2.txt.gz 251.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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