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Sample GSM232765 Query DataSets for GSM232765
Status Public on Oct 01, 2007
Title NA19209_across_population_normalised
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics HapMap YRI_parent, Female
Biomaterial provider Coriell http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19209
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 Female
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

Data table header descriptions
ID_REF ILLUMINA PROBE NAME
VALUE NORMALISED DATA:log quantile across replicates + median normalised across all individuals data.

Data table
ID_REF VALUE
GI_10047089-S 5.872865
GI_10047091-S 6.488811
GI_10047093-S 9.199342
GI_10047099-S 7.641518
GI_10047103-S 11.678457
GI_10047105-S 6.322104
GI_10047121-S 5.906955
GI_10047123-S 9.526692
GI_10047133-A 5.958945
GI_10047133-I 6.394010
GI_10092578-S 5.979323
GI_10092585-S 7.177935
GI_10092596-S 6.834933
GI_10092600-S 9.251819
GI_10092602-S 5.957253
GI_10092603-S 5.880983
GI_10092611-A 8.394837
GI_10092616-S 6.339403
GI_10092618-S 12.992946
GI_10092638-S 6.506329

Total number of rows: 47293

Table truncated, full table size 1009 Kbytes.




Supplementary file Size Download File type/resource
GSM232765_NA19209_1_1.txt.gz 256.6 Kb (ftp)(http) TXT
GSM232765_NA19209_1_2.txt.gz 254.0 Kb (ftp)(http) TXT
GSM232765_NA19209_2_1.txt.gz 253.5 Kb (ftp)(http) TXT
GSM232765_NA19209_2_2.txt.gz 248.4 Kb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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