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Sample GSM159718 Query DataSets for GSM159718
Status Public on Feb 09, 2007
Title NA19209
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°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 YRI_parent Female
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 5.891805
GI_10047091-S 6.507751
GI_10047093-S 9.218282
GI_10047099-S 7.660458
GI_10047103-S 11.697397
GI_10047105-S 6.341044
GI_10047121-S 5.925895
GI_10047123-S 9.545632
GI_10047133-A 5.977885
GI_10047133-I 6.412950
GI_10092578-S 5.998263
GI_10092585-S 7.196875
GI_10092596-S 6.853873
GI_10092600-S 9.270759
GI_10092602-S 5.976193
GI_10092603-S 5.899923
GI_10092611-A 8.413777
GI_10092616-S 6.358343
GI_10092618-S 13.011886
GI_10092638-S 6.525269

Total number of rows: 47293

Table truncated, full table size 1009 Kbytes.




Supplementary file Size Download File type/resource
GSM159718_NA19209_1_1.txt.gz 256.6 Kb (ftp)(http) TXT
GSM159718_NA19209_1_2.txt.gz 254.0 Kb (ftp)(http) TXT
GSM159718_NA19209_2_1.txt.gz 253.5 Kb (ftp)(http) TXT
GSM159718_NA19209_2_2.txt.gz 248.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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