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Sample GSM159720 Query DataSets for GSM159720
Status Public on Feb 09, 2007
Title NA19222
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=NA19222
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 5.948931
GI_10047091-S 6.358622
GI_10047093-S 9.932209
GI_10047099-S 6.649114
GI_10047103-S 12.085914
GI_10047105-S 6.746165
GI_10047121-S 6.095579
GI_10047123-S 9.359858
GI_10047133-A 5.905634
GI_10047133-I 6.363445
GI_10092578-S 6.083927
GI_10092585-S 7.147802
GI_10092596-S 7.112672
GI_10092600-S 9.015464
GI_10092602-S 5.924212
GI_10092603-S 6.025837
GI_10092611-A 8.287577
GI_10092616-S 6.512370
GI_10092618-S 13.558828
GI_10092638-S 6.376200

Total number of rows: 47293

Table truncated, full table size 1009 Kbytes.




Supplementary file Size Download File type/resource
GSM159720_NA19222_1_1.txt.gz 257.1 Kb (ftp)(http) TXT
GSM159720_NA19222_1_2.txt.gz 255.5 Kb (ftp)(http) TXT
GSM159720_NA19222_3_1.txt.gz 248.2 Kb (ftp)(http) TXT
GSM159720_NA19222_3_2.txt.gz 246.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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