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Sample GSM399346 Query DataSets for GSM399346
Status Public on Apr 30, 2012
Title NA12802
Sample type RNA
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_children
coriell sample: NA12802
Biomaterial provider Coriell sample NA12802
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 Cy5
Label protocol 1.5 ug of total RNA from each sample was used in cDNA synthesis and IVT reaction using the Amino Allyl MessageAmpTMII aRNA Amplification kit (Ambion, Austin, TX 78744-1832, cat. no.1753). Single stranded aRNA labeled with Cy5 was generated using the Cy5 Mono-Reactive dye pack (Amersham. PA25001)
Hybridization protocol Ten micrograms of Cy5- labeled aRNA was fragmented (Ambion cat# 8740) and hybridized 16 hrs to Phalanx HOA arrays according to manufacturer’s instructions
Scan protocol Arrays were scanned using Agilent DNA Microarray Scanner G2565B (Agilent Technologies, Inc. CA, USA) at settings of 60 PMT (for Cy5) and of 10 micron, and the resulting images were quantified using the software ProbeArrayer (an in-house tool developed by ITRI)
Description no additional information
Data processing log2 transformed intensities were normalized across technical replicates for each individual using a ComBat (Johnson et al. 2007) normalization. The normalized replicate values were merged by median as one chip per sample, and then sample-based chips were normalized by median across individuals (n=60 for parent or n=30 for children).
Submission date Apr 30, 2009
Last update date Apr 30, 2012
Contact name Li-Lan Li
Organization name Industrial Technology Research Institute
Street address 195,Sec. 4, Chung Hsing Rd. Chutung
City Hsinchu
ZIP/Postal code 310
Country Taiwan
Platform ID GPL6254
Series (1)
GSE15905 A new genome wide expression array and its application to eQTL mapping, synergy to other platforms

Data table header descriptions
VALUE Normalized, log2 signal intensity

Data table
PH_hs_0004877 7.038498634
PH_hs_0033433 7.011481271
PH_hs_0026582 5.479607731
PH_hs_0035481 13.98999745
PH_hs_0025134 8.188125653
PH_hs_0023499 12.75871419
PH_hs_0025293 7.758083902
PH_hs_0023725 9.43976315
PH_hs_0032109 10.39978953
PH_hs_0010306 8.708272897
PH_hs_0001352 7.908403229
PH_hs_0022361 8.563738984
PH_hs_0014165 13.37082986
PH_hs_0032993 1.815026265
PH_hs_0021034 14.26639345
PH_hs_0011065 7.87275112
PH_hs_0041074 2.348810949
PH_hs_0004580 9.27973014
PH_hs_0000364 7.772071829
PH_hs_0012615 6.253464149

Total number of rows: 30968

Table truncated, full table size 778 Kbytes.

Supplementary file Size Download File type/resource
GSM399346_H0601014606.txt.gz 345.7 Kb (ftp)(http) TXT
GSM399346_H0601014607.txt.gz 347.3 Kb (ftp)(http) TXT
GSM399346_H0601014611.txt.gz 341.5 Kb (ftp)(http) TXT
GSM399346_H0601014805.txt.gz 349.0 Kb (ftp)(http) TXT
GSM399346_H0601014888.txt.gz 347.9 Kb (ftp)(http) TXT
GSM399346_H0601014891.txt.gz 347.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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