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Sample GSM399339 Query DataSets for GSM399339
Status Public on Apr 30, 2012
Title NA10861
Sample type RNA
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_children
coriell sample: NA10861
Biomaterial provider Coriell sample NA10861
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 6.840716495
PH_hs_0033433 6.369951533
PH_hs_0026582 5.031895887
PH_hs_0035481 13.76518994
PH_hs_0025134 8.052255298
PH_hs_0023499 12.01138854
PH_hs_0025293 6.351085415
PH_hs_0023725 8.879639412
PH_hs_0032109 9.0784594
PH_hs_0010306 7.98449282
PH_hs_0001352 7.468926351
PH_hs_0022361 8.119286436
PH_hs_0014165 11.93657289
PH_hs_0032993 3.047005649
PH_hs_0021034 13.5739132
PH_hs_0011065 7.47204675
PH_hs_0041074 3.311046829
PH_hs_0004580 7.386764368
PH_hs_0000364 7.466666119
PH_hs_0012615 6.141928394

Total number of rows: 30968

Table truncated, full table size 779 Kbytes.

Supplementary file Size Download File type/resource
GSM399339_H0601014717.txt.gz 348.6 Kb (ftp)(http) TXT
GSM399339_H0601014718.txt.gz 350.3 Kb (ftp)(http) TXT
GSM399339_H0601014731.txt.gz 351.0 Kb (ftp)(http) TXT
GSM399339_H0601014990.txt.gz 348.1 Kb (ftp)(http) TXT
GSM399339_H0601015000.txt.gz 349.0 Kb (ftp)(http) TXT
GSM399339_H0601015002.txt.gz 350.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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