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Sample GSM399261 Query DataSets for GSM399261
Status Public on Apr 30, 2012
Title NA11830
Sample type RNA
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_parent
coriell sample: NA11830
Biomaterial provider Coriell sample NA11830
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 6.437274697
PH_hs_0033433 7.402123877
PH_hs_0026582 5.541174081
PH_hs_0035481 13.03246812
PH_hs_0025134 8.048295212
PH_hs_0023499 13.60222675
PH_hs_0025293 7.118854631
PH_hs_0023725 10.46652226
PH_hs_0032109 10.52637716
PH_hs_0010306 8.918470958
PH_hs_0001352 7.365987384
PH_hs_0022361 9.060468804
PH_hs_0014165 13.62072366
PH_hs_0032993 2.706551699
PH_hs_0021034 14.90206006
PH_hs_0011065 7.589292101
PH_hs_0041074 3.680609996
PH_hs_0004580 10.41309561
PH_hs_0000364 7.871280453
PH_hs_0012615 6.085370181

Total number of rows: 30968

Table truncated, full table size 773 Kbytes.

Supplementary file Size Download File type/resource
GSM399261_H0601021269.txt.gz 335.2 Kb (ftp)(http) TXT
GSM399261_H0601021271.txt.gz 338.1 Kb (ftp)(http) TXT
GSM399261_H0601021557.txt.gz 341.0 Kb (ftp)(http) TXT
GSM399261_H0601021558.txt.gz 341.8 Kb (ftp)(http) TXT
GSM399261_H0601021575.txt.gz 337.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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