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Sample GSM399302 Query DataSets for GSM399302
Status Public on Apr 30, 2012
Title NA07034
Sample type RNA
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_parent
coriell sample: NA07034
Biomaterial provider Coriell sample NA07034
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 7.458215297
PH_hs_0033433 6.538074746
PH_hs_0026582 4.919174787
PH_hs_0035481 13.86197064
PH_hs_0025134 7.445865133
PH_hs_0023499 13.25020298
PH_hs_0025293 7.257392388
PH_hs_0023725 10.37192165
PH_hs_0032109 10.2368407
PH_hs_0010306 9.300206993
PH_hs_0001352 7.004395786
PH_hs_0022361 8.44332412
PH_hs_0014165 12.91352226
PH_hs_0032993 1.593323796
PH_hs_0021034 14.63098883
PH_hs_0011065 6.946932149
PH_hs_0041074 2.910186941
PH_hs_0004580 10.79797666
PH_hs_0000364 7.041787873
PH_hs_0012615 5.348360974

Total number of rows: 30968

Table truncated, full table size 775 Kbytes.

Supplementary file Size Download File type/resource
GSM399302_H0601014566.txt.gz 342.3 Kb (ftp)(http) TXT
GSM399302_H0601014568.txt.gz 344.3 Kb (ftp)(http) TXT
GSM399302_H0601014668.txt.gz 339.4 Kb (ftp)(http) TXT
GSM399302_H0601021550.txt.gz 334.4 Kb (ftp)(http) TXT
GSM399302_H0601021738.txt.gz 337.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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