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Sample GSM399271 Query DataSets for GSM399271
Status Public on Apr 30, 2012
Title NA12057
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_parent
coriell sample: NA12057
Biomaterial provider Coriell sample NA12057
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12057
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
E-mail(s) lilanli@itri.org.tw
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
ID_REF
VALUE Normalized, log2 signal intensity

Data table
ID_REF VALUE
PH_hs_0004877 6.54245351
PH_hs_0033433 7.210079469
PH_hs_0026582 5.192999367
PH_hs_0035481 13.26853574
PH_hs_0025134 7.961710397
PH_hs_0023499 13.54980346
PH_hs_0025293 7.044636933
PH_hs_0023725 10.52607212
PH_hs_0032109 10.33984554
PH_hs_0010306 9.072844764
PH_hs_0001352 6.954703105
PH_hs_0022361 8.96526101
PH_hs_0014165 13.19390847
PH_hs_0032993 2.542650279
PH_hs_0021034 14.58845922
PH_hs_0011065 7.377841116
PH_hs_0041074 3.472660821
PH_hs_0004580 9.19407731
PH_hs_0000364 7.625039721
PH_hs_0012615 6.017006732

Total number of rows: 30968

Table truncated, full table size 770 Kbytes.




Supplementary file Size Download File type/resource
GSM399271_H0601021288.txt.gz 339.3 Kb (ftp)(http) TXT
GSM399271_H0601021298.txt.gz 336.3 Kb (ftp)(http) TXT
GSM399271_H0601021810.txt.gz 339.0 Kb (ftp)(http) TXT
GSM399271_H0601021813.txt.gz 331.8 Kb (ftp)(http) TXT
GSM399271_H0601021814.txt.gz 335.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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