NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM399262 Query DataSets for GSM399262
Status Public on Apr 30, 2012
Title NA11831
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: lymphoblastoid cell line
parent/child: HapMap CEU_parent
coriell sample: NA11831
Biomaterial provider Coriell sample NA11831
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA11831
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 6.709448919
PH_hs_0033433 6.85630063
PH_hs_0026582 5.403792097
PH_hs_0035481 12.75704507
PH_hs_0025134 7.57331617
PH_hs_0023499 11.92049084
PH_hs_0025293 6.602054351
PH_hs_0023725 9.875692125
PH_hs_0032109 11.40190604
PH_hs_0010306 8.728973162
PH_hs_0001352 7.939420109
PH_hs_0022361 8.215727912
PH_hs_0014165 12.96858468
PH_hs_0032993 2.331581113
PH_hs_0021034 14.21161753
PH_hs_0011065 6.645022192
PH_hs_0041074 2.677688638
PH_hs_0004580 9.702050442
PH_hs_0000364 8.02090949
PH_hs_0012615 6.218694136

Total number of rows: 30968

Table truncated, full table size 776 Kbytes.




Supplementary file Size Download File type/resource
GSM399262_H0601006516.txt.gz 347.3 Kb (ftp)(http) TXT
GSM399262_H0601006519.txt.gz 344.8 Kb (ftp)(http) TXT
GSM399262_H0601021723.txt.gz 342.8 Kb (ftp)(http) TXT
GSM399262_H0601021751.txt.gz 339.6 Kb (ftp)(http) TXT
GSM399262_H0601021755.txt.gz 343.9 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap