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Sample GSM189024 Query DataSets for GSM189024
Status Public on May 31, 2007
Title GM12865 (2)
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics Coriell cell line repository identifier: GM12865
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM12865
CEPH sample
Gender: Female
Associated family: 1459-2
Family relationship: mother
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12865
Treatment protocol Untreated, baseline expression data.
Growth protocol Each sample was collected while in exponential growth.
Lymphoblastoid cell lines were centrifuged at 400 × g to remove media and 5 mL fresh lymphoblastoid cell media (LCL media) containing RPMI 1640 (Mediatech)/1% l-glutamine (Mediatech) plus 20% FBS (HyClone Laboratories) for the initial passage and then passaged every 48 h with LCL medium and 15% FBS. Cell suspensions were transferred to 25 cm2 flasks and incubated at 37oC in a 90% humidified 5% CO2 atmosphere. Cell lines were maintained at a concentration of 3.5-4.0×105 cells/mL and harvested following the 4th passage, only if viability >= 85%.
Extracted molecule total RNA
Extraction protocol Lymphoblastoid cell line suspensions were spun at 400 × g for 5 min to remove media. Cell pellets were washed twice with ice-cold PBS and stored at -80°C. Total RNA was extracted using RNeasy Plus Kits according to the manufacturers protocol.
Label biotin
Label protocol Ribosomal RNA was depleted from 1µg of total RNA using the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen Corp., Carlsbad, CA). cDNA was generated using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA) per manufacturer's instructions. cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labeling Kit (Affymetrix, Inc.).
 
Hybridization protocol Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45oC for 16 hours per manufacturers recommendation (see http://www.affymetrix.com/products/arrays/exon_application.affx for additional information). Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.
Scan protocol All samples were scanned on a GCS3000 Scanner (Affymetrix, Inc.).
Description Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array.
Data processing Gene expression profiles were assessed by using Affymetrix GeneChip Human Exon 1.0 ST array. Probe-signal intensities were sketch normalized using a subset of the 1.4 million probe sets. Transcript expression was summarized by using a robust multiarray average method (RMA) with the core set of well annotated exons (~200,000). The ExACT program developed by Affymetrix was used to determine gene signal estimates
 
Submission date May 14, 2007
Last update date Apr 26, 2009
Contact name Eileen Dolan
E-mail(s) edolan@medicine.bsd.uchicago.edu
Phone 773-702-4441
Fax 773-702-0963
Organization name University of Chicago
Department Medicine
Lab Dolan Lab
Street address 5841 S. Maryland
City Chicago
State/province IL
ZIP/Postal code 60657
Country USA
 
Platform ID GPL5175
Series (1)
GSE7792 A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
Relations
Alternative to GSM188842
Alternative to GSM245651

Data table header descriptions
ID_REF Transcript_probeset_id
VALUE Probe-signal intensities were sketch normalized using a subset of the 1.4 million probe sets. Transcript expression was summarized by using a robust multiarray average method (RMA) with the core set of well annotated exons (~200,000). The ExACT program developed by Affymetrix was used to determine gene signal estimates

Data table
ID_REF VALUE
4054117 6.9039416
4041923 7.083357
2390976 6.045334
4052881 8.034998
4054612 5.0801115
4053415 5.1378517
4054639 9.167279
4053462 6.349223
4053495 6.241341
4054681 5.3138876
4054690 5.8223276
4053534 7.8971214
2391005 6.007783
2315554 5.8761916
2391150 6.450784
2391172 5.841763
2391188 7.537552
2315633 6.5088987
2391255 6.746786
4042392 6.6564064

Total number of rows: 17879

Table truncated, full table size 303 Kbytes.




Supplementary file Size Download File type/resource
GSM189024.CEL.gz 37.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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