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Sample GSM188944 Query DataSets for GSM188944
Status Public on May 31, 2007
Title GM19208 (2)
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics Coriell cell line repository identifier: GM19208
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM19208
Yoruban sample
Gender: Male
Associated family: Y051-1
Family relationship: child
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19208
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 GSM188762
Alternative to GSM245571

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 6.335353
4041923 7.7682915
2390976 6.4500895
4052881 7.998518
4054612 5.049495
4053415 5.1083536
4054639 9.552955
4053462 6.404294
4053495 6.1107116
4054681 5.596679
4054690 6.1090813
4053534 8.269304
2391005 6.209629
2315554 5.873499
2391150 6.372056
2391172 6.042779
2391188 7.491753
2315633 7.1484513
2391255 7.14005
4042392 6.7821007

Total number of rows: 17879

Table truncated, full table size 302 Kbytes.




Supplementary file Size Download File type/resource
GSM188944.CEL.gz 37.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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