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Sample GSM188963 Query DataSets for GSM188963
Status Public on May 31, 2007
Title GM10856 (2)
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics Coriell cell line repository identifier: GM10856
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM10856
CEPH sample
Gender: Male
Associated family: 1350-1
Family relationship: father
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM10856
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 GSM188781
Alternative to GSM245590

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 6.578681
4041923 7.20611
2390976 6.3365865
4052881 7.8946595
4054612 5.0941815
4053415 5.227678
4054639 9.530043
4053462 6.560754
4053495 6.241341
4054681 5.4690375
4054690 5.992763
4053534 6.504939
2391005 6.249278
2315554 6.211562
2391150 7.123587
2391172 6.028508
2391188 7.3699594
2315633 6.8102417
2391255 6.9969873
4042392 6.814198

Total number of rows: 17879

Table truncated, full table size 303 Kbytes.




Supplementary file Size Download File type/resource
GSM188963.CEL.gz 37.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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