|
| Status |
Public on May 31, 2007 |
| Title |
GM19239 (2) |
| Sample type |
RNA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
Coriell cell line repository identifier: GM19239
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM19239
Yoruban sample
Gender: Male
Associated family: Y117-3
Family relationship: father
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19239
|
| 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 |
GSM188771 |
| Alternative to |
GSM245580 |
