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Sample GSM291953 Query DataSets for GSM291953
Status Public on May 29, 2008
Title S003623
Sample type RNA
 
Source name Lymphoblastoid cell line
Organism Pan troglodytes
Characteristics SAHA drug response: NA
Simva drug response: NA
6MP drug response: NA
5FU drug response: NA
MTX drug response: NA
Growth protocol EBV-transformed lymphoblastoid cell lines were acquired from the NHGRI Sample Repository for Human Genetic Research in frozen aliquots. Cells were thawed in 5mL culture medium (RPMI medium 1640 (Invitrogen) supplemented with 10% FetalPlex (Gemini), 2mM L-Glutamine (Invitrogen), and 1x penicillin/streptomycin (Invitrogen)). Cell lines were counted daily using Z2 Coulter Counter (Beckman Coulter) and passaged as needed to maintain a concentration of 2-5 x 1e5 cells/ml at 37C in a 95% humidified 5% CO2 atmosphere. Initially, cells were grown until 5 x 1e5 cells/ml were reached in 50 mL total volume. Then, ten identical aliquots were frozen in 1 mL freezing media containing 50% FetalPlex, 40% RPMI 1640 medium, and 10% DMSO (Sigma) at -80C for 24 hrs and transferred to liquid nitrogen. These aliquots were used to provide biologic replicates for the experiments described below. Aliquots were thawed on experiment day #1 as described above. Cell lines were counted daily and passaged as need to maintain a concentration of 4-8 x 1e5 cells/ml in 10 mL culture medium. On experiment day #7, cells were counted and distributed for use in the various experiments described below. One cc of culture was used for immediate immunophenotyping via FACS and Luminex beads. One cc of culture was used for RNA and DNA extraction using Trizol (Invitrogen) following the manufacturer's protocol. The remaining eight cc of culture were used for drug response assays described below.
Extracted molecule total RNA
Extraction protocol All LCLs were cultured in the fashion described above. Prior to the plating of cells for the Drug Response Assay, 5 x 10^5 cells were set aside for RNA extraction. Cells were immediately lysed with Trizol Reagent (Invitrogen). RNA was collected according to the manufacturer instructions.
Label biotin
Label protocol As per manufactureer's protocol. 1.25 ug total RNA (OD>1.8) was diluted to a total volume of 10uL.
 
Hybridization protocol RNA was processed and hybridized onto Affymetrix Human U133A whole genome RNA expression genechip arrays according to the manufacturer’s protocol.
Scan protocol As per manufacturer's protocol
Description S003623
Data processing RMA; Gene expression summary values for the whole dataset were computed by RMA[36,37] and log-transformed. Measurements were successfully obtained for 257 HapMap cell lines in the main experiment, for 64 biological replicates, for 24 cell lines originally thawed at the WTSI, as well as multiple replicates of 5 cell lines derived from chimpanzees. (raw data in “all broad cell line expression data.zip” online)
 
Submission date May 28, 2008
Last update date May 29, 2008
Contact name Roman Yelensky
E-mail(s) ryelensky@gmail.com
Organization name MGH
Street address Massachusetts General Hospital Department of Molecular Biology 185 Cambridge St., Simches Ctr., CPZN-6818
City Boston
State/province MA
ZIP/Postal code 02114-2790
Country USA
 
Platform ID GPL96
Series (1)
GSE11582 Genetic Analysis of Human Traits In-Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 6.56465991858139
1053_at 7.11960392042712
117_at 5.26882546975548
121_at 7.1979314351445
1255_g_at 3.52573254293390
1294_at 7.35146499363371
1316_at 3.99621016151868
1320_at 4.13686474928994
1405_i_at 4.69716825073214
1431_at 3.68414391081250
1438_at 5.80453045770369
1487_at 6.65983986551707
1494_f_at 5.49018190571963
1598_g_at 7.08223026794072
160020_at 6.6137605638633
1729_at 7.52644210063095
177_at 4.73955224532856
1773_at 5.31666530661351
179_at 8.09764991607708
1861_at 5.76165095726385

Total number of rows: 22283

Table truncated, full table size 605 Kbytes.




Supplementary file Size Download File type/resource
GSM291953.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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