NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM188748 Query DataSets for GSM188748
Status Public on Jun 06, 2007
Title GM19172
Sample type RNA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics Coriell cell line repository identifier: GM19172
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM19172
Yoruban sample
Gender: Female
Associated family: Y047-2
Family relationship: mother
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19172
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 dbSNP in Probe Filtering and Background Correction Protocol: The start and end coordinates of all probes of the Exon array were queried against the human genome (hg17). The coordinates for all SNPs were then queried in the dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP/) (release 126) and then based on location, we identified probes harboring SNPs. In total, ~400,000 probes contained SNPs within their structure. Of the ~1.4 million probesets of the exon array, 255,676 contained at least one probe with SNP. Among these affected probesets, 105,000 harbored 2 or more probes with SNPs. Resulting probe signal intensity files were filtered by removing this group of 105,000probesets. After filtering, individual probe intensities were background corrected by subtracting the median intensity of a population of non-genomic probes with the same GC content to account for any non-specific hybridization. The resulting probe signal intensities were sketch quantile normalized over all 176 samples and gene-level expressions were summarized using the robust multi-array average (RMA) method with signals generated on a core set of exons. A constant of 16 was added to all probeset intensities for variance stabilization and summarized signals were then log2 transformed with a median polish.
 
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 (2)
GSE7761 Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach
GSE7851 Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations
Relations
Alternative to GSM188930
Alternative to GSM245557

Data table header descriptions
ID_REF Transcript_probeset_id
VALUE Probe signal intensities were sketch quantile normalized over all 176 samples and gene-level expressions were summarized using the robust multi-array average (RMA) method with signals generated on a core set of exons. A constant of 16 was added to all probeset intensities for variance stabilization and summarized signals were then log2 transformed with a median polish.

Data table
ID_REF VALUE
3881686 9.175483485
2672712 8.097818099
2842570 8.963496731
3526544 6.763357556
2902531 5.957119114
2402942 6.266202447
3382216 5.220086663
3771800 10.41698337
2427469 4.71715836
2392945 7.171702916
2453006 6.060820685
2562821 7.596029031
3416651 6.288426482
3552083 6.303956255
3721851 8.253683412
2477438 4.885443508
2926969 4.565562697
3026969 6.822400079
3442176 7.849708185
3796335 8.07099815

Total number of rows: 17745

Table truncated, full table size 344 Kbytes.




Supplementary file Size Download File type/resource
GSM188748.CEL.gz 38.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap