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Series GSE11767 Query DataSets for GSE11767
Status Public on Jun 13, 2008
Title Gene expression profiling of fibroblasts and lymphoblastoid cells derived from four individuals
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Fibroblasts and lymphoblastoid cells (LCLs) are the most widely used cells in genetic, genomic, and transcriptomic studies in relation to human diseases. Examining the gene expression patterns in these two cell types will provide valuable information regarding the validity of using them to study gene expression related to various human diseases.
Fibroblasts and LCLs from four members of the Old Order Amish family 884 were purchased from Coriell cell repositories (Coriell Institute for Medical Research, Camden, NJ). We used microarrays to profile the patterns of gene expression in these eight cell lines. By employing the PennCNV algorithm to the Illumina HumanHap550 SNP genotyping data, we detected 13 Copy Number Variants (CNV) that exist in these four individuals. CNV-expression association analysis revealed that seven of these 13 CNVs were associated with the expression of genes within or near (<2Mb sweep) these CNVs at a nominal regression P value of 0.05.
 
Overall design Fibroblast GM05930 and LCL GM05931 were from individual GM05930/5931, fibroblast GM05932 and LCL GM05933 were from individual GM05932/5933, fibroblast GM05934 and LCL GM05935 were from individual GM05934/5935, fibroblast GM05936 and LCL GM05937 were from individual GM05936/5937. These four individuals are siblings within a large sibship; two of them (GM05932/5933 and GM05934/5935) have bipolar type I disorder (BPI). Five μg of total RNA from each cell line was subjected to microarray experiments using HG U133A 2.0 Array (Affymetrix, Santa Clara, CA). Affymetrix Microarray Suite 5.0 was used to quantitate expression levels and assign Calls (Flags of present, marginal, and absent) for each probe set. The CEL files were used to generate normalized expression data that were corrected by the GCRMA algorithm in GeneSpring7.2.
 
Contributor(s) Yang S, Bucan M
Citation(s) 19214233
Submission date Jun 12, 2008
Last update date Dec 06, 2018
Contact name Maja Bucan
E-mail(s) bucan@pobox.upenn.edu
Organization name UPENN
Street address 415 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (8)
GSM298008 fibroblast 5930
GSM298009 fibroblast 5932
GSM298010 fibroblast 5934
Relations
BioProject PRJNA105949

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11767_RAW.tar 17.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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