NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE8919 Query DataSets for GSE8919
Status Public on Nov 04, 2007
Title A Survey of Genetic Human Cortical Gene Expression
Organism Homo sapiens
Experiment type Expression profiling by array
Summary It is widely assumed that genetic differences in gene expression will underpin much of the differences between individuals and many of the quantitative traits of interest to geneticists. Despite this, there has been little work on genetic variability in human gene expression and almost none in the human brain. This is because the tools for assessing this genetic variability were not available. With whole genome SNP genotyping arrays and whole transcriptome expression arrays, these experiments have now become feasible. We have carried out whole genome genotyping and expression analysis on a series of 193 neuropathologically normal human brain samples using the Affymetrix GeneChip Human Mapping 500K Array Set and Illumina HumanRefseq-8 Expression BeadChip platforms. Here we present data showing that 58% of the transcriptome is cortically expressed in at least 5% of our samples, and of these cortically expressed transcripts 21% have expression profiles that correlate with their genotype. These genetic expression effects should be useful in determining the underlying biology of associations with common diseases of the human brain and in guiding the analysis of the genomic regions involved in the control of normal gene expression.
Keywords: neuropathologically normal cortex
 
Overall design RNA ws isolated from human cortical samples by standard protocols. RNA expression was assessed using the Illumina HumanRefseq-8 Expression BeadChip system. Transcripts that were detected in less than 5% of the series were excluded from our study. All expression profiles were extracted and rank invariant normalized (Workman et al 2002, Shadt et al 2001, Tseng et al 2001) using the BeadStudio software available from Illumina (http://www.illumina.com/pages.ilmn?ID=170).
 
Contributor(s) Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J
Citation(s) 17982457
Submission date Aug 30, 2007
Last update date Mar 17, 2012
Contact name Amanda Myers
Organization name Miller School of Medicine, University of Miami
Department Psychiatry and Behavioral Sciences
Street address 1600 NW 10th Ave
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platforms (1)
GPL2700 Sentrix HumanRef-8 Expression BeadChip
Samples (200)
GSM225652 WGACON-1
GSM225662 WGACON-6
GSM225664 WGACON-7
Relations
BioProject PRJNA102323

Supplementary table header descriptions
GEO accession
Group
Member
gender
age at death
Postmortem interval days
transcripts_detected_rate(24354) Average Transcript detection rate for sample (out of all 24354 probes)
trans_det_rate(14078) Average Transcript detection rate for sample (out of all 14078 brain expressed probes)
exp_hyb_date Date of chip hybridizitation
institute_sample_source Institute from where sample was obtained
brain_region

Data table
GEO accession Group Member gender age at death Postmortem interval transcripts_detected_rate(24354) trans_det_rate(14078) exp_hyb_date institute_sample_source brain_region
GSM225683 WGACON 37 male 82 unknown 0.468 0.808 6/22/2006 B frontal
GSM225684 WGACON 38 female 94 9.75 0.487 0.84 9/7/2006 B frontal
GSM225685 WGACON 40 female 87 3 0.462 0.796 9/7/2006 B frontal
GSM225686 WGACON 42 male 74 unknown 0.497 0.855 6/22/2006 B frontal
GSM225720 WGACON 83 male 76 30 0.386 0.665 3/9/2006 F frontal
GSM225721 WGACON 84 male 75 6 0.457 0.787 2/22/2006 F frontal
GSM225941 WGACON 181 male 77 unknown 0.455 0.781 2/22/2006 J frontal
none WGACON 185 female 74 unknown 0.429 0.737 2/22/2006 J frontal
GSM225942 WGACON 186 male 96 6 0.483 0.829 2/22/2006 K frontal
GSM225943 WGACON 188 female 78 6 0.53 0.901 2/22/2006 K frontal
GSM225944 WGACON 189 male 77 6 0.448 0.767 9/7/2006 K frontal
GSM225949 WGACON 198 female 97 2.75 0.444 0.766 9/13/2006 M frontal
GSM225950 WGACON 199 female 86 2.25 0.518 0.886 6/22/2006 M frontal
GSM225951 WGACON 201 male 77 3.5 0.515 0.877 6/22/2006 M frontal
GSM225952 WGACON 202 male 87 2 0.479 0.826 6/22/2006 M frontal
GSM225953 WGACON 203 female 72 3.75 0.478 0.825 6/22/2006 M frontal
GSM225954 WGACON 204 female 91 4 0.418 0.72 6/22/2006 M frontal
GSM225955 WGACON 205 female 85 1.66 0.471 0.795 9/7/2006 M frontal
GSM225956 WGACON 206 male 88 5 0.485 0.835 6/22/2006 M frontal
GSM225957 WGACON 207 female 86 3.75 0.49 0.845 6/22/2006 M frontal

Total number of rows: 201

Table truncated, full table size 13 Kbytes.




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

Supplementary data files not provided
Raw data not provided for this record
Processed data included within Sample table

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