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Sample GSM1249634 Query DataSets for GSM1249634
Status Public on Oct 29, 2013
Title FCHL-CHD patient 4 [GPL94]
Sample type RNA
 
Source name subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4
Organism Homo sapiens
Characteristics chd status: CHD: patient undergoing coronary artery bypass surgery
fchl status: FCHL
tg rsponse to statins status: reduced TG
Treatment protocol Tissue was excised from upper abdominal subcutaneous region and immediately snap-frozen in the operating room.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, cRNA was hybridized to Affymetrix Genechips for 16 hr at 45°C and GeneChips were washed and stained in an Affymetrix Fluidics Station according to standard Affymetrix protocols.
Scan protocol Performed according to standard Affymetrix protocols.
Description Gene expression data from upper abdominal subcutaneous adipose tissue of CHD patient with FCHL
Data processing Image-files were analysed with Bioconductor in R using the pmonly and rma algorithms implemented in expresso. Normalisation of chip sets was performed by the ‘quantiles’ approach and probe sets summarised using ‘median polish’. Probes were labelled ‘absent’ or ‘present’ according to the Affymetrix Microarray Suite 5.0 algorithm. Probes returning absent calls in all cel files were removed. Differences in probe values were detected by the Significance Analysis of Microarray (SAM) procedure at specified false detection rates (FDR).
 
Submission date Oct 23, 2013
Last update date Oct 29, 2013
Contact name Carol Shoulders
Organization name QMUL
Department Centre for Endocrinology
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL94
Series (1)
GSE51625 Expression data from human abdominal, subcutaneous adipose tissue

Data table header descriptions
ID_REF
VALUE Rma quantile normalized MAS5.0 signal intensity

Data table
ID_REF VALUE
67020_at
67021_at 4.16581
67023_at
67025_at
67027_at
67029_at
67031_at 3.956529
67033_at
67034_at
67036_at
67037_at
67039_g_at
67041_at
67043_at
67045_r_at
67047_at
67051_r_at 4.129542
67053_at 5.915718
67054_at 5.251851
67056_at

Total number of rows: 12644

Table truncated, full table size 155 Kbytes.




Supplementary file Size Download File type/resource
GSM1249634_18D.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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