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Sample GSM474496 Query DataSets for GSM474496
Status Public on Mar 01, 2010
Title human_LIMA_artery_patient2_control
Sample type RNA
 
Source name Human LIMA artery from patient 2, control (unstented)
Organism Homo sapiens
Characteristics gender: male
individual: patient 2
treatment: control
Treatment protocol Thereafter, a bare metal stent (Express2, 2.5 x 16 mm stent, Boston Scientific Corporation, MA, USA) was implanted (1 min, 10 bar) into one of the three LIMA pieces and a paclitaxel-eluting stent (TAXUS Express2 2.5 x 16 mm stent, Boston Scientific Corporation, MA, USA) was implanted into another. The third part was left as unstented control. Forty-eight hours post stent implantation, the stents were removed and the LIMA samples snap frozen in liquid nitrogen.
Growth protocol As part of elective Coronary Artery Bypass Graft Surgery procedures performed at Lund University Hospital, Sweden, tissues containing parts of the LIMA from four coronary artery bypass graft (CABG) patients (68-73 year old males with stable angina and 3-vessel coronary atheroslerosis, two had hypertension, none were diabetic) were collected and stored in DMEM low glucose at 4C. Each LIMA (n=4) was dissected free of surrounding tissues, cut into three equal parts and incubated under tissue culture conditions in serum-free DMEM. All LIMA vessel segments were approximately 2 mm in diameter. The vessel segments were incubated for 24 h to induce quiescence.
Extracted molecule total RNA
Extraction protocol Tissues were homogenized in TRIzol and RNA purified as described in Amisten et al 2008 (PMID 17920662).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Hu133Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description stable angina and 3-vessel coronary atheroslerosis
Data processing The data were analyzed with Expression Console ver.1 using Affymetrix default analysis settings followed by MAS5 as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Nov 23, 2009
Last update date Nov 23, 2009
Contact name Ann-Sofie Albrekt
E-mail(s) ann-sofie.albrekt@immun.lth.se
Phone +46462229818
Organization name Lund University
Street address Solvegatan 19
City Lund
ZIP/Postal code 22184
Country Sweden
 
Platform ID GPL570
Series (1)
GSE19136 Gene expression response to implanted drug (paclitaxel)-eluting or bare metal stents in denuded human LIMA arteries

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 237.8914
AFFX-BioB-M_at 412.6411
AFFX-BioB-3_at 216.9546
AFFX-BioC-5_at 565.6325
AFFX-BioC-3_at 623.524
AFFX-BioDn-5_at 1466.931
AFFX-BioDn-3_at 2685.111
AFFX-CreX-5_at 7289.021
AFFX-CreX-3_at 8852.027
AFFX-DapX-5_at 119.7596
AFFX-DapX-M_at 218.7128
AFFX-DapX-3_at 399.946
AFFX-LysX-5_at 2.716785
AFFX-LysX-M_at 35.21596
AFFX-LysX-3_at 54.7388
AFFX-PheX-5_at 26.1657
AFFX-PheX-M_at 46.49403
AFFX-PheX-3_at 73.672
AFFX-ThrX-5_at 37.22334
AFFX-ThrX-M_at 41.04392

Total number of rows: 54675

Table truncated, full table size 1054 Kbytes.




Supplementary file Size Download File type/resource
GSM474496.CEL.gz 7.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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