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Sample GSM1033598 Query DataSets for GSM1033598
Status Public on Nov 09, 2012
Title Peripheral Blood, MI 5, 14hrs fasting , rep 1
Sample type RNA
Source name Peripheral Blood, case, 14hrs fasting , replicate 1
Organism Homo sapiens
Characteristics tissue: whole blood
gender: male
age (y): 48
disease state: coronary artery disease
Extracted molecule total RNA
Extraction protocol A total of 3ml of peripheral blood was collected in EDTA coated tubes from each participant after overnight fast. Total RNA was extracted from the blood samples using QIAamp RNA Blood mini kit (Qiagen, USA) using the protocol recommended by the manufacturer. For the microarray experiment, the extracted RNA was cleaned up using the RNeasy Mini Elute cleanup kit (Qiagen, USA). RNA was quantified by NanoDrop ND-1000 Spectrophotometer (NanoDrop,Wilmington,DE, USA) , while the quality was determined using a Bioanalyzer 2100 (Agilent Technologies, CA, USA).
Label Cy3
Label protocol cDNA was synthesized from 200ng of total RNA, and cRNA was synthesized from cDNA and incorporated with Cy3-dUTP through in vitro transcription of the cDNA. Labeled probes were purified using RNAeasy mini kit (Qiagen, USA) and Dye incorporation and cRNA yield were verified with the NanoDrop ND-1000 Spectrophotometer and concentrated to the desired volume
Hybridization protocol 5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1ul of 25x Agilent fragmentation buffer and 5ul of 10x Agilent blocking agent following the manufacturer’s instructions. 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent G4851A , human genome G3 Hmn GE 8X60K microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned on the Agilent DNA Microarray Scanner (G2505-64250) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in case samples
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Nov 08, 2012
Last update date Nov 09, 2012
Contact name prathima arvind
Fax 080-27835302
Organization name Thrombosis Research Institute
Department Functional Genomics
Street address #258/A, Bommasandra Industrial Area, Anekal Taluk
City Bangalore
ZIP/Postal code 560099
Country India
Platform ID GPL13607
Series (1)
GSE42148 Global gene expression profile of coronary artery disease in Asian Indians

Data table header descriptions
VALUE Normalized log2 signal intensity

Data table
1 16.780
2 3.944
3 2.756
4 8.351
5 5.583
6 8.132
7 9.716
8 12.359
9 2.961
10 4.032
11 2.019
12 13.160
13 9.949
14 9.363
15 8.327
16 2.019
17 6.146
18 2.019
19 3.923
20 11.795

Total number of rows: 62972

Table truncated, full table size 739 Kbytes.

Supplementary file Size Download File type/resource
GSM1033598_US90403632_252800411153_S01_GE1_107_Sep09_1_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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