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Sample GSM1228084 Query DataSets for GSM1228084
Status Public on Jan 01, 2014
Title SVPs3
Sample type RNA
Source name pericytes
Organism Homo sapiens
Characteristics celltype: SVPs
Extracted molecule total RNA
Extraction protocol RNeasy AllPrep column extraction (Qiagen) using the manufacturers protocols
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.65 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 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 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 immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Sep 11, 2013
Last update date Jan 01, 2014
Contact name Klemens Vierlinger
Organization name AIT
Department HMD
Street address Giefinggasse 4
City Vienna
ZIP/Postal code 1210
Country Austria
Platform ID GPL13607
Series (1)
GSE50758 Gene expression from pericytes and endothelial cells

Data table header descriptions
VALUE background subtracted and spatially detrended processed signal intensities

Data table
1 83570
2 41.5833333333333
3 34.25
4 139.75
5 1089.08333333333
6 86.5
7 4644.45833333333
8 458.666666666667
9 72.3333333333333
10 58.75
11 91.2916666666667
12 610.166666666667
13 756.916666666667
14 168.25
15 7468.66666666667
16 45.8333333333333
17 260.25
18 30.5833333333333
19 202.166666666667
20 1960.75

Total number of rows: 62976

Table truncated, full table size 1164 Kbytes.

Supplementary file Size Download File type/resource
GSM1228084_US83703555_252800414017_S03_GE1_105_Dec08_2_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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