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Sample GSM324265 Query DataSets for GSM324265
Status Public on Sep 19, 2009
Title IPA220_day2
Sample type RNA
 
Channel 1
Source name Gastric cell line treated with siRNA UPF-1
Organism Homo sapiens
Characteristics Gastric cell line treated with siRNA UPF-1
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each cell line using the RNeasy kit (Qiagen) including a DNase digestion step, according to the manufacturer’s instructions
Label Cy3
Label protocol 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name Gastric cell line treated with control siRNA
Organism Homo sapiens
Characteristics Gastric cell line treated with control siRNA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each cell line using the RNeasy kit (Qiagen) including a DNase digestion step, according to the manufacturer’s instructions
Label Cy5
Label protocol 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol 825ng of Cy3 and Cy5 labeled cRNA were hybridized for 16 hrs at 65 C (hybridization oven G2545A, Agilent), according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Arrays were scanned at on an Agilent DNA Microarray Scanner using the default settings for 4x44k format two-color arrays.
Description IPA220_day2
Data processing Image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings. All data pre-processing and analysis was performed using the R-Bioconductor package Limma20. A robust Edwards background correction was applied
 
Submission date Sep 25, 2008
Last update date Sep 29, 2008
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL4133
Series (1)
GSE12928 NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of the test (Cy3)/ reference (Cy5) sample

Data table
ID_REF VALUE
1 -0.00509499
2 0.091185202
3 -0.011552993
4 0.096690082
5 0.018519941
6 0.006080199
7 0.132879179
8 0.222634095
9 0.287014684
10 -0.053964789
11 0.220948485
12 -0.318752481
13 -0.132183092
14 0.14223613
15 -0.063477238
16 -0.072043553
17 0.183137479
18 -0.41477764
19 0.299370886
20 0.016601352

Total number of rows: 45015

Table truncated, full table size 796 Kbytes.




Supplementary file Size Download File type/resource
GSM324265.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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