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Sample GSM1380338 Query DataSets for GSM1380338
Status Public on May 08, 2014
Title ovarian OV-167 Mock/AZA Day3
Sample type RNA
 
Channel 1
Source name Control ovarian OV-167 Day3
Organism Homo sapiens
Characteristics cell line: OV-167
cell type: ovarian cancer cell line
time point: Day 3
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol 400 ng total RNA was amplified and labeled using Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.
 
Channel 2
Source name AZA-treated ovarian OV-167 Day3
Organism Homo sapiens
Characteristics cell line: OV-167
cell type: ovarian cancer cell line
time point: Day 3
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol 400 ng total RNA was amplified and labeled using Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.
 
 
Hybridization protocol 825 ng labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.
Scan protocol Arrays were scanned by Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 Software.
Description ovarian OV167 d3 Mock/OV167 d3 AZA
Data processing Data were extracted with Agilent Feature Extraction Software.
 
Submission date May 06, 2014
Last update date May 08, 2014
Contact name Stephen Baylin
E-mail(s) sbaylin@jhmi.edu
Phone 4109558506
Organization name Johns Hopkins UniversityJohns Hopkins Medical Institutions
Department Oncology
Street address 1650 Orleans St CRB I RM 541
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
Platform ID GPL4133
Series (2)
GSE57341 Effect of AZA on gene expression of multiple breast, colon, and ovarian cell lines [expression]
GSE57343 Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers

Data table header descriptions
ID_REF
VALUE normalized log10 ratio representing (reference/test)

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12 0.028799607
13 -0.032266377
14 -0.256932121
15 -0.032609299
16 0.111765545
17 0.100249759
18 -0.01218061
19 0.180545525
20 0.050874944

Total number of rows: 45015

Table truncated, full table size 790 Kbytes.




Supplementary file Size Download File type/resource
GSM1380338_jhu_251485077096_S01_GE2_107_Sep09_1_3_OV167_d3_Mock-Cy3_OV167_d3_AZA-Cy5.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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