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Sample GSM1380251 Query DataSets for GSM1380251
Status Public on May 08, 2014
Title colon CACO2 Mock/AZA Day14
Sample type RNA
 
Channel 1
Source name Control colon CACO2 Day14
Organism Homo sapiens
Characteristics cell line: CACO2
cell type: colon cancer cell line
time point: Day 14
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 colon CACO2 Day14
Organism Homo sapiens
Characteristics cell line: CACO2
cell type: colon cancer cell line
time point: Day 14
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 colon CACO2_Mock_D14/CACO2_Aza_D14
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 0.01572074
13 0.194043459
14 -0.020134794
15 0.111927397
16 -0.02714414
17 0.180705006
18 -0.127156399
19 0.598797499
20 0.382401055

Total number of rows: 45015

Table truncated, full table size 791 Kbytes.




Supplementary file Size Download File type/resource
GSM1380251_jhu_251485070598_S01_GE2_107_Sep09_1_4_CACO2_Mock_D14-Cy3_CACO2_Aza_D14-Cy5.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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