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Sample GSM1380218 Query DataSets for GSM1380218
Status Public on May 08, 2014
Title breast EFM192A Mock/AZA Day7
Sample type RNA
 
Channel 1
Source name Control breast EFM192A Day7
Organism Homo sapiens
Characteristics cell line: EFM192A
cell type: breast cancer cell line
time point: Day 7
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 breast EFM192A Day7
Organism Homo sapiens
Characteristics cell line: EFM192A
cell type: breast cancer cell line
time point: Day 7
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 breast EFM192A Mock Day7/EFM192A AZA Day7
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 -0.068453873
13 -0.017427572
14 0.143223089
15 0.00492039
16 0.113323924
17 0.169066601
18 0.008573466
19 0.360198021
20 -0.031042385

Total number of rows: 45015

Table truncated, full table size 791 Kbytes.




Supplementary file Size Download File type/resource
GSM1380218_jhu_251485071039_S01_GE2_107_Sep09_1_3_EFM192A_Mock_Day7_RNA-Cy3_EFM192A_AZA_Day7_RNA-Cy5.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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