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Sample GSM1380242 Query DataSets for GSM1380242
Status Public on May 08, 2014
Title breast MDA436 Mock/AZA Day7
Sample type RNA
 
Channel 1
Source name Control breast MDA436 Day7
Organism Homo sapiens
Characteristics cell line: MDA436
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 MDA436 Day7
Organism Homo sapiens
Characteristics cell line: MDA436
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 MDA436 Mock Day7/MDA436 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 0.01417307
13 -0.111286784
14 -0.193114708
15 0.068709569
16 0.251998292
17 0.086283357
18 -0.116604176
19 0.459507489
20 -0.032186003

Total number of rows: 45015

Table truncated, full table size 790 Kbytes.




Supplementary file Size Download File type/resource
GSM1380242_jhu_251485071079_S01_GE2_107_Sep09_1_3_MDA436_Mock_Day7_RNA-Cy3_MDA436_AZA_Day7_RNA-Cy5.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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