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Sample GSM1380239 Query DataSets for GSM1380239
Status Public on May 08, 2014
Title breast SKBR3 Mock/AZA Day10
Sample type RNA
 
Channel 1
Source name Control breast SKBR3 Day10
Organism Homo sapiens
Characteristics cell line: SKBR3
cell type: breast cancer cell line
time point: Day 10
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 SKBR3 Day10
Organism Homo sapiens
Characteristics cell line: SKBR3
cell type: breast cancer cell line
time point: Day 10
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 SKBR3 Mock Day10/SKBR3 AZA Day10
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 0.188243445
13 -0.09307738
14 0.017610238
15 0.095020557
16 0.444893133
17 0.144880216
18 0.042043498
19 0.233775296
20 0.050972973

Total number of rows: 45015

Table truncated, full table size 790 Kbytes.




Supplementary file Size Download File type/resource
GSM1380239_jhu_251485071078_S01_GE2_107_Sep09_1_4_SKBR3_Mock_Day10_RNA-Cy3_SKBR3_AZA_Day10_RNA-Cy5.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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