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Sample GSM849880 Query DataSets for GSM849880
Status Public on Dec 17, 2011
Title MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_133574_SIMIN
Sample type RNA
 
Channel 1
Source name Mouse reference
Organism Mus musculus
Characteristics reference: Whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
Extracted molecule total RNA
Extraction protocol Total RNA was purified from 20-30 mg tissue of end-stage tumors using the Qiagen RNeasy Mini Kit according to the manufacturer’s protoco.
Label Cy3
Label protocol Two micrograms of total RNA was reverse transcribed, amplified and labeled using the Low RNA Input Amplification kit (Agilent).
 
Channel 2
Source name MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_133574_SIMIN
Organism Mus musculus
Characteristics test: mammary tumor
Biomaterial provider Karl Simin
Extracted molecule total RNA
Extraction protocol Total RNA was purified from 20-30 mg tissue of end-stage tumors using the Qiagen RNeasy Mini Kit according to the manufacturer’s protoco.
Label Cy5
Label protocol Two micrograms of total RNA was reverse transcribed, amplified and labeled using the Low RNA Input Amplification kit (Agilent).
 
 
Hybridization protocol The amplified sample and reference were co-hybridized overnight to Agilent Mouse Oligo Microarrays (G4121A) according the manufacturer's protocol.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner.
Description MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_133574_SIMIN
Data processing Image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software. Data for both channels were Lowess-normalized and then log(2) ratio was taken.
 
Submission date Dec 15, 2011
Last update date Dec 17, 2011
Contact name Karl Simin
E-mail(s) karl.simin@umassmed.edu
Organization name UMass Medical School
Street address 364 Plantation St.
City Worcester
State/province MA
ZIP/Postal code 01606
Country USA
 
Platform ID GPL891
Series (1)
GSE34479 Cooperativity of Rb, Brca1, and p53 and malignant breast cancer evolution

Data table header descriptions
ID_REF
VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN (flagged values removed)

Data table
ID_REF VALUE
1 -0.01
2 -0.203
3 0.306
4 0.034
5 0.458
6 -3.006
7 0.341
8 -0.593
9 0.106
10 -0.18
11 1.301
12 0.171
13 0.062
14 0.248
15 1.703
16 -0.061
17 0.282
18 -0.612
19 0.332
20 -0.148

Total number of rows: 22575

Table truncated, full table size 261 Kbytes.




Supplementary file Size Download File type/resource
GSM849880_43779.txt.gz 798.8 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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