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Sample GSM1823825 Query DataSets for GSM1823825
Status Public on Jul 01, 2016
Title CM435-normal
Sample type RNA
Source name breast tissue adjacent to tumor
Organism Homo sapiens
Characteristics sample id: CM435.N.c2
tissue: normal
er: neg
her2: neg
cohort: cohort_2
age_in_years: 43
bmi: 24.8
tumor_size_cm: 1.5
array_scan_date: 2013-02-13
Extracted molecule total RNA
Extraction protocol Tissue samples were stabilized with RNAlater at the time of surgery. After surgery, RNAlater was removed and tissue was stored at -80°C. RNA was extracted with TRIzol (Invitrogen, Carlsbad CA) or TRI reagent (Life Technologies, Gaithersburg MD) and further purified on RNeasy columns in combination with the RNeasy Mini Kit (Qiagen, Valenca, CA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE) and quality checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
Hybridization protocol Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
Scan protocol Scanning on Agilent scanner G2505C
Description CM435.N.c2
gene expression from breast tissue adjacent to tumor
Data processing Expression data were background-corrected and quantile normalized using limma in R. Features flagged as non-uniform or below-background were excluded.
Submission date Jul 15, 2015
Last update date Jul 01, 2016
Contact name David Quigley
Organization name UCSF
Department Helen Diller Comprehensive Cancer Center
Lab Ashworth Lab
Street address 1450 Third St. Room 207
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL13607
Series (2)
GSE70947 Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_2]
GSE70951 Paired Breast Adenocarcinoma and Adjacent Normal tissue

Data table header descriptions
VALUE log2 quantile normalized signal intensity

Data table
1 16.245
2 6.022
3 5.955
4 9.09
5 8.119
6 7.123
7 11.741
8 9.441
9 6.56
10 7.009
11 6.399
12 11.402
13 11.174
14 8.226
15 7.147
16 5.928
17 7.402
18 6.065
19 6.238
20 9.424

Total number of rows: 62976

Table truncated, full table size 719 Kbytes.

Supplementary file Size Download File type/resource
GSM1823825_252800417017_S01_GE1_107_Sep09_2_1.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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