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Sample GSM1823814 Query DataSets for GSM1823814
Status Public on Jul 01, 2016
Title CM411-normal
Sample type RNA
Source name breast tissue adjacent to tumor
Organism Homo sapiens
Characteristics sample id: CM411.N.c2
tissue: normal
er: pos
her2: pos
cohort: cohort_2
age_in_years: 48.8
bmi: 38.6
tumor_size_cm: 2.1
array_scan_date: 2012-10-10
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 CM411.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
5 7.636
6 6.778
7 11.54
8 8.133
9 5.084
10 6.454
11 5.004
12 11.317
13 10.674
14 7.264
15 9.407
16 4.983
17 6.599
18 4.113
19 5.121
20 9.31

Total number of rows: 62976

Table truncated, full table size 726 Kbytes.

Supplementary file Size Download File type/resource
GSM1823814_252800416925_S01_GE1_107_Sep09_2_1.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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