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Sample GSM1821560 Query DataSets for GSM1821560
Status Public on Jul 01, 2016
Title CM009-tumor
Sample type RNA
Source name breast adenocarcinoma
Organism Homo sapiens
Characteristics sample id: CM9T
tissue: tumor
er: pos
her2: neg
cohort: cohort_1
age_in_years: 39
bmi: 21
tumor_size_cm: 4.5
array_scan_date: 2008-09-23
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 G2505B
Description CM9T
gene expression from breast adenocarcinoma
Data processing Expression data were background-corrected and quantile normalized using limma in R. Features flagged as non-uniform or below-background were excluded. Batch effect from Scan Date was corrected using ComBat.
Submission date Jul 14, 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 GPL4133
Series (2)
GSE70905 Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_1]
GSE70951 Paired Breast Adenocarcinoma and Adjacent Normal tissue

Data table header descriptions
VALUE log2 quantile normalized signal intensity

Data table
1 null
2 null
3 6.731
4 6.839
5 6.74
6 6.59
7 6.635
8 6.648
9 6.821
10 6.651
11 6.721
12 8.563
13 7.261
14 9.373
15 6.799
16 13.784
17 6.917
18 8.178
19 14.56
20 7.092

Total number of rows: 45015

Table truncated, full table size 521 Kbytes.

Supplementary file Size Download File type/resource
GSM1821560_9T_251485027975_S01_GE1_107_Sep09_1_2.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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