NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1821545 Query DataSets for GSM1821545
Status Public on Jul 01, 2016
Title CM128-normal
Sample type RNA
 
Source name breast tissue adjacent to tumor
Organism Homo sapiens
Characteristics sample id: CM128N
tissue: normal
er: pos
her2: neg
cohort: cohort_1
age_in_years: 86
bmi: NA
tumor_size_cm: 3.1
array_scan_date: 2010-11-11
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 CM128N
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. 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
ID_REF
VALUE log2 quantile normalized signal intensity

Data table
ID_REF VALUE
1 16.301
2 6.676
3 6.606
4 null
5 null
6 null
7 6.57
8 6.633
9 6.754
10 6.693
11 null
12 7.583
13 null
14 10.574
15 6.815
16 12.657
17 6.949
18 null
19 null
20 6.966

Total number of rows: 45015

Table truncated, full table size 522 Kbytes.




Supplementary file Size Download File type/resource
GSM1821545_128N_251485046071_S01_GE1_107_Sep09_1_2.txt.gz 8.7 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap