GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1821608 Query DataSets for GSM1821608
Status Public on Jul 01, 2016
Title RP003-reduction
Sample type RNA
Source name mammaplastic reduction
Organism Homo sapiens
Characteristics sample id: RP3
tissue: reduction
er: NA
her2: NA
cohort: cohort_1
age_in_years: NA
bmi: NA
tumor_size_cm: NA
array_scan_date: 2008-10-15
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 RP3
gene expression from mammaplastic reduction
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 16.648
2 6.572
3 6.552
4 6.525
5 6.583
6 6.561
7 6.575
8 6.621
9 6.443
10 6.59
11 6.665
12 7.62
13 7.004
14 9.692
15 6.934
16 12.305
17 6.751
18 7.792
19 14.71
20 6.731

Total number of rows: 45015

Table truncated, full table size 521 Kbytes.

Supplementary file Size Download File type/resource
GSM1821608_RP3_251485027965_S01_GE1_107_Sep09_1_3.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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