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Sample GSM1821641 Query DataSets for GSM1821641
Status Public on Jul 01, 2016
Title RP058-reduction
Sample type RNA
 
Source name mammaplastic reduction
Organism Homo sapiens
Characteristics sample id: RP58
tissue: reduction
er: NA
her2: NA
cohort: cohort_1
age_in_years: NA
bmi: NA
tumor_size_cm: NA
array_scan_date: 2009-12-16
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 RP58
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
ID_REF
VALUE log2 quantile normalized signal intensity

Data table
ID_REF VALUE
1 null
2 7.355
3 7.042
4 7.302
5 7.299
6 7.215
7 7.493
8 7.301
9 7.205
10 6.958
11 7.31
12 8.017
13 7.682
14 9.09
15 7.766
16 10.652
17 7.619
18 7.734
19 12.741
20 6.898

Total number of rows: 45015

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM1821641_RP58_251485040497_S01_GE1_107_Sep09_1_1.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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