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Sample GSM593730 Query DataSets for GSM593730
Status Public on Nov 04, 2010
Title breast tumor part_IDC_rep1 4391
Sample type RNA
 
Channel 1
Source name Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-).
Organism Homo sapiens
Characteristics er/pr/her status: ER(-) PR(-)HER(-)
status: ER(-), PR(-)
gender: female
tissue: primary tumor
Treatment protocol The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.
Growth protocol The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.
Extracted molecule total RNA
Extraction protocol Trizol reagent combined with RNAeasy mini kit
Label Cy5
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0
 
Channel 2
Source name Commercially available.
Organism Homo sapiens
Characteristics sample type: Stratagene's human common reference RNA
Treatment protocol The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.
Growth protocol The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.
Extracted molecule total RNA
Extraction protocol Trizol reagent combined with RNAeasy mini kit
Label Cy3
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0
 
 
Hybridization protocol Agilent Oligo Microarray Kit, hybridization protocol version 5.0
Scan protocol Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.
Description breast tumor part_IDC_rep1

Data processing Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0. The log2 ratio for each gene was centered by subtracting the median across all samples to discriminate the subclass of the dataset.
 
Submission date Sep 14, 2010
Last update date Oct 19, 2011
Contact name Fon-Jou Hsieh
E-mail(s) fjhsieh@ntu.edu.tw
Organization name National Taiwan University
Department Department of obstetrics and gynecology
Street address No. 7, Chung-Shan South Rd
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL887
Series (2)
GSE24124 The inferred mechanisms for prognostic features of signal transducer and activator of transcription 3 in an ER(+) breast cancer model system
GSE32641 Major functional transcriptome of an inferred center regulator of an ER(-) breast cancer model system
Relations
Reanalyzed by GSE33095

Data table header descriptions
ID_REF
VALUE rank-invariant linear LOWESS normalized log2 Ratio (test/ref)

Data table
ID_REF VALUE
1 0.259809989
2 0
3 -0.745214773
4 -0.117333822
5 0.891479267
6 -3.466365528
7 0.013725775
8 -1.345942284
9 -0.496797669
10 0.502136007
11 -0.978334399
12 -2.510028937
13 0.674660343
14 0.019059861
15 1.174358054
16 -0.145063949
17 0
18 0.037759028
20 0
21 0

Total number of rows: 22153

Table truncated, full table size 375 Kbytes.




Supplementary file Size Download File type/resource
GSM593730.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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