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Sample GSM378116 Query DataSets for GSM378116
Status Public on Mar 06, 2009
Title Breast Cancer_Pre-Treatment_Patient 307
Sample type genomic
 
Channel 1
Source name patient germline DNA
Organism Homo sapiens
Characteristics tissue: whole blood or cell pellets
Treatment protocol Samples were taken from patients prior to treatment.
Growth protocol Tissue biopsies were frozen in oct and stored in liquid nitrogen.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using Qiagen DNA Isolation kits.
Label Cy3
Label protocol Agilent Genomic DNA Labeling kit.
 
Channel 2
Source name DNA from patient breast biopsy
Organism Homo sapiens
Characteristics disease: breast cancer
tissue: breast
tumor cellularity: at least 70%
storage: oct embedded
Treatment protocol Samples were taken from patients prior to treatment.
Growth protocol Tissue biopsies were frozen in oct and stored in liquid nitrogen.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using Qiagen DNA Isolation kits.
Label Cy5
Label protocol Agilent Genomic DNA Labeling kit.
 
 
Hybridization protocol Agilent Direct Method.
Scan protocol Agilent Scan Control Software.
Description 307B
Data processing A process control algorithm was used to flag log cgh probe ratios and calculate Z' scores. Z' scores >=2 were used to identify probable copy gains and Z' scores <= -2 were used to identify probable copy loss. Z' scores for the genes of interest are available on the Series record.
 
Submission date Mar 05, 2009
Last update date Dec 26, 2023
Contact name Cynthia Ma
E-mail(s) cynthiaxma@wustl.edu
Phone 3143628903
Organization name Washington University
Department Medical Oncology
Lab Dr. Cynthia Ma Lab
Street address 4515 Mckinley, 4515 Mckinley
City st louis
State/province Missouri
ZIP/Postal code 63627
Country USA
 
Platform ID GPL4091
Series (2)
GSE15130 PIK3CB aCGH Patient Results
GSE15134 PI3K inhibition in ER+ breast cancer microarray data

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 3.362306728e-002
2 0.000000000e+000
3 0.000000000e+000
4 9.735262131e-003
5 -2.974133581e-002
6 1.714018117e-001
7 4.613369933e-002
8 1.806089008e-002
9 3.207614017e-002
10 -1.663354451e-002
11 -6.432063966e-002
12 1.569619256e-001
13 -2.176081269e-002
14 1.076811967e-001
15 -3.059989667e-002
16 1.259169432e-002
17 3.560294103e-002
18 -6.708246842e-002
19 -6.839794768e-002
20 -4.022518285e-002

Total number of rows: 243430

Table truncated, full table size 5729 Kbytes.




Supplementary file Size Download File type/resource
GSM378116.txt.gz 67.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record
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