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Sample GSM193829 Query DataSets for GSM193829
Status Public on Nov 24, 2008
Title Case 8, DCIS, Grade 2, CGH experiment
Sample type genomic
 
Channel 1
Source name Case 8, DCIS, Grade 2, CGH experiment
Organism Homo sapiens
Characteristics Sample Type:DCIS;Grade:2
Extracted molecule genomic DNA
Extraction protocol DCIS foci were isolated from 10 micrometer serial frozen tissue sections by laser capture microdissection (PALM Microlaser Technologies AG, Bernried, Germany), guided by interval sections stained with haematoxylin and eosin. In addition, LCIS and co-existing areas of atypical ductal hyperplasia (ADH), proliferative disease without atypia (PDWA) and benign epithelium were sampled from a proportion of cases. For in situ lesions care was taken to capture pure intraduct cell populations. Benign epithelium samples were lobular tissue collected with intralobular stroma.

DNA was extracted from laser microdissected material using the QIAamp DNA Micro Kit (Qiagen Inc., Valencia, CA, USA) and quantitated using the PicoGreen dsDNA Quantitation Reagent (Molecular Probes) both according to the manufacturers instructions. Ten nanograms of DNA was amplified using the GenomiPhi DNA Amplification Kit (Amersham Biosciences, Piscataway, NJ, NY) according to the manufacturer’s instructions.
Label Cy3
Label protocol DNA was labelled with the Bioprime Kit (Invitrogen) using a modified protocol. Briefly, 3 micrograms of amplified test and reference DNA were directly labelled with either Cy3-dUTP or Cy5-dUTP (see Supplementary Methods for detailed description of labelling protocol). Samples were hybridised to the same oligonucleotide microarrays used for gene expression profiling.
 
Channel 2
Source name Promega Normal male genomic DNA
Organism Homo sapiens
Characteristics Promega Normal male DNA
Extracted molecule genomic DNA
Extraction protocol DCIS foci were isolated from 10 micrometer serial frozen tissue sections by laser capture microdissection (PALM Microlaser Technologies AG, Bernried, Germany), guided by interval sections stained with haematoxylin and eosin. In addition, LCIS and co-existing areas of atypical ductal hyperplasia (ADH), proliferative disease without atypia (PDWA) and benign epithelium were sampled from a proportion of cases. For in situ lesions care was taken to capture pure intraduct cell populations. Benign epithelium samples were lobular tissue collected with intralobular stroma.

DNA was extracted from laser microdissected material using the QIAamp DNA Micro Kit (Qiagen Inc., Valencia, CA, USA) and quantitated using the PicoGreen dsDNA Quantitation Reagent (Molecular Probes) both according to the manufacturers instructions. Ten nanograms of DNA was amplified using the GenomiPhi DNA Amplification Kit (Amersham Biosciences, Piscataway, NJ, NY) according to the manufacturer’s instructions.
Label Cy5
Label protocol DNA was labelled with the Bioprime Kit (Invitrogen) using a modified protocol. Briefly, 3 micrograms of amplified test and reference DNA were directly labelled with either Cy3-dUTP or Cy5-dUTP (see Supplementary Methods for detailed description of labelling protocol). Samples were hybridised to the same oligonucleotide microarrays used for gene expression profiling.
 
 
Hybridization protocol See label protocol
Scan protocol Agilent scanner
Description Case 8, DCIS, Grade 2, CGH experiment
Data processing Median-centered Log2 ratio
 
Submission date May 23, 2007
Last update date Nov 18, 2008
Contact name Sean Davis
E-mail(s) sdavis2@mail.nih.gov
Phone 301-435-2652
Organization name National Cancer Institute
Lab Genetics Branch
Street address 37 Convent Drive, Room 6138
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL5326
Series (1)
GSE7882 Gene Expression and Comparative Genomic Hybridization of Ductal Carcinoma In Situ of the Breast

Data table header descriptions
ID_REF ID in platform
Red Intensity Background-subtracted Red Intensity
Green Intensity Background-subtracted Green Intensity
VALUE Log2 Ratio

Data table
ID_REF Red Intensity Green Intensity VALUE
1 394.7 329.7 0.146312960266123
2 2773.4 1291 0.908222590787245
3 1245 613.5 0.437713904437246
4 873.1 835.8 0.525137372442764
5 4132.9 2312.9 -0.556085519621675
6 985.8 642.2 -0.76367971779808
7 691.1 544.7 -0.0788445085628346
8 2261.8 914.9 -0.367361642168204
9 1814.3 785.9 -0.429241790184493
10 868.2 424.1 -1.96990936186842
11 1096.4 712.3 -0.898696784846278
12 1295 952.1 0.111686535801608
13 890.8 401.1 0.26453589185061
14 1619.4 412.5 -0.386442926486685
15 657.2 459.6 -0.131922343119745
16 462.2 329.1 -0.713325381334423
17 578.6 259.9 -1.74562407873774
18 1606.8 949.8 -1.86446673782729
19 2642.1 1082 -1.81334673375353
20 556.2 410 0.6120197868964

Total number of rows: 36288

Table truncated, full table size 1281 Kbytes.




Supplementary file Size Download File type/resource
GSM193829.txt.gz 586.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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