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Sample GSM193840 Query DataSets for GSM193840
Status Public on Nov 24, 2008
Title Case 18, DCIS, Grade 2, CGH experiment
Sample type genomic
 
Channel 1
Source name Case 18, 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 18, 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
1 514.8 470.4 -0.140027458210294
2 3012.2 1312.1 0.00286837515806582
3 1597.5 664.7 0.275391720013451
4 1961.1 1264.4 0.278376403240344
5 4108 2639.5 -0.186427663750624
6 1166.5 753.2 0.12596054057766
7 1483 932.3 0.0980920902567544
8 1737.4 1053.7 1.37581184643617
9 2097.4 927.7 -0.546493740345909
10 1255.3 485.3 -1.50133793647608
11 1064.3 704.6 -0.671051164616088
12 1958.8 1393.8 -0.472401071749298
13 1407.5 563.1 -0.251300984374852
14 1291.8 394.5 -0.0759095470132518
15 938.9 453.1 -0.143377617347568
16 703.1 418.1 -0.263948584862733
17 899.3 333.1 -0.523412039097318
18 2319.4 1042.4 -0.85873816138605
19 2325.9 916 -0.956522187494373
20 552.6 287.2 -0.484736802484893

Total number of rows: 36288

Table truncated, full table size 1302 Kbytes.




Supplementary file Size Download File type/resource
GSM193840.txt.gz 595.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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