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Sample GSM267199 Query DataSets for GSM267199
Status Public on Feb 01, 2009
Title IDC6
Sample type genomic
 
Channel 1
Source name IDC without known metastases into axillary lymph nodes
Organism Homo sapiens
Characteristics Microdissected sections of fresh fixed paraffin embedded tissue
Extracted molecule genomic DNA
Extraction protocol DNA extracted using a QIAGEN DNA Mini Kit (QUIAGEN Inc., Canada) after a 72 hr period in lysis buffer at 56°C. DNA from 12 normal lymph nodes was prepared similarly and pooled for the reference sample. The single cell comparative genomic hybridization protocol (SCOMP) was used for genome amplification
Label Cy5
Label protocol 1.0μg of amplified test and reference DNA was mixed with 21.5μl ddH2O and 20μl of 2.5X Random Primer/Reaction Mix Buffer (Invitrogen, www.invitrogen.com), boiled for 5 min. and 5μl of ‘low C’ dNTP mix with either 2.5μl Cy5-dCTP (Amersham Biosciences, USA) for test or Cy3 for the reference DNA with 1μl of Klenow solution, then incubated at 37°C for 2 hrs. The reaction was stopped by adding EDTA, then 450μl of TE pH 7.4 added and the mix loaded onto a micron-30 filter (Fisher/Millipore), spun for 8-10 min. at 10,000 rpm, inverted and spun for 1 min to recover the purified probe.
 
Channel 2
Source name Pooled normal lymph nodes
Organism Homo sapiens
Characteristics Microdissected sections of fresh fixed paraffin embedded tissue
Extracted molecule genomic DNA
Extraction protocol DNA extracted using a QIAGEN DNA Mini Kit (QUIAGEN Inc., Canada) after a 72 hr period in lysis buffer at 56°C. DNA from 12 normal lymph nodes was prepared similarly and pooled for the reference sample. The single cell comparative genomic hybridization protocol (SCOMP) was used for genome amplification
Label Cy3
Label protocol 1.0μg of amplified test and reference DNA was mixed with 21.5μl ddH2O and 20μl of 2.5X Random Primer/Reaction Mix Buffer (Invitrogen, www.invitrogen.com), boiled for 5 min. and 5μl of ‘low C’ dNTP mix with either 2.5μl Cy5-dCTP (Amersham Biosciences, USA) for test or Cy3 for the reference DNA with 1μl of Klenow solution, then incubated at 37°C for 2 hrs. The reaction was stopped by adding EDTA, then 450μl of TE pH 7.4 added and the mix loaded onto a micron-30 filter (Fisher/Millipore), spun for 8-10 min. at 10,000 rpm, inverted and spun for 1 min to recover the purified probe.
 
 
Hybridization protocol Labeled products were combined, 80μg of Human Cot-1 DNA and 200mg of yeast tRNA (Invitrogen) were added. The mixture was concentrated in a speed-vac at 37°C down to 10μl and resuspended in 80μl of DIG Easy Hybe buffer (Roche, Switzerland), denatured at 100°C for 1.5 min., cooled on ice and incubated for 30 min at 37°C, then hybridized to 19K human cDNA arrays (University Health Network Microarray Centre, Toronto, Canada, www.microarrays.ca) for 16 hours at 42°C.
Scan protocol GenePix 4000B slide scanner and GenePix Pro 6.0 software package (Molecular Devices, California, USA)
Description run in duplicate
Data processing Samples run in duplicate, Log2 ratios of duplicates averaged, filtered to exclude cDNA clones without mapping info and those spots flagged as anomalous, cenetered by the median and scale normalized.
 
Submission date Feb 21, 2008
Last update date Feb 28, 2008
Contact name Susan Done
E-mail(s) sdone@uhnres.utoronto.ca
Organization name Ontario Cancer Institute
Street address 610 University Ave
City Toronto
ZIP/Postal code M5G2M9
Country Canada
 
Platform ID GPL6514
Series (1)
GSE10600 aCGH study of invasive duct carcinoma (IDC) of the breast without axillary lymph node LN and with sentinel LN metastasis

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3)(test/pooled)
INV_VALUE normalized log2 ratio (Cy3/Cy5)

Data table
ID_REF VALUE INV_VALUE
1 0.0645377 -0.06453774
2 0.565209 -0.565209155
3 0.520278 -0.520278087
4 0.695494 -0.69549355
5 -0.0446588 0.044658833
6 0.0317612 -0.031761173
7 0.356899 -0.356898662
8 0.407178 -0.407177656
9 0.407805 -0.407804818
10 0.0632409 -0.063240853
11 1.10372 -1.103716552
12 0.792955 -0.79295537
13 0.743512 -0.743511842
14 0.124605 -0.12460461
15 0.137644 -0.137643565
16 0.567894 -0.567893811
17 -0.839476 0.839475932
18 0.369589 -0.369589168
19 0.186428 -0.186428487
20 -0.206093 0.206093018

Total number of rows: 9697

Table truncated, full table size 253 Kbytes.




Supplementary file Size Download File type/resource
GSM267199_IDC6a.norm_parsed.gpr.gz 782.0 Kb (ftp)(http) GPR
GSM267199_IDC6b.norm_parsed.gpr.gz 778.4 Kb (ftp)(http) GPR
Processed data included within Sample table

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