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Sample GSM1081729 Query DataSets for GSM1081729
Status Public on Jul 01, 2014
Title M368662_IU
Sample type genomic
 
Channel 1
Source name Gastrointestinal Tissue with active Crohn's Fistula
Organism Homo sapiens
Characteristics Sex: Male
patient age: 21
clinical comments: Large bowel fistula
Treatment protocol Samples were selected from patients presenting with Crohn’s Disease fistulae at Eastern Health Department of Gastroenterology and Hepatology (Arnold Street, Box Hill, Victoria, Australia). The 8 samples used in this study were formalin-fixed paraffin-embedded (FFPE) specimens resected as part of a surgical intervention to remove fistula tissue. To focus on changes within the individual patient we used tissue taken from the same surgery at an uninvolved region of the intestine.
Extracted molecule genomic DNA
Extraction protocol Total gDNA was extracted and RNase treated with the QIAmp® DNA FFPE kit (Qiagen, Australia) following the manufacturer’s instructions. For each sample approximately 8 FFPE sections (20mm x 20mm x 10µm per section) were used. gDNA was further treated using the MiniElute PCR purification kit (Qiagen, Australia) followed by whole genome amplification (WGA) using the Ovation® WGA FFPE System (Nugen, USA). For each WGA 200 ng of starting material was used. The amplified DNA product was purified using the MiniElute PCR purification kit (Qiagen, Australia). Patient samples were interrogated for CNV using 4 x 180K (60-mer) genome-wide microarrays (Agilent Technologies, USA). Sample Quality Analysis, hybridisation and data generation were performed by the Australian Genome Research Facility (WEHI, Melbourne, Australia).
Label Cy3
Label protocol Human gDNA was quality ascertained using the Nanodrop ND-1000 spectrophotometer and standard agarose gel electrophoresis. A total of 500ng was fragmented and labelled using the ULS cydye (Cy3 or Cy5) coupling method (Agilent – 5190-0419). The cydye incorporation was determined using the Nanodrop ND-1000 spectrophotometer.
 
Channel 2
Source name Uninvolved Control Gastrointestinal tissue from same individual as test sample
Organism Homo sapiens
Characteristics Sex: Male
patient age: 21
tissue: uninvolved control tissue for large bowel fistula
Treatment protocol Samples were selected from patients presenting with Crohn’s Disease fistulae at Eastern Health Department of Gastroenterology and Hepatology (Arnold Street, Box Hill, Victoria, Australia). The 8 samples used in this study were formalin-fixed paraffin-embedded (FFPE) specimens resected as part of a surgical intervention to remove fistula tissue. To focus on changes within the individual patient we used tissue taken from the same surgery at an uninvolved region of the intestine.
Extracted molecule genomic DNA
Extraction protocol Total gDNA was extracted and RNase treated with the QIAmp® DNA FFPE kit (Qiagen, Australia) following the manufacturer’s instructions. For each sample approximately 8 FFPE sections (20mm x 20mm x 10µm per section) were used. gDNA was further treated using the MiniElute PCR purification kit (Qiagen, Australia) followed by whole genome amplification (WGA) using the Ovation® WGA FFPE System (Nugen, USA). For each WGA 200 ng of starting material was used. The amplified DNA product was purified using the MiniElute PCR purification kit (Qiagen, Australia). Patient samples were interrogated for CNV using 4 x 180K (60-mer) genome-wide microarrays (Agilent Technologies, USA). Sample Quality Analysis, hybridisation and data generation were performed by the Australian Genome Research Facility (WEHI, Melbourne, Australia).
Label Cy5
Label protocol Human gDNA was quality ascertained using the Nanodrop ND-1000 spectrophotometer and standard agarose gel electrophoresis. A total of 500ng was fragmented and labelled using the ULS cydye (Cy3 or Cy5) coupling method (Agilent – 5190-0419). The cydye incorporation was determined using the Nanodrop ND-1000 spectrophotometer.
 
 
Hybridization protocol The fragmented labelled DNA was then prepared for hybridisation to the Agilent 4x180k Human CGH arrays using the aCGH hybridisation kit (Agilent – 5188-5220) where each hybridisation reaction had a final volume of 110ul. The Agilent hybridisation chambers were prepared according to manufacturer’s instructions. Each sample was loaded on to the Agilent hybridisation gaskets slide which is placed into a hybridisation chamber. The 4x180k array slide was carefully lowered onto the gasket to create a sealed array for each sample. The hybridisation chambers were then placed in a rotating hybridisation oven at 65C for 24 hours.
Scan protocol Scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Description US83403541_252206023757_S01_CGH_107_Sep09_2_1_4
uninvolved control tissue for large bowel fistula
Data processing Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Feb 12, 2013
Last update date Jul 01, 2014
Contact name phillip david parker
Organization name Deakin University
Department Health
Lab CPAN
Street address 221 Burwood Highway
City Burwood
State/province Victoria
ZIP/Postal code 3125
Country Australia
 
Platform ID GPL10123
Series (1)
GSE44275 Analysis of whole-genome copy-number variation in Crohn's disease fistula tissue

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
23 1.53963
24 1.87392
25 1.92947
26 1.94001
27 2.00429
28 1.8481
29 1.93733
30 2.09979
31 2.02286
32 1.72831
33 1.92063
34 2.18414
35 1.73578
36 1.83683
37 2.10065
38 1.97956
39 2.03347
40 1.93586
41 2.06606
42 2.01121

Total number of rows: 174334

Table truncated, full table size 2430 Kbytes.




Supplementary file Size Download File type/resource
GSM1081729_US83403541_252206023757_S01_CGH_107_Sep09_2_1_4.txt.gz 56.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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