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Sample GSM2412382 Query DataSets for GSM2412382
Status Public on Jan 01, 2018
Title kidney 10y
Sample type genomic
 
Channel 1
Source name Frozen tissue biopsy
Organism Homo sapiens
Characteristics disease state: Urothelial cancer
tissue: tumor (Frozen tissue biopsy)
location: kidney
timepoint: 10y
Treatment protocol None
Growth protocol Tumor samples from the patient from different locations and different timepoints with urothelial carcinoma were either snap-frozen and maintaned at -80 degrees C or FFPE archived until processed for flow sorting
Extracted molecule genomic DNA
Extraction protocol 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care).
Label Cy5
Label protocol A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
 
Channel 2
Source name Reference pooled 46XX
Organism Homo sapiens
Characteristics reference: Normal female genome
Treatment protocol None
Growth protocol Tumor samples from the patient from different locations and different timepoints with urothelial carcinoma were either snap-frozen and maintaned at -80 degrees C or FFPE archived until processed for flow sorting
Extracted molecule genomic DNA
Extraction protocol 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care).
Label Cy3
Label protocol A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
 
 
Hybridization protocol Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol
Scan protocol All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.
Data processing Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visualized and analyzed using DNA Analytics 4.0.85 and the ADM2 step gram algorithm.
For normalization, we applied GC-correction and diploid peak-centralization using the Agilent Workbench 7.0.4.0.
 
Submission date Dec 01, 2016
Last update date Jan 01, 2018
Contact name David Christian M├╝ller
E-mail(s) david.mueller@usb.ch
Organization name University Hospital Basel
Department Institute for Pathology
Street address Sch├Ânbeinstrasse 40
City Basel
ZIP/Postal code 4031
Country Switzerland
 
Platform ID GPL10123
Series (1)
GSE90778 Array-CGH data of aneuploid tumor populations of different urothelial cancer sites in one patient

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

Data table
ID_REF VALUE
1 4.18E-02
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 0.00E+00
13 0.00E+00
14 0.00E+00
15 0.00E+00
16 0.00E+00
17 0.00E+00
18 0.00E+00
19 0.00E+00
20 0.00E+00

Total number of rows: 180880

Table truncated, full table size 2798 Kbytes.




Supplementary file Size Download File type/resource
GSM2412382_US11203904_252206041441_S01_CGH_1010_Sep10_1_2.txt.gz 18.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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