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Sample GSM2892269 Query DataSets for GSM2892269
Status Public on Mar 01, 2018
Title PatientE_2000_AN
Sample type genomic
 
Channel 1
Source name Prostate
Organism Homo sapiens
Characteristics amplification: phi29
year: 2000
ploidy: AN
Growth protocol Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C 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 pooled 46, XX DNA (Promega, Madison, WI)
Organism Homo sapiens
Characteristics amplification: phi29
sample type: reference
Growth protocol Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C 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 microarray slides were scanned using an Agilent G2505C DNA 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 analysed using the Limma package in the R environment. With minimum background correction and printtiploess normalization.
 
Submission date Dec 18, 2017
Last update date Mar 01, 2018
Contact name Joël Roman Federer-Gsponer
Organization name University Hospital Basel
Department Department of Pathology
Street address Tangentenweg 34
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL9777
Series (1)
GSE108203 Tumor evolution in the context of castration resistance in prostate cancer

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference.

Data table
ID_REF VALUE
1 -0.19307891
2 1.896474076
3 2.420062164
4 0.066933186
5 0.957165591
6 -1.42473459
7 0.980941681
8 0.827230848
9 -0.182916088
10 1.088225044
11 0.479223212
12 -0.692831479
13 -1.247723394
14 -1.529080235
15 0.728546875
16 1.026226622
17 -0.567396786
18 0.349920161
19 1.258312692
20 0.426113669

Total number of rows: 420288

Table truncated, full table size 7849 Kbytes.




Supplementary file Size Download File type/resource
GSM2892269_US12302336_252185016859_S01_CGH_107_Sep09_1_1.txt.gz 44.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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