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Sample GSM3954346 Query DataSets for GSM3954346
Status Public on Oct 11, 2019
Title DU145 radioresistant vs. Normal
Sample type genomic
 
Channel 1
Source name Radioresistant DU145
Organism Homo sapiens
Characteristics cell line: derived from DU145
phenotype: radioresistant
Sex: Male
Treatment protocol Radioresistant sub-line was generated from original (parental) DU145 or LNCaP cell line by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses. Prior to RNA isolation cells were stained with Aldefluor kit (Stem Cell Technologies) and sorted by FACS.
Growth protocol Prostate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the manufacturers recommendations in a humidified 37°C incubator supplemented with 5% CO2. DU145 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) (Sigma-Aldrich) and LNCaP cells in RPMI-1640 medium (Sigma-Aldrich) containing 10% fetal bovine serum (FBS, PAA Laboratories) and 1mM L-glutamine (Sigma-Aldrich).
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cell cultures and normal tumor tissue by phenol:chloroform extraction using standard protocols.
Label Cy3
Label protocol Labeling was done according to the manufacturer‘s instructions with the exception that the labeling of reference and test DNA was reversed.
 
Channel 2
Source name Agilent Euro Male
Organism Homo sapiens
Characteristics tissue: Normal tissue
Sex: Male
Treatment protocol Radioresistant sub-line was generated from original (parental) DU145 or LNCaP cell line by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses. Prior to RNA isolation cells were stained with Aldefluor kit (Stem Cell Technologies) and sorted by FACS.
Growth protocol Prostate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the manufacturers recommendations in a humidified 37°C incubator supplemented with 5% CO2. DU145 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) (Sigma-Aldrich) and LNCaP cells in RPMI-1640 medium (Sigma-Aldrich) containing 10% fetal bovine serum (FBS, PAA Laboratories) and 1mM L-glutamine (Sigma-Aldrich).
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cell cultures and normal tumor tissue by phenol:chloroform extraction using standard protocols.
Label Cy5
Label protocol Labeling was done according to the manufacturer‘s instructions with the exception that the labeling of reference and test DNA was reversed.
 
 
Hybridization protocol Hybridization was done according to the manufacturer‘s instructions.
Scan protocol Arrays were scanned using the Agilent Technologies Scanner G2505C according to the manufacturer‘s instructions.
Description aCGH profiling
DU145_RR
Data processing Feature extraction and processing of raw data were done with Agilent’s CytoGenomics Editions 2.7 (DU145) and 2.9 (LNCaP).
 
Submission date Jul 18, 2019
Last update date Oct 11, 2019
Contact name Michael Seifert
Organization name TU Dresden
Street address Fetscherstr. 74
City Dresden
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL11357
Series (2)
GSE134498 DNA copy number alteration analysis of radioresistant and radiosensitive prostate cancer cell lines
GSE134500 DNA copy number alteration analysis and gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines

Data table header descriptions
ID_REF
VALUE Log2-ratio of tumor cell line versus normal

Data table
ID_REF VALUE
225922 -0.276783312764499
384535 0.100659805318465
171588 -0.625311016216088
263762 -0.0901428017161145
88377 -0.061510249224957
78171 0.488089426886949
23645 -0.349144334578254
185975 -0.367162597076155
122023 -0.466860830038489
269613 -0.349209240105827
10215 -0.86098427929399
318487 -0.480123132964845
174080 -0.369795785604406
332313 -0.805473808952565
260176 -0.929673722358985
203116 -0.863482499733395
360063 -0.837504755283216
353151 -0.495867346853181
85572 -1.45354618394475
240806 -0.461506400664376

Total number of rows: 294426

Table truncated, full table size 7278 Kbytes.




Supplementary file Size Download File type/resource
GSM3954346_DU145_RR_aCGH.txt.gz 43.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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