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Sample GSM3954347 Query DataSets for GSM3954347
Status Public on Oct 11, 2019
Title DU145 radiosensitive vs. Normal
Sample type genomic
 
Channel 1
Source name Radiosensitive DU145
Organism Homo sapiens
Characteristics cell line: parental DU145
phenotype: radiosensitive
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_RS
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 -0.460645901539515
384535 -0.0863325523408316
171588 -0.500722876154754
263762 -0.0561160094328691
88377 -0.142092139164506
78171 0.117269406386325
23645 -0.225239652754769
185975 -0.394018733858861
122023 -0.21856485248908
269613 -0.239197159555349
10215 -0.301525700278358
318487 -0.259924383313162
174080 -0.365527857095433
332313 -0.467664351233755
260176 -0.302951580524162
203116 -0.425031416845908
360063 -0.545468657197886
353151 -0.352204589973244
85572 -0.64780310803856
240806 -0.316981413073458

Total number of rows: 294426

Table truncated, full table size 7289 Kbytes.




Supplementary file Size Download File type/resource
GSM3954347_DU145_RS_aCGH.txt.gz 43.9 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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