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Sample GSM3954349 Query DataSets for GSM3954349
Status Public on Oct 11, 2019
Title LNCaP radiosensitive vs. Normal
Sample type genomic
 
Channel 1
Source name Radiosensitive LNCaP
Organism Homo sapiens
Characteristics cell line: parental LNCaP
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
LNCaP_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 -0.729656585965528
384535 -0.492348595162234
171588 -0.879193850667573
263762 0.0531586008748169
88377 0.0880603758126798
78171 0.257823645131062
23645 0.0487615592564332
185975 -0.210763149857908
122023 -0.0394425467962301
269613 -0.0374233382785096
10215 -0.245178449961277
318487 0.0154965582444428
174080 0.170223206233583
332313 0.0564862301016844
260176 0.307908563369018
203116 -0.0256188090122859
360063 -0.058554971916484
353151 -0.0614693510527346
85572 0.0239701250933223
240806 0.182102636723447

Total number of rows: 294426

Table truncated, full table size 7325 Kbytes.




Supplementary file Size Download File type/resource
GSM3954349_LNCaP_RS_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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