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Sample GSM3954348 Query DataSets for GSM3954348
Status Public on Oct 11, 2019
Title LNCaP radioresistant vs. Normal
Sample type genomic
 
Channel 1
Source name Radioresistant LNCaP
Organism Homo sapiens
Characteristics cell line: derived from LNCaP
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
LNCaP_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 -0.771616385135764
384535 -0.49906454706757
171588 -0.880595324245315
263762 0.22436526234073
88377 -0.0270979865116994
78171 0.190266293557393
23645 0.0866754375511818
185975 -0.177802126558427
122023 0.0363271758344303
269613 3.01558025928065
10215 0.0799847977831535
318487 0.0627439681830003
174080 2.64403024698635
332313 1.69283865719108
260176 1.50518697234845
203116 2.10422804078645
360063 2.44099278241808
353151 0.0621706250260968
85572 0.265623757879794
240806 0.493060748206264

Total number of rows: 294426

Table truncated, full table size 7312 Kbytes.




Supplementary file Size Download File type/resource
GSM3954348_LNCaP_RR_aCGH.txt.gz 43.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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