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Sample GSM3954358 Query DataSets for GSM3954358
Status Public on Oct 11, 2019
Title LNCaP radioresistant replicate 3
Sample type RNA
 
Source name Radioresistant LNCaP
Organism Homo sapiens
Characteristics cell line: derived from LNCaP
phenotype: Radioresistant
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 total RNA
Extraction protocol RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C wit GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)
Description Gene expression profiling
Data processing Quantile normalization was used to normalize the hybridization signals (gProcessedSignal). This was done separately for all DU145 and LNCaP samples to account for differences between DU145 and 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 GPL17077
Series (2)
GSE134499 Comparative analysis of gene expression profiles comparing radioresistant to 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 of normalized hybridization signal

Data table
ID_REF VALUE
A_19_P00315452 2.0264992489751
A_19_P00315459 6.91738329126969
A_19_P00315482 3.51504491909304
A_19_P00315492 4.38123130967663
A_19_P00315493 1.94523790868094
A_19_P00315502 4.09846389448587
A_19_P00315506 7.95790937338854
A_19_P00315518 2.02893131340298
A_19_P00315519 1.81674468181285
A_19_P00315524 4.62025016094922
A_19_P00315528 1.90131819712053
A_19_P00315529 2.46230772031354
A_19_P00315538 1.81327543234571
A_19_P00315541 1.93746267842903
A_19_P00315543 6.89877821057793
A_19_P00315550 7.39305510943037
A_19_P00315551 6.22744213229801
A_19_P00315554 1.9547617611418
A_19_P00315581 11.3895577947112
A_19_P00315583 3.12219548170911

Total number of rows: 50579

Table truncated, full table size 1502 Kbytes.




Supplementary file Size Download File type/resource
GSM3954358_LNCaP_RR_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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