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Sample GSM1348305 Query DataSets for GSM1348305
Status Public on Oct 17, 2014
Title PC3, rep2 [set 2]
Sample type RNA
 
Source name PC3 prostate cancer cells
Organism Homo sapiens
Characteristics cell line: PC3
cell type: Prostate Cancer cells
Treatment protocol After prostatectomy, the pathologist examined tumor part and adjacent normal part of prostate. Two biopsy needle amount tissues were obtained from 10 pair of samples and tissues were immersed in RNAlater (Ambion, Austin TX). After 24 hr at 4C, samples were stored at -80C.
Growth protocol Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. Cells were harvested at confluency 70%.
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared using the RNeasy kit (QAIGEN, Valencia CA) following the manufacturer's recommendations. The prostate epithelial cell RNA was purchased from Biochain (Cat # R1234201-50, Newark CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol The samples were labeled using One Color Quick Amp Labeling kit following Manufacturer's (Agilent Technologies) protocol. The protocol incorporates Cyanine 3-CTP to the target (aRNA) material.
 
Hybridization protocol The fragmented and labeled aRNA (600ng) were hybridized onto Agilent’s 8x60k format Human LINC RNA array using Agilent Technologies Gene Hybridization protocol.
Scan protocol The arrays were scanned using Agilent's C Scanner following the scan protocol
Description PC3-2
Gene expression in androgen insensitive prostate cancer cells
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain mean signals which were background corrected, log transformed and normalized using using Limma package.
 
Submission date Mar 14, 2014
Last update date Apr 23, 2018
Contact name Jian-Liang Li
Organization name NIEHS
Street address 111 TW Alexander Dr
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL16699
Series (2)
GSE55909 Long noncoding RNA as putative biomarkers for protstate cancer detection [Set 2]
GSE55910 Long noncoding RNA as putative biomarkers for protstate cancer detection
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Log2-transformed normalized signal intensity

Data table
ID_REF VALUE
50168 5.957646712
21536 7.749543027
29227 6.061587208
2485 6.091570907
41993 9.296662713
20928 6.897425061
44908 9.72850396
40143 5.94013125
34800 5.785191098
12324 6.18705093
16599 6.019752685
1985 5.905130245
3006 6.559338888
55937 6.022552314
9151 6.538050254
62423 8.016517886
60614 8.567449922
55235 6.025544705
14519 12.30644395
45622 6.912392223

Total number of rows: 58717

Table truncated, full table size 1015 Kbytes.




Supplementary file Size Download File type/resource
GSM1348305_PC_0953_1_3.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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