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Sample GSM187290 Query DataSets for GSM187290
Status Public on Aug 07, 2007
Title LNCaP_dye
Sample type RNA
 
Channel 1
Source name LNCaP
Organism Homo sapiens
Characteristics prostate cancer cell line, androgen sensitive
Treatment protocol Cells were not treated prior to RNA extraction.
Growth protocol LNCaP was grown in RPMI with 10% fetal bovine serum. C4-2B was grown in T-medium (Invitrogen) with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.
Label Cy3
Label protocol One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name Clontech prostate pool (CPP)
Organism Homo sapiens
Characteristics Commercially available pooled benign prostate tissue total RNA
Treatment protocol Cells were not treated prior to RNA extraction.
Growth protocol LNCaP was grown in RPMI with 10% fetal bovine serum. C4-2B was grown in T-medium (Invitrogen) with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.
Label Cy5
Label protocol One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.
Description na
Data processing Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. Only features passing standard Agilent Feature Extraction filtering on all four arrays were used to identify differentially expressed features between LNCaP and C4-2B
 
Submission date May 03, 2007
Last update date Aug 07, 2007
Contact name Scott Tomlins
E-mail(s) tomlinss@med.umich.edu
Phone 734-615-1417
Organization name University of Michigan
Department Pathology
Lab Chinnaiyan Lab
Street address 1400 E. Medical Center Dr., 5410 CCGC
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL4133
Series (1)
GSE7702 Comparison of the prostate cancer cell line LNCaP and its androgen insensitive derivative C4-2B

Data table header descriptions
ID_REF
VALUE linear-lowess normalized log10 ratio test/reference
INV_VALUE linear-lowess normalized log10 ratio (Cy5 (channel 2) /Cy3 (channel 1)), LogRatio

Data table
ID_REF VALUE INV_VALUE
1 -0.405817 0.4058174286
2 null null
3 null null
4 null null
5 null null
6 null null
7 null null
8 null null
9 null null
10 null null
11 null null
12 1.27327 -1.273268094
13 0.362092 -0.3620923397
14 0.1093 -0.109299919
15 -0.176838 0.1768379867
16 0.0923707 -0.09237070078
17 -0.734757 0.7347570911
18 0.457277 -0.4572771211
19 0.0492038 -0.04920380746
20 0.169184 -0.1691844926

Total number of rows: 45015

Table truncated, full table size 1196 Kbytes.




Supplementary file Size Download File type/resource
GSM187290.txt.gz 13.1 Mb (ftp)(http) TXT

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