NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM256985 Query DataSets for GSM256985
Status Public on Dec 31, 2009
Title Sarcosine (duplicate)
Sample type RNA
 
Channel 1
Source name untreated PrEC cells
Organism Homo sapiens
Characteristics PrEC cells from Lonza (Cat No CC-0310)
Treatment protocol The cells are grown to 60-70% confluence and treated with 50 uM concentration of either alanine, leucine, glycine or sarcosine (Sigma, St Louis, MO), all resuspended in water for a period of 24h.
Growth protocol The cells are grown in Prostate Epithelial Cell Medium (Lonza Walkersville Inc. Walkersville, MD, Cat No CC-0310) supplemented with Bovine Pitutary extract, Hydrocortisone, human Epidermal Growth factor, Transferrin, Insulin, retinoic Acid, Triiodothyronine, and GA-1000 as per manufacturers instruction.
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 Sarcosine treated PrEC cells, rep2
Organism Homo sapiens
Characteristics 50 uM sarcosine added to PrEC cells
Treatment protocol The cells are grown to 60-70% confluence and treated with 50 uM concentration of either alanine, leucine, glycine or sarcosine (Sigma, St Louis, MO), all resuspended in water for a period of 24h.
Growth protocol The cells are grown in Prostate Epithelial Cell Medium (Lonza Walkersville Inc. Walkersville, MD, Cat No CC-0310) supplemented with Bovine Pitutary extract, Hydrocortisone, human Epidermal Growth factor, Transferrin, Insulin, retinoic Acid, Triiodothyronine, and GA-1000 as per manufacturers instruction.
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 Samples 1 and 2 are technical replicates
Data processing Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.5.1.1). Spot values were normalized using the default linear-lowess normalization. Samples M5a and M5b were isolated from the same patient and normalized values were averaged before data analysis.
 
Submission date Jan 14, 2008
Last update date Dec 31, 2008
Contact name Laila M Poisson
E-mail(s) lpoisso1@hfhs.org
Organization name Henry Ford Health Systems
Department Biostatistics and Research Epidemiology
Street address 1 Ford Place
City Detroit
State/province MI
ZIP/Postal code 48202
Country USA
 
Platform ID GPL4133
Series (1)
GSE10164 PrEC response to Alanine or Sarcosine at 6 hours

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

Data table
ID_REF VALUE
1 -6.33E-02
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 0.00E+00
8 0.00E+00
9 -1.31E+00
10 -1.13E+00
11 0.00E+00
12 8.33E-02
13 0.00E+00
14 -2.13E-01
15 0.00E+00
16 7.61E-01
17 0.00E+00
18 -4.47E-01
19 2.23E-01
20 -2.22E-01

Total number of rows: 45015

Table truncated, full table size 664 Kbytes.




Supplementary file Size Download File type/resource
GSM256985.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap