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Sample GSM11742 Query DataSets for GSM11742
Status Public on Jun 01, 2004
Title CCFAlmasan_CaP1_0B
Sample type RNA
 
Source name LNCaP C4-2 cells, human prostate cancer androgen insensitive cultured cell line
Organism Homo sapiens
Extracted molecule total RNA
 
Description SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, control: no irradiation, Affymetrix HGU-95B GeneChip(R).
DESIGN: The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells. The parent LNCaP cell lines were obtained from ATCC (Manassas, VA). The derived LNCaP cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083. (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.) The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION: This sample was not irradiated.
EXTRACTION: PolyA+ mRNA was prepared from total RNA by using QIAGEN Oligotex kits.
PROCESSING: Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual. Double-stranded cDNA was prepared from the PolyA+ mRNA using the GIBCO BRL SuperScript Choice system. An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit. The sample was then purified using the QIAGEN RNA MiniKit and then fragmented. A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY: Affymetrix HGU-95B GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING: Affymetrix Fluidics Station 400, FlexGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2. Original calibration. The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm: Statistical
Corner+ Avg:1190, Count:32
Corner- Avg:45230, Count:32
Background Avg:484.37, Stdev:26.85, Max:535.9, Min:395.3
Noise Avg:15.38, Stdev:1.16, Max:19.2, Min:13.1
RawQ 19.20
Alpha1 0.04
Alpha2 0.06
Tau 0.015
Gamma1H 0.0025
Gamma1L 0.0025
Gamma2H 0.003
Gamma2L 0.003
Perturbation 1.1
TGT 300
NF 1.000000
SF 1.500825
SFGene All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333. The Microarray Suite 5 output data was further processed with GeneSpring(R). Each chip (A-E) was normalized separately. Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample. The percentile was calculated with all normalized measurements above 0. Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
 
Submission date Oct 18, 2003
Last update date May 28, 2005
Contact name John Gilmary Hissong
E-mail(s) hissonj@ccf.org
Phone 216-445-7105
Fax 216-445-6269
URL http://www.lerner.ccf.org/cancerbio/almasan/
Organization name Lerner Research Institute Cleveland Clinic Foundation
Department Cancer Biology
Lab Almasan Lab NB40
Street address 9500 Euclid Ave.
City Cleveland
State/province OH
ZIP/Postal code 44195
Country USA
 
Platform ID GPL92
Series (1)
GSE762 CCFAlmasan_CaP1

Data table header descriptions
ID_REF Affymetrix defined probe set names
STAT_PAIRS the number of probe pairs available for measuring the transcript abundance
STAT_PAIRS_USED the number of probe pairs actually used for measuring the transcript abundance
MAS5_VALUE Microarray Suite 5 output measure for transcript abundance, scaled so that the trimmed mean signal is 300
ABS_CALL Microarray Suite 5 statistical assessment of whether the transcript was present (P), absent (A), marginal (M), or no call (NC)
P_VALUE Microarray Suite 5 p-value of finding transcript at this level or higher from background fluctuations
VALUE GeneSpring 6 output measure of the transcript abundance, normalized so that the median is equal to 1.0

Data table
ID_REF STAT_PAIRS STAT_PAIRS_USED MAS5_VALUE ABS_CALL P_VALUE VALUE
AFFX-MurIL2_at 20 20 51 A 0.699394 0.96937436
AFFX-MurIL10_at 20 20 41 A 0.58862 0.6189893
AFFX-MurIL4_at 20 20 37.9 A 0.60308 0.25791448
AFFX-MurFAS_at 20 20 43.8 A 0.5 0.64671254
AFFX-BioB-5_at 20 20 866.4 P 0.002867 9.286474
AFFX-BioB-M_at 20 20 1656.3 P 0.000225 14.067329
AFFX-BioB-3_at 20 20 1126 P 0.000857 10.036753
AFFX-BioC-5_at 20 20 3343.8 P 0.00007 33.478783
AFFX-BioC-3_at 20 20 3099.9 P 0.000052 27.893955
AFFX-BioDn-5_at 20 20 4131.5 P 0.000052 40.065353
AFFX-BioDn-3_at 20 20 16129.6 P 0.000095 155.03804
AFFX-CreX-5_at 20 20 32877.7 P 0.000044 308.61554
AFFX-CreX-3_at 20 20 41574.1 P 0.000044 430.9062
AFFX-BioB-5_st 20 20 231.9 A 0.275146 1.3607283
AFFX-BioB-M_st 20 20 55.3 A 0.724854 1.3009155
AFFX-BioB-3_st 20 20 47.3 A 0.916408 0.5752387
AFFX-BioC-5_st 20 20 27.7 A 0.891021 0.43678063
AFFX-BioC-3_st 20 20 10.3 A 0.58862 0.23870885
AFFX-BioDn-5_st 20 20 23 A 0.737173 1.5147645
AFFX-BioDn-3_st 20 20 300.9 A 0.131361 2.6770988

Total number of rows: 12620

Table truncated, full table size 513 Kbytes.




Supplementary data files not provided

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