title: P-3h-11-B

description: RNA from polysomal fraction #11 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-8-B

status: Public on Jun 02 2004

type: RNA

city: Baltimore

first: Myriam

last: Gorospe

state: MD

address: 5600 Nathan Shock Drive

country: USA

institute: NIA

description: RNA from polysomal fraction #8 from cells collected 3h after UVC treatment. Biological repeat 2

molecule: total RNA

organism: Homo sapiens

source_name: RKO cells


title: P-3h-9-B

description: RNA from polysomal fraction #9 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-5-B

description: RNA from polysomal fraction #5 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-7-B

description: RNA from polysomal fraction #7 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-6-B

description: RNA from polysomal fraction #6 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-8-A

description: RNA from polysomal fraction #8 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-1-B

description: RNA from polysomal fraction #1 from cells collected 3h after UVC treatment. Biological repeat 2.


title: P-3h-10-A

description: RNA from polysomal fraction #10 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-c-11-C

description: RNA from polysomal fraction #11 collected from untreated cells. Biological repeat 3.


title: P-3h-11-A

description: RNA from polysomal fraction #11 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-7-A

description: RNA from polysomal fraction #7 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-4-B

description: RNA from polysomal fraction #4 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-2-B

description: RNA from polysomal fraction #2 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-c-8-C

description: RNA from polysomal fraction #8 collected from untreated cells. Biological repeat 3.


title: P-3h-3-B

description: RNA from polysomal fraction #3 from cells collected 3h after UVC treatment. Biological repeat 2


title: P-3h-1-A

description: RNA from polysomal fraction #1 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-6-A

description: RNA from polysomal fraction #6 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-2-A

description: RNA from polysomal fraction #2 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-4-A

description: RNA from polysomal fraction #4 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-5-A

description: RNA from polysomal fraction #5 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-3-A

description: RNA from polysomal fraction #3 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-3h-9-A

description: RNA from polysomal fraction #9 from cells collected 3h after UVC treatment. Biological repeat 1.


title: P-c-9-C

description: RNA from polysomal fraction #9 collected from untreated cells. Biological repeat 3.


title: P-c-7-C

description: RNA from polysomal fraction #7 collected from untreated cells. Biological repeat 3.


title: P-c-10-C

description: RNA from polysomal fraction #10 collected from untreated cells. Biological repeat 3.


title: P-c-5-C

description: RNA from polysomal fraction #5 collected from untreated cells. Biological repeat 3.


title: P-c-4-C

description: RNA from polysomal fraction #4 collected from untreated cells. Biological repeat 3.


title: P-c-6-C

description: RNA from polysomal fraction #6 collected from untreated cells. Biological repeat 3.


title: P-c-10-B

description: RNA from polysomal fraction #10 collected from untreated cells. Biological repeat 2.


title: P-c-9-B

description: RNA from polysomal fraction #9 collected from untreated cells. Biological repeat 2.


title: P-c-6-B

description: RNA from polysomal fraction #6 collected from untreated cells. Biological repeat 2.


title: P-c-11-B

description: RNA from polysomal fraction #11 collected from untreated cells. Biological repeat 2.


title: P-c-2-B

description: RNA from polysomal fraction #2 collected from untreated cells. Biological repeat 2.


title: P-c-1-B

description: RNA from polysomal fraction #1 collected from untreated cells. Biological repeat 2.


title: P-c-3-B

description: RNA from polysomal fraction #3 collected from untreated cells. Biological repeat 2.


title: P-c-7-B

description: RNA from polysomal fraction #7 collected from untreated cells. Biological repeat 2.


title: P-c-4-B

description: RNA from polysomal fraction #4 collected from untreated cells. Biological repeat 2.


title: P-c-2-A

description: RNA from polysomal fraction #2 collected from untreated cells. Biological repeat 1.


title: P-c-3-C

description: RNA from polysomal fraction #3 collected from untreated cells. Biological repeat 3.


title: P-c-5-B

description: RNA from polysomal fraction #5 collected from untreated cells. Biological repeat 2.


title: P-c-8-B

description: RNA from polysomal fraction #8 collected from untreated cells. Biological repeat 2.


title: P-c-9-A

description: RNA from polysomal fraction #9 collected from untreated cells. Biological repeat 1.


title: P-c-2-C

description: RNA from polysomal fraction #2 collected from untreated cells. Biological repeat 3.


title: P-c-11-A

description: RNA from polysomal fraction #11 collected from untreated cells. Biological repeat 1.


title: P-c-10-A

description: RNA from polysomal fraction #10 collected from untreated cells. Biological repeat 1.


title: P-c-5-A

description: RNA from polysomal fraction #5 collected from untreated cells. Biological repeat 1.


title: P-c-6-A

description: RNA from polysomal fraction #6 collected from untreated cells. Biological repeat 1.


title: P-12h-10-C

description: RNA from polysomal fraction #10 from cells collected 12h after UVC treatment. Biological repeat 3


title: P-c-3-A

description: RNA from polysomal fraction #3 collected from untreated cells. Biological repeat 1.


title: P-c-4-A

description: RNA from polysomal fraction #4 collected from untreated cells. Biological repeat 1.


title: P-c-1-A

description: RNA from polysomal fraction #1 collected from untreated cells. Biological repeat 1.


title: T-12h-C

description: Total RNA from cells collected 12 h after UVC treatment. Biological repeat 3.


title: T-12h-A

description: Total RNA from cells collected 12 h after UVC treatment. Biological repeat 1.


title: T-12h-B

description: Total RNA from cells collected 12 h after UVC treatment. Biological repeat 2.


title: T-6h-B

description: Total RNA from cells collected 6 h after UVC treatment. Biological repeat 2.


title: T-3h-B

description: Total RNA from cells collected 3 h after UVC treatment. Biological repeat 2.


title: T-3h-C

description: Total RNA from cells collected 3 h after UVC treatment. Biological repeat 3.


title: T-3h-A

description: Total RNA from cells collected 3 h after UVC treatment. Biological repeat 1.


title: T-6h-A

description: Total RNA from cells collected 6 h after UVC treatment. Biological repeat 1.


title: T-c-A

description: Total RNA from untreated cells. Biological repeat 1.


title: T-6h-C

description: Total RNA from cells collected 6 h after UVC treatment. Biological repeat 3.


title: T-c-B

description: Total RNA from untreated cells. Biological repeat 2.


title: T-c-C

description: Total RNA from untreated cells. Biological repeat 3.


title: aa4

status: Public on Jun 01 2004

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: HY-TCR RTOC 10-5M Smcy, day 6

organism: Mus musculus

source_name: RTOC thymocyte


title: aa2

description: HY-TCR RTOC 10-5M Smcy, day 6


title: ab3

description: HY-TCR RTOC 10-7M Smcy, day 6


title: ab4

description: HY-TCR RTOC 10-7M Smcy, day 6


title: aa3

description: HY-TCR RTOC 10-5M Smcy, day 6


title: CCFAlmasan_CaP1_24B

city: Cleveland

first: John

middle: Gilmary

last: Hissong

state: OH

address: 9500 Euclid Ave.

department: Cancer Biology

institute: Lerner Research Institute Cleveland Clinic Foundation

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, 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:  Harvested 24 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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:1458, Count:32
Corner-  Avg:45449, Count:32
Background  Avg:476.25, Stdev:3.19, Max:486.6, Min:470.1
Noise  Avg:14.27, Stdev:0.45, Max:15.5, Min:12.2
RawQ  19.08
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  1.509654
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

source_name: LNCaP C4-2 cells, human prostate cancer androgen insensitive cultured cell line


title: ab2

description: HY-TCR RTOC 10-7M Smcy, day 6


title: aa1

description: HY-TCR RTOC 10-5M Smcy, day 6


title: CCFAlmasan_CaP1_LB

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP, polyA+ mRNA extracted, 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 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP C4-2 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:1223, Count:32
Corner-  Avg:45420, Count:32
Background  Avg:497.50, Stdev:2.38, Max:505.2, Min:493.0
Noise  Avg:15.19, Stdev:0.52, Max:17.4, Min:14.3
RawQ  19.71
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  1.416113
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

source_name: LNCaP, human prostate cancer androgen dependent cultured cell line


title: CCFAlmasan_CaP1_FB

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, fractionated: harvested 6 hr after the fourth of four sequential daily 2.5 Sv radiation doses, 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:  The sample was irradiated to a dose of 10 Sv in four equal fractions of 2.5 Sv given over four consecutive days; the sample was harvested 6 hr after the final dose.  The radiation source was a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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:1044, Count:32
Corner-  Avg:43971, Count:32
Background  Avg:486.66, Stdev:3.61, Max:495.7, Min:477.1
Noise  Avg:14.06, Stdev:0.48, Max:15.3, Min:12.9
RawQ  19.33
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  1.713592
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


title: ab1

description: HY-TCR RTOC 10-7M Smcy, day 6


title: ot4

description: OT1-TCR thymocytes, RTOC day 6


title: CCFAlmasan_CaP1_FD

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, fractionated: harvested 6 hr after the fourth of four sequential daily 2.5 Sv radiation doses, Affymetrix HGU-95D 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:  The sample was irradiated to a dose of 10 Sv in four equal fractions of 2.5 Sv given over four consecutive days; the sample was harvested 6 hr after the final dose.  The radiation source was a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95D 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:846, Count:32
Corner-  Avg:36288, Count:32
Background  Avg:443.55, Stdev:2.92, Max:449.4, Min:435.4
Noise  Avg:12.82, Stdev:0.33, Max:13.9, Min:11.8
RawQ  18.29
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  4.135726
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


title: CCFAlmasan_CaP1_6B

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, 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:  Harvested 6 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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:1098, Count:32
Corner-  Avg:41784, Count:32
Background  Avg:506.13, Stdev:4.05, Max:517.7, Min:496.6
Noise  Avg:13.90, Stdev:0.57, Max:15.9, Min:12.1
RawQ  19.19
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  1.914078
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


title: CCFAlmasan_CaP1_LD

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP, polyA+ mRNA extracted, no irradiation, Affymetrix HGU-95D 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 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP C4-2 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-95D 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:973, Count:32
Corner-  Avg:37100, Count:32
Background  Avg:469.74, Stdev:5.56, Max:480.9, Min:453.8
Noise  Avg:13.51, Stdev:0.34, Max:14.7, Min:12.7
RawQ  18.91
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  3.934490
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


title: CCFAlmasan_CaP1_0B

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


title: ot3

description: OT1-TCR thymocytes, RTOC day 6


title: CCFAlmasan_CaP1_24D

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95D 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:  Harvested 24 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95D 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:1310, Count:32
Corner-  Avg:44373, Count:32
Background  Avg:457.07, Stdev:4.19, Max:465.9, Min:445.3
Noise  Avg:13.19, Stdev:0.21, Max:13.7, Min:12.5
RawQ  18.60
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  3.954699
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


title: CCFAlmasan_CaP1_LE

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP, polyA+ mRNA extracted, no irradiation, Affymetrix HGU-95E 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 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP C4-2 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-95E 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:799, Count:32
Corner-  Avg:35840, Count:32
Background  Avg:451.26, Stdev:19.89, Max:540.9, Min:378.3
Noise  Avg:15.11, Stdev:2.37, Max:24.6, Min:11.7
RawQ  18.15
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  3.114513
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


title: CCFAlmasan_CaP1_FE

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, fractionated: harvested 6 hr after the fourth of four sequential daily 2.5 Sv radiation doses, Affymetrix HGU-95E 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:  The sample was irradiated to a dose of 10 Sv in four equal fractions of 2.5 Sv given over four consecutive days; the sample was harvested 6 hr after the final dose.  The radiation source was a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95E 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:832, Count:32
Corner-  Avg:35095, Count:32
Background  Avg:414.13, Stdev:5.46, Max:426.4, Min:398.7
Noise  Avg:12.35, Stdev:0.40, Max:13.9, Min:11.5
RawQ  17.92
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  4.387765
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


title: ot2

description: OT1-TCR thymocytes, RTOC day 6


title: CCFAlmasan_CaP1_6D

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95D 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:  Harvested 6 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95D 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:1202, Count:32
Corner-  Avg:42847, Count:32
Background  Avg:429.20, Stdev:2.91, Max:435.5, Min:421.1
Noise  Avg:12.56, Stdev:0.37, Max:13.8, Min:11.3
RawQ  17.87
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  4.601868
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


title: CCFAlmasan_CaP1_0D

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, control: no irradiation, Affymetrix HGU-95D 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-95D 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:1127, Count:32
Corner-  Avg:42869, Count:32
Background  Avg:471.09, Stdev:2.91, Max:480.6, Min:464.3
Noise  Avg:13.84, Stdev:0.50, Max:15.5, Min:12.7
RawQ  19.06
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  3.645765
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


title: R6/2 (triple treatment) 5211

city: Cardiff

first: Lesley

last: Jones

address: Heath Park

department: Psychological Medicine

country: United Kingdom

institute: Cardiff University School of Medicine

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5211

source_name: Whole brain hemispheres


title: ot1

description: OT1-TCR thymocytes, RTOC day 6


title: R6/2 (untreated) 5270

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5270


title: R6/2 (triple treatment) 5185


title: R6/2 (triple treatment) 5253

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5253


title: CCFAlmasan_CaP1_6E

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95E 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:  Harvested 6 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95E 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:1174, Count:32
Corner-  Avg:44246, Count:32
Background  Avg:427.27, Stdev:5.03, Max:437.0, Min:413.7
Noise  Avg:12.23, Stdev:0.40, Max:13.4, Min:11.1
RawQ  17.75
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  3.872409
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


title: CCFAlmasan_CaP1_LC

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP, polyA+ mRNA extracted, no irradiation, Affymetrix HGU-95C 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 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP C4-2 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-95C 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:1356, Count:32
Corner-  Avg:45385, Count:32
Background  Avg:471.22, Stdev:3.70, Max:481.1, Min:461.2
Noise  Avg:14.93, Stdev:0.66, Max:17.3, Min:13.7
RawQ  19.18
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  1.920943
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


title: CCFAlmasan_CaP1_0E

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, control: no irradiation, Affymetrix HGU-95E 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-95E 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:981, Count:32
Corner-  Avg:38210, Count:32
Background  Avg:465.00, Stdev:6.06, Max:475.7, Min:452.2
Noise  Avg:13.78, Stdev:0.61, Max:15.2, Min:12.1
RawQ  19.14
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  2.961084
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


title: CCFAlmasan_CaP1_24C

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95C 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:  Harvested 24 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95C 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:1126, Count:32
Corner-  Avg:41218, Count:32
Background  Avg:447.02, Stdev:3.35, Max:452.3, Min:433.2
Noise  Avg:13.02, Stdev:0.44, Max:14.3, Min:11.1
RawQ  18.75
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  2.865989
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


title: CCFAlmasan_CaP1_FC

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, fractionated: harvested 6 hr after the fourth of four sequential daily 2.5 Sv radiation doses, Affymetrix HGU-95C 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:  The sample was irradiated to a dose of 10 Sv in four equal fractions of 2.5 Sv given over four consecutive days; the sample was harvested 6 hr after the final dose.  The radiation source was a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95C 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:958, Count:32
Corner-  Avg:41942, Count:32
Background  Avg:454.20, Stdev:5.76, Max:466.1, Min:438.5
Noise  Avg:13.20, Stdev:0.39, Max:14.5, Min:12.2
RawQ  18.81
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  2.756703
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


title: R6/2 (untreated) 5197

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5197


title: CCFAlmasan_CaP1_24E

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95E 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:  Harvested 24 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95E 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:1281, Count:32
Corner-  Avg:43770, Count:32
Background  Avg:437.12, Stdev:5.96, Max:450.7, Min:425.0
Noise  Avg:13.30, Stdev:0.59, Max:14.8, Min:11.7
RawQ  18.29
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  3.700992
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


title: W/type (triple treatment) 5267

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5267


title: W/type (triple treatment) 5289

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5289


title: R6/2 (untreated) 5227

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5227


title: CCFAlmasan_CaP1_6C

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95C 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:  Harvested 6 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95C 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:1146, Count:32
Corner-  Avg:40500, Count:32
Background  Avg:423.33, Stdev:3.34, Max:432.8, Min:414.2
Noise  Avg:12.53, Stdev:0.38, Max:13.8, Min:11.0
RawQ  17.83
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  2.941873
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


title: Wild type (untreated) 5241

description:
Tacrine 2.7mg/kg/day from 5 weeks, from 5 weeks. Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5241


title: CCFAlmasan_CaP1_LA

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP, polyA+ mRNA extracted, no irradiation, Affymetrix HGU-95Av1 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 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP C4-2 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-95Av1 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:618, Count:32
Corner-  Avg:29779, Count:32
Background  Avg:442.78, Stdev:7.80, Max:459.7, Min:425.1
Noise  Avg:13.72, Stdev:0.65, Max:15.2, Min:12.4
RawQ  18.24
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  1.186709
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


title: CCFAlmasan_CaP1_FA

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, fractionated: harvested 6 hr after the fourth of four sequential daily 2.5 Sv radiation doses, Affymetrix HGU-95Av1 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:  The sample was irradiated to a dose of 10 Sv in four equal fractions of 2.5 Sv given over four consecutive days; the sample was harvested 6 hr after the final dose.  The radiation source was a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95Av1 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:1001, Count:32
Corner-  Avg:43570, Count:32
Background  Avg:473.42, Stdev:3.05, Max:482.3, Min:465.6
Noise  Avg:14.77, Stdev:0.51, Max:16.1, Min:13.3
RawQ  19.40
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  0.943573
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


title: Wild type (untreated) 5296

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5296


title: R6/2 (untreated) 5213

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5213


title: CCFAlmasan_CaP1_24A

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 24 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95Av1 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:  Harvested 24 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
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-95Av1 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:1311, Count:32
Corner-  Avg:43663, Count:32
Background  Avg:532.33, Stdev:6.32, Max:552.6, Min:516.7
Noise  Avg:16.04, Stdev:0.59, Max:17.6, Min:15.0
RawQ  20.90
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  0.720930
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


title: W/type (triple treatment) 5217

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5217


title: Wildtype (untreated) 5176

description:
Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5176

source_name: Whole brain hemispheres, harvested at 8 weeks