title: CCFAlmasan_CaPK_1

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 1 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, 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 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:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA 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 HG-U95Av2 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, EukGE: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:677, Count:32
Corner-  Avg:38369, Count:32
Background  Avg:336.43, Stdev:5.01, Max:345.8, Min:325.4
Noise  Avg:10.88, Stdev:0.30, Max:11.9, Min:10.2
RawQ  14.06
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  0.775541
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 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: Week 7 - High Glucose

status: Public on May 31 2004

type: RNA

city: St. Louis

first: Matthew

middle: Alan

last: Roberts

state: MO

address: 1 Checkerboard Square

department: Global Strategic Business Unit and R&D

country: USA

institute: Nestle Research Center

description: Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d’Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF).  Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere.

molecule: total RNA

organism: Homo sapiens

source_name: muscle biopsy primary cell culture


title: CCFAlmasan_CaPK_4

status: Public on Jun 01 2004

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: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 4 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, 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 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:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA 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 HG-U95Av2 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, EukGE: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:603, Count:32
Corner-  Avg:38917, Count:32
Background  Avg:358.36, Stdev:3.41, Max:367.7, Min:348.7
Noise  Avg:10.83, Stdev:0.24, Max:11.4, Min:10.0
RawQ  13.82
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  0.857604
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 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: Week 5 - High Glucose


title: Week 4 - High Glucose


title: 38 year old female

status: Public on Jul 21 2004

city: Boston

first: Tao

last: Lu

state: MA

address: 300 Longwood Ave

department: Neurology

institute: The Children's Hospital

description:
The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals.
Keywords = human brain aging

source_name: human frontal cortex


title: Week 1 Control

description:
Human muscle cultures were prepared from progenitor satellite cells isolated from a muscle biopsy of a 16-donor subject through an explant-reexplant technique (5). Biopsies were obtained with informed consent and approval of the Human Use Committee of the Hospital Vall d’Hebrón, Barcelona. A batch of cells isolated after 1 explant and 4 consecutive subcultures at dilution (1:3) were induced to differentiate for 15 days and then weekly monitored for the stated parameters. Growth medium was DMEM:MEM-199 3:1, supplemented with 10 % fetal bovine serum (FBS), 10 µg/ml insulin, 2 mM glutamine, 25 ng/ml fibroblast growth factor (FGF) and 10 ng/ml epidermal growth factor (EGF).  Differentiating medium had the same composition except FGF and EGF. Cultures were kept at 37ºC in a humidified 5% CO2 atmosphere.

After week 1, myotubes were incubated with "low" 10 mM [14C]-glucose (100 µCi/mmol) (synthesis rate) or "high" 25 mM glucose (glycogen content); .

RNA was extracted from cells cultured in 10 cm plates with Nucleospin II (Macherey Nagel, Duren, Switzerland) including DNAase treatment. All RNA samples were quantified with the RiboGreen RNA Quantification Kit (Molecular Probes, Eugene Oregon), then monitored with the Agilent 2100 Bioanalyser (Agilent Biotechnologies, Germany) and consistently demonstrated high-quality RNA (28S/18S ratio approximately 2, but always less than 3). Total RNA (7 µg) was converted to biotinylated cRNA as previously described.


title: CCFAlmasan_CaPK_2

description:
SUMMARY: Kinetic response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, total RNA extracted, harvested 2 hr after irradiation to a dose of 10 Sv, Affymetrix HG-U95Av2 GeneChip(R).
DESIGN: The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation.  The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, 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 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:  Harvested at specified intervals after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Mark 1 Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 emits a gamma ray with an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  Total RNA was extracted from cells using the Trizol reagent (GIBCO BRL).
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from total RNA 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 HG-U95Av2 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, EukGE: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:667, Count:32
Corner-  Avg:38136, Count:32
Background  Avg:341.82, Stdev:5.93, Max:358.3, Min:328.8
Noise  Avg:11.04, Stdev:0.44, Max:12.3, Min:10.0
RawQ  14.33
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  0.886110
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 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: Week 2 - High Glucose


title: Organ confined prostate cancer (R310)

status: Public on May 26 2004

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

country: China

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

description: Human prostate cancer tissues analyses

source_name: Human prostate cancer tissues


title: Organ confined prostate cancer (R308)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R306)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R309)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R307)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R305)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R303)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R301)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R292)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R304)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R291)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R302)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R290)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R288)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R289)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R286)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R287)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R261)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R285)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R262)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R260)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R257)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R254)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R259)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R255)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R251)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R264)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R258)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R252)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R256)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R250)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R246)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R248)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R245)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R247)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R249)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R244)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R243)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R228)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R229)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R223)

description: Human prostate cancer tissues analyses


title: ERDNp63a primary keratinocytes, 220 min after Tamoxifen

status: Public on Mar 01 2008

city: Naples

first: Diego

last: di Bernardo

address: Via P Castellino 111

country: Italy

institute: Telethon Institute of Genetics and Medicine

description: Primary keratinocytes infected with a retrovirus carryng the DNp63alpha isform fused to estrogen receptor domain, and induced with tamoxifen

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with dChip

label: biotin

organism: Mus musculus

source_name: Primary keratinocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: Organ confined prostate cancer (R226)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R222)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R241)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R225)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R221)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R216)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R219)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R213)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R214)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R215)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R210)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R212)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R209)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R206)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R203)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R207)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R204)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R208)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R202)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R205)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R201)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R165)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R167)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R164)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R166)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R163)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R263)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R161)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R162)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R155)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R152)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R151)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R154)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R149)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R146)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R147)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R150)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R148)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R144)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R143)

description: Human prostate cancer tissues analyses


title: Organ confined prostate cancer (R153)

description: Human prostate cancer tissues analyses


title: HIV IMR90 2

status: Public on May 19 2004

city: La Jolla

first: Richard

middle: Steven

last: Mitchell

state: CA

address: 10010 North Torrey Pines Rd

department: Infectious Disease Laboratory

institute: The Salk Institute

description: IMR90 cells (passaged 36 times) infected with an HIV-1 based vector (see Schroder et al., Cell 110:521-9).  RNA isolated 48 hours after infection.  Sample 2.

source_name: HIV vector infected IMR90


title: HIV IMR90 1

description: IMR90 cells (passaged 36 times) infected with an HIV-1 based vector (see Schroder et al., Cell 110:521-9).  RNA isolated 48 hours after infection.  Sample 1.

source_name: HIV vector infected IMR90 cells


title: Organ confined prostate cancer (R145)

description: Human prostate cancer tissues analyses


title: InfSup#1

description:
SupT1 cells were infected with an HIV-1-based vector (see Schroder et al., Cell 110:521-529) and the RNA isolated 48 hours after infection.
Keywords = HIV SupT1

source_name: HIV-1 vector infected SupT1 cells


title: infPBMC#3

description:
Human female PBMC were infected with an HIV-based vector (see Schroder et al., Cell 110:521-9) and RNA isolated 48 hours after infection.
Sample #3

source_name: HIV vector infected PBMC


title: patient 3, time 48h

status: Public on Apr 28 2004

city: Heidelberg

first: Matthias

last: Nees

address: Im Neuenheimer Feld 156

department: Pediatric Oncology & Hematology

country: Germany

institute: Heidelberg University, Children's Hospital

description:
Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48h after aspiration. However, storage of BM has dramatic effects on mRNA expression of individual transcripts.
Keywords = mRNA stability
Keywords = transport and storage of clinical samples

source_name: bone marrow aspirate, stored at room temperature for 48h


title: InfSupt1#2

description:
SupT1 cells were infected with an HIV-1-based vector (see Schroder et al., Cell 110:521-529) and the RNA isolated 48 hours after infection.  Sample #2
Keywords = HIV SupT1

source_name: HIV-based vector infected SupT1 cells


title: Organ confined prostate cancer (R141)

description: Human prostate cancer tissues analyses


title: infPBMC#2

description:
Human female PBMC were infected with an HIV-based vector (see Schroder et al., Cell 110:521-9) and RNA isolated 48 hours after infection.
sanple #2


title: patient 3, time 24h

source_name: bone marrow aspirate, stored at room temperature for 24h


title: Organ confined prostate cancer (R142)

description: Human prostate cancer tissues analyses


title: Week 3 - High Glucose


title: patient 2, time 48h


title: patient 2, time 0h (fresh)

source_name: bone marrow aspirate, fresh (time 0h)


title: infPBMC_1

description:
Human female PBMC were infected with an HIV-based vector (see Schroder et al., Cell 110:521-9) and RNA isolated 48 hours after infection.
sample #1


title: patient 2, time 24h


title: patient 1, time 48h


title: PCNSL biopsy (PCNSL23)

status: Public on Dec 16 2007

city: Cologne

first: Manuel

last: Montesinos-Rongen

state: NRW

address: Kerpenerstr. 62

department: Institute for Neuropathology

institute: University Hospital Cologne

description: PCNSL biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

data_processing: obtained by using GCOS1.2

label: Biotin

source_name: PCNSL biopsy

tag: Primary CNS lymphoma (PCNSL) biopsy.


title: patient 1 time 0h (fresh)

source_name: bone marrow aspirate


title: patient 1 time 24h

source_name: bone marrow aspirate,stored at room temperature for 24h


title: LungFibrobl_AMyb

status: Public on Apr 16 2004

city: Albuquerque

first: Scott

middle: A.

last: Ness

state: NM

department: Internal Medicine

institute: U. of New Mexico HSC

description:
Primay human lung fibroblast cells were grown in tissue culture and infected with an adenovirus expressing Green Fluorescent Protein and chicken A-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, fibroblast, Myb oncogene

source_name: Primary human lung fibroblast cells


title: LungEpith_AdCont

description:
Lung epithelial cells were infected with adenovirus expressing Green Fluorescent Protein. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, epithelial, Myb oncogene

source_name: Primary human lung small airway epithelial cells


title: patient 3, time 0h (fresh)

source_name: bone marrow aspirate, fresh (0h)


title: LungEpith_cmyb

description:
Lung epithelial cells were infected with adenovirus expressing Green Fluorescent Protein and chicken c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, epithelial, Myb oncogene


title: LungFibrobl_Uninf

description:
Primay human lung fibroblast cells were grown in tissue culture. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, fibroblast, Myb oncogene


title: LungFibrobl_cMyb

description:
Primay human lung fibroblast cells were grown in tissue culture and infected with an adenovirus expressing Green Fluorescent Protein and chicken c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, fibroblast, Myb oncogene


title: Organ confined prostate cancer (R227)

description: Human prostate cancer tissues analyses


title: MCF7_AMyb1

description:
MCF-7 cells were infected with adenovirus expressing Green Fluorescent Protein and chicken A-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, MCF-7, breast cancer, Myb oncogene

source_name: MCF-7 cells


title: LungEpith_Amyb

description:
Lung epithelial cells were infected with adenovirus expressing Green Fluorescent Protein and chicken A-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, epithelial, Myb oncogene


title: MCF7_AMyb2


title: MCF7_AdCont2

description:
MCF-7 cells were infected with adenovirus expressing Green Fluorescent Protein. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, MCF-7, breast cancer, Myb oncogene


title: MCF7_cMyb2

description:
MCF-7 cells were infected with adenovirus expressing Green Fluorescent Protein and chicken c-Myb. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, MCF-7, breast cancer, Myb oncogene


title: LungFibrobl_AdCont

description:
Primay human lung fibroblast cells were grown in tissue culture and infected with an adenovirus expressing Green Fluorescent Protein. After 16 hours, RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, lung, fibroblast, Myb oncogene


title: MCF7_Uninf1

description:
Uninfected MCF-7 cells. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. Initial data analysis was performed using Affymetrix MAS software.
Keywords = Human, MCF-7, breast cancer, Myb oncogene


title: 95a GW7845_1

status: Public on Apr 13 2004

first: Brig

last: Mecham

address: 20 Shattuck St

institute: Harvard Medical School

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 1

source_name: human primary trophoblast


title: 95a GW7845_4

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 4


title: Organ confined prostate cancer (R284)

description: Human prostate cancer tissues analyses

source_name: Human prostate cancer tissues


title: 95a GW7845_5

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 5


title: 95a GW7845_3

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 3


title: MCF7_AdCont1


title: MCF7_Uninf2


title: 95a Troglitazone_5

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This  sample was treated with 10 uM Troglitazone .  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 2, replicate 5


title: 95a Control_3

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with DMSO as a vehicle control.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 1, replicate 3


title: 95a Troglitazone_3

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This  sample was treated with 10 uM Troglitazone .  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 2, replicate 3


title: 95a GW7845_2

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with 1 uM GW7845.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 3, replicate 2


title: 95a Troglitazone_4

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This  sample was treated with 10 uM Troglitazone .  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 2, replicate 4


title: 95a Troglitazone_2

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This  sample was treated with 10 uM Troglitazone .  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 2, replicate 2


title: MCF7_cMyb1


title: 95a Troglitazone_1

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This  sample was treated with 10 uM Troglitazone .  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation.  Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 2, replicate 1


title: 95a Control_5

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with DMSO as a vehicle control.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 1, replicate 5


title: Normal Breast Epithelium Control replicate 2 95A

description: Human mammary epithelial cells were purchased from Cambrex Bio Science and cultured according to the manufacturer's instructions. Cells were solubilized in TRIzol LS and RNA was extracted using the Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 7 ug of total RNA.

source_name: Human Mammary Epithelial Cells


title: 95a Control_2

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with DMSO as a vehicle control.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 1, replicate 2


title: 95a Control_1

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with DMSO as a vehicle control.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 1, replicate 1


title: Normal Breast Epithelium Control replicate 1 95A


title: HGPC, monolayer, 0.5% serum, sample 3

city: Jacksonville

first: Robert

middle: C.

last: Olney

state: FL

address: 807 Children's Way

department: Pediatrics

institute: Nemours Children's Clinic

description:
Human growth plate chondrocytes were isolated from the distal femoral growth plate from an adolescent undergoing epiphysiodesis.  Cell were isolated and grown in monolayers, long term, in 20% serum.  Cells replated and grown in 0.5% serum for 48 h.
Keywords = chondrocytes
Keywords = cartilage
Keywords = growth plate

source_name: Human long-bone growth plate chondrocytes, in vitro


title: Breast Cancer cells HCC1954 replicate 1 95A

description: The HCC1954 human breast cancer derived cell line was purchased from American Tissue Type Collection and cultured according to the manufacturer's instructions. Cells were solubilized in TRIzol LS and RNA was extracted using the Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 7 ug of total RNA.

source_name: HCC1954 Breast Cancer cell line


title: Breast Cancer cells HCC1954 replicate 2 95A


title: Breast Cancer cells MDA-MB-436 replicate 2 95A

description: The MDA-MB-436 human breast cancer derived cell line was purchased from American Tissue Type Collection and cultured according to the manufacturer's instructions. Cells were solubilized in TRIzol LS and RNA was extracted using the Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 7 ug of total RNA.

source_name: MDA-MB436 Breast Cancer cell line


title: HGPC, monolayer, 20% serum, unamplified

description:
Human growth plate chondrocytes were isolated from the distal femoral growth plate from an adolescent undergoing epiphysiodesis.  Cell were isolated and grown in monolayers, long term, in 20% serum.
Keywords = chondrocytes
Keywords = cartilage
Keywords = growth plate


title: HGPC, monolayer, 0.5% serum, sample 2


title: HGPC, monolayer, 0.5% serum, sample 1

description:
Human growth plate chondrocytes were isolated from the distal femoral growth plate from an adolescent undergoing epiphysiodesis.  Cell were isolated and grown in monolayers, long term, in 20% serum.  Cell replated and grown in 0.5% serum for 48 h.
Keywords = chondrocytes
Keywords = cartilage
Keywords = growth plate


title: Diabetes 1b

status: Public on Apr 01 2004

city: Leiden

first: Hans

last: Baelde

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description:
mRNA from isolated glomeruli from kidneys with diabetic nephropathy
Keywords = Kidney

source_name: kidney


title: Diabetes 2

description:
mRNA from isolated glomeruli from kidneys with diabetic nephropathy
Keywords = Kidney
Keywords = diabetes


title: Control 2

description:
mRNA from isolated glomeruli from normal kidney
Keywords = Kidney


title: Diabetes 1a


title: Control 1b


title: scott_replicate2

status: Public on Mar 05 2004

city: Le Kremlin-Bicetre

first: Daniele

last: Kerbiriou-Nabias

country: France

institute: INSERM U143

description: B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection. Scott phenotype is lack of exposure of procoagulant phosphatidylserine

source_name: B lymphocytes U143 from scott


title: scott_iono_replicate2

description: B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection. Scott phenotype is lack of exposure of procoagulant phosphatidylserine. B lymphocytes were treated with A23187 Ca2+ ionophore (200 nM final concentration)


title: scott_iono_replicate1

description:
B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection. Scott phenotype is lack of exposure of procoagulant phosphatidylserine.
B lymphocytes were treated with A23187 Ca2+ ionophore (200 nM final concentration)


title: daughter_replicate_2

description: B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection. B lymphocytes from Scott daughter exhibit in vitro functional properties coinciding with heterozygous status

source_name: B lymphocytes U143 from Scott daughter


title: daughter_iono_replicate_1

description: B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection. B lymphocytes from Scott daughter exhibit in vitro functional properties coinciding with heterozygous status. B lymphocytes were treated with A23187 Ca2+ ionophore (200 nM final concentration)


title: Control 1a

description:
mRNA from isolated glomeruli from normal kidney
Keywords = kidney

source_name: Kidney


title: daughter_iono_replicate_2

description: B lymphocytes obtained from scott patient daughter.  B lymphoblasts were generated by EBV-infection. B lymphoblasts from daughter exhibit in vitro functional properties coinciding with heterozygous status. B lymphoblasts were treated with A23187 Ca2+ ionophore (200 nM final concentration)


title: scott_replicate1


title: Organ confined prostate cancer (R220)

description: Human prostate cancer tissues analyses


title: daughter_replicate_1

description:
B lymphocytes Scott daughter. B Lymphocytes were generated by EBV-infection.
B lymphocytes from Scott daughter exhibit in vitro functional properties coinciding with heterozygous status


title: control_B replicate2

description: B lymphocytes from volunteers unrelated to the patient. B Lymphocytes were generated by EBV-infection

source_name: B lymphocytes U143


title: control_B_iono replicate2

description: B lymphocytes from volunteers unrelated to the patient. B Lymphocytes were generated by EBV-infection. B lymphocytes were treated with A23187 CA2+ ionophore (200 nM final concentration)


title: control_B_iono replicate1

description:
B lymphocytes from volunteers unrelated to the patient. B Lymphocytes were generated by EBV-infection
B lymphocytes were treated with A23187 Ca2+ ionophore (200 nM final concentration)


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 10

status: Public on Jan 29 2004

first: Judith

last: Haslett

description:
biopsy sample obtained from a male Duchenne Muscular Dystrophy patient(age: unknown)
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array

source_name: Quadriceps


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 7

description:
biopsy sample obtained from a 0.8-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 8

description:
biopsy sample obtained from a 6-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: control_B replicate1


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 11

description:
biopsy sample obtained from a 4-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 4

description:
biopsy sample obtained from a 3-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 5

description:
biopsy sample obtained from a 3.5-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: 95a Control_4

description: Primary cultures of human trophoblasts were established from normal, term placenta.  Cells were treated five hours after plating.  This sample was treated with DMSO as a vehicle control.  RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.  This sample is also known as Treatment 1, replicate 4


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 9

description:
biopsy sample obtained from a male Duchenne Muscular Dystrophy patient(unknown age)
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Breast Cancer cells MDA-MB-436 replicate 1 95A

description: The MDA-MB-436 human breast cancer derived cell line was purchased from American Tissue Type Collection and cultured according to the manufacturer's instructions. Cells were solubilized in TRIzol LS and RNA was extracted using the Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 7 ug of total RNA.


title: normal human skeletal muscle sample 11

description:
biopsy sample obtained from 36-year-old female individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 10

description:
biopsy sample obtained from 58-year-old female individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 2

description:
biopsy sample obtained from a 1.5-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 1

description:
biopsy sample obtained from a 1-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 9

description:
biopsy sample obtained from 5-year-old female individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 12


title: Duchenne muscular dystrophy (DMD) patient’s skeletal muscle sample 6

description:
biopsy sample obtained from a 1-year-old Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 8

description:
biopsy sample obtained from 4-year-old female individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 6

description:
biopsy sample obtained from 10-year-old male individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 4

description:
biopsy sample obtained from 2-year-old male individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: Duchenne muscular dystrophy (DMD) patient's skeletal muscle sample 3

description:
biopsy sample obtained from a 7-year-old male Duchenne Muscular Dystrophy patient
Keywords = gene expression profile of duchenne muscular dystrophy patient skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 7

description:
biopsy sample obtained from 1-year-old male individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: normal human skeletal muscle sample 3


title: normal human skeletal muscle sample 1

description:
Biopsy skeletal muscle sample obtained from 17-year-old female individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A


title: normal  human skeletal muscle sample 2

description:
biopsy sample obtained from 13-year-old male individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A


title: V5-P600

status: Public on Jan 01 2004

city: Little Rock

middle: D.

last: Shaughnessy

state: AR

address: 4301 West Markham St., Slot 776

department: Division of Basic Sciences

institute: Myeloma Institute for Research and Therapy

description:
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining.
MRI-lytic-lesion sample
Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1

source_name: bone marrow


title: V5-P596


title: V5-P599


title: V5-P598


title: V5-P604


title: V5-P565


title: V5-P568


title: V5-P566


title: V5-P562


title: V5-P582


title: V5-P588


title: V5-P597


title: V5-P556


title: V5-P594


title: V5-P575


title: V5-P577


title: V5-P564


title: V5-P536


title: V5-P561


title: V5-P524


title: V5-P522


title: V5-P549


title: V5-P517


title: V5-P511


title: V5-P504


title: V5-P502


title: V5-P495


title: V5-P487


title: V5-P503


title: V5-P501


title: V5-P481


title: V5-P508


title: V5-P492-2


title: V5-P482


title: V5-P490


title: V5-P465


title: V5-P478


title: V5-P463


title: V5-P480


title: V5-P447


title: V5-P451


title: V5-P592


title: V5-P446


title: V5-P433


title: V5-P427


title: V5-P421


title: V5-P426


title: V5-P385


title: V5-P392


title: V5-P420


title: V5-P418


title: V5-P399


title: V5-P368


title: V5-P374


title: V5-P401


title: V5-P405


title: V5-P366


title: V5-P397


title: V5-P364


title: V5-P355


title: V5-P313


title: V5-P332


title: V5-P307


title: V5-P303


title: V5-P296


title: V5-P299


title: V5-P354


title: V5-P288


title: V5-P291


title: V5-P343


title: V5-P324


title: V5-P283


title: KBGem

status: Public on Aug 30 2007

city: Duarte

first: Xiyong

last: Liu

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutic Research

institute: City of Hope

description: total RNA was extracted from KBGem cells. Hybridization and scan was performed in USC Microarray co-facilty

data_processing: GCOS and Genespring

label: KBGem

source_name: Gemcitabine Drug resistant KB clone

tag: This clone is selected from KB cell step-wise exposed to Gemcitabine. LC50 of KBGem is 32uM, which is almost 100 folds than parental KB cell.


title: V5-P347


title: V5-P281


title: V5-P391


title: V5-P280


title: V5-P278


title: normal human skeletal muscle sample 5

description:
biopsy sample obtained from 4-year-old male individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array


title: V5-P285


title: V5-P276


title: V5-P255


title: V5-P257


title: V5-P260


title: V5-P259


title: V5-P237


title: V5-P271


title: V5-P250


title: V5-P541


title: V5-P208


title: V5-P222


title: V5-P254


title: V5-P176


title: V5-P226


title: V5-P187


title: V5-P266


title: V5-P249


title: V5-P175


title: V5-P251


title: V5-P163


title: V5-P122


title: V5-P256


title: V5-P158


title: V5-P474


title: V5-P131


title: V5-P170


title: V5-P120


title: V5-P154


title: V5-P171


title: V5-P117


title: V5-P101


title: V5-P096


title: V5-P124


title: V5-P092


title: V5-P107


title: V5-P091


title: V5-P085


title: V5-P104


title: V5-P066


title: V5-P061


title: V5-P083


title: V5-P069


title: V5-P077


title: V5-P057


title: V5-P065


title: V5-P052


title: V5-P055


title: V5-P075


title: V5-P054


title: V5-P063


title: V5-P056


title: V5-P053


title: V5-P051


title: V5-P048


title: V5-P037


title: V5-P584

description:
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining.
MRI-no-lytic-lesion sample
Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1


title: V5-P569


title: V5-P408


title: V5-P457


title: V5-P043


title: V5-P415


title: V5-P103


title: V5-P357


title: V5-P393


title: V5-P535


title: V5-P510


title: V5-P381


title: V5-P387


title: V5-P340


title: V5-P379


title: V5-P330


title: V5-P335


title: V5-P563


title: V5-P390


title: V5-P270


title: V5-P155


title: V5-P301


title: V5-P241


title: V5-P213


title: V5-P239


title: V5-P165


title: V5-P157


title: V5-P212


title: V5-P102


title: V5-P127


title: V5-P119


title: V5-P144


title: V5-P025


title: V5-P029


title: V5-P121


title: V5-P084


title: 1791 HP48_22

city: Chicago

first: M Rosario

last: Hernandez

state: IL

address: 330 Chicago Avenue

department: Ophthalmology

institute: Northwestern University

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 48 h to hydrostatic pressure (HP48), pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE2, HP48


title: 1788 CP48_22

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 48 h to ambient pressure (CP48) and harvested with cells exposed for 48 h to hydrostatic pressure, pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE2, CP48


title: 1789 CP48_23


title: 1284 HP48_12

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and  exposed 48 h to hydrostatic pressure (HP48), pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, HP48


title: 1790 HP48_21


title: 1283 HP48_11


title: 1787 CP48_21


title: 1301 CP48_11

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 48 h to ambient pressure (CP48) and harvested with cells exposed for 48 h to hydrostatic pressure, pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, CP48


title: 1282 CP48_12


title: 2533 HP24_32

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 24 h to hydrostatic pressure (HP24), pressure experiment # 3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE3, HP24


title: 2534 HP24_33


title: 2532 HP24_31


title: 1786 HP24_23

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 24 h to hydrostatic pressure (HP24), pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE2, HP24


title: V5-P079


title: 1285 HP24_12

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and  exposed 24 h to hydrostatic pressure (HP24), pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, HP24


title: 1785 HP24_22

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 6 h to hydrostatic pressure (HP24), pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: 1784 HP24_21


title: 1240 HP24_11


title: 2531 CP24_33

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE3, CP24


title: 540T1 || K-ras Lkb1 L/- || primary lung tumor || Sq

status: Public on Aug 28 2007

city: boston

first: kwok-kin

last: wong

address: 44 binney street

department: medical oncology

institute: dana farber cancer institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

label_protocol: Affymetrix standard protocol

extract_protocol: Affymetrix standard protocol

tag: 540-T1 Tumor T1 LSL-Kras, Lkb1L/- Squamous carcinoma


title: 2530 CP24_32


title: 2529 CP24_31


title: 3073 HP6_42

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and  exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 4 (PE4).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE4, HP6


title: 1238 CP24_11

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, CP24


title: 1239 CP24_12


title: 3072 HP6_41


title: 1781 CP24_21

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE2, CP24


title: 1782 CP24_22


title: 2526 HP6_31

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 6 h to hydrostatic pressure (HP6), pressure experiment # 3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE3, HP6


title: 2627 HP6_32


title: 2528 HP6_33


title: 3074 HP6_43

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and  exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 4 (PE4)
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: 1243 HP6_11

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed 6 h to hydrostatic pressure (HP6), pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, HP6


title: 3068 CP0_43

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #4 (PE4).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE4, CP0


title: 1242 CP6_12

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, CP6


title: 3066 CP0_41

description:
Description Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #4 (PE4).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: 2525 CP6_32

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP), exposed 6 h more to ambient pressure (CP6) and harvested with cells exposed for 6 h to hydrostatic pressure, pressure experiment # 3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE3, CP6


title: 1241 CP6_11


title: 3067 CP0_42


title: 2522 CP0_31

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning  (0 h) of pressure experiment #3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE3, CP0


title: 1236 CP0_11

description:
Description Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 99-10RC5 P4 (donor age 19, gender M), PE1, CP0


title: 1237 CP0_12

description:
Primary optic nerve head astrocytes (99-10RC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment # 1 (PE1).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: 2523 CP0_32

description:
Description Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure (CP) and harvested at the beginning (0 h) of pressure experiment #3 (PE3).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: sample =XCGD6 treatment=Control time=0 (min)

status: Public on Dec 31 2003

city: Hamilton

first: Frank

middle: R.

last: DeLeo

state: MT

address: 903 South 4th Street

department: Laboratory of Human Bacterial Pathogenesis

institute: National Institute of Allergy and Infectious Diseases

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, XCGD6). "time" indicates time at which transcript levels were analyzed. "treatment" indicates whether the polymorphonuclear leukocytes were resting (Control) or activated by phagocytosis (Stimulated)
Sample_PMN_treatment = Control
Affymetrix MAS version = MAS5
GeneSpring (version 5.0)normalization protocol:
1.  Data Transformation:  Set measurements less than 0.0 to 0.0
2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
3.  Per Gene:  Normalize to median
Keywords = GENE PROFILING IN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS

source_name: Human polymorphonuclear (PMN) leukocytes


title: sample =XCGD6 treatment=Control time=360 (min)


title: sample =XCGD6 treatment=Stimulated time=360 (min)

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, XCGD6). "time" indicates time at which transcript levels were analyzed. "treatment" indicates whether the polymorphonuclear leukocytes were resting (Control) or activated by phagocytosis (Stimulated)
Sample_PMN_treatment = Stimulated
Affymetrix MAS version = MAS5
GeneSpring (version 5.0)normalization protocol:
1.  Data Transformation:  Set measurements less than 0.0 to 0.0
2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
3.  Per Gene:  Normalize to median
Keywords = GENE PROFILING IN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS


title: V5-P221

first: John

description:
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining.
MRI-no-lytic-lesion sample
Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1

source_name: bone marrow


title: sample =XCGD5 treatment=Stimulated time=360 (min)


title: sample =XCGD5 treatment=Control time=90 (min)


title: sample =XCGD6 treatment=Control time=180 (min)


title: sample =XCGD5 treatment=Stimulated time=180 (min)


title: sample =XCGD6 treatment=Stimulated time=180 (min)


title: sample =XCGD5 treatment=Stimulated time=90 (min)


title: V5-P371


title: sample =XCGD5 treatment=Control time=360 (min)


title: sample =XCGD5 treatment=Control time=180 (min)


title: sample =XCGD5 treatment=Control time=0 (min)


title: 2524 CP6_31


title: sample =XCGD4 treatment=Stimulated time=360 (min)


title: sample =XCGD4 treatment=Control time=360 (min)


title: sample =XCGD3 treatment=Control time=360 (min)


title: sample =XCGD4 treatment=Stimulated time=180 (min)


title: sample =XCGD4 treatment=Control time=180 (min)


title: sample =XCGD3 treatment=Control time=90 (min)


title: sample =XCGD2 treatment=Stimulated time=90 (min)


title: sample =XCGD3 treatment=Control time=0 (min)


title: sample =XCGD4 treatment=Control time=0 (min)


title: sample =XCGD3 treatment=Stimulated time=90 (min)


title: sample =XCGD3 treatment=Stimulated time=360 (min)


title: sample =XCGD2 treatment=Stimulated time=180 (min)


title: sample =XCGD2 treatment=Control time=90 (min)


title: sample =XCGD2 treatment=Stimulated time=360 (min)


title: sample =XCGD2 treatment=Control time=360 (min)


title: sample =XCGD2 treatment=Control time=0 (min)


title: sample =XCGD2 treatment=Control time=180 (min)


title: sample =XCGD1 treatment=Stimulated time=180 (min)


title: sample =XCGD1 treatment=Stimulated time=90 (min)


title: sample =Healthy4 treatment=Control time=90 (min)


title: sample =XCGD1 treatment=Control time=90 (min)


title: V5-P090


title: sample =Healthy3 treatment=Stimulated time=90 (min)

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, XCGD6). "time" indicates time at which transcript levels were analyzed. "treatment" indicates whether the polymorphonuclear leukocytes were resting (Control) or activated by phagocytosis (Stimulated)
Sample_PMN_treatment = Stimulated
Affymetrix MAS version = MAS4
GeneSpring (version 5.0)normalization protocol:
1.  Data Transformation:  Set measurements less than 0.0 to 0.0
2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
3.  Per Gene:  Normalize to median
Keywords = GENE PROFILING IN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS


title: sample =Healthy4 treatment=Control time=180 (min)


title: 1792 HP48_23

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure and exposed for 48 h to hydrostatic pressure (HP48), pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure

source_name: Primary optic nerve head astrocytes 00-1LC5 P4 (donor age 15, gender M), PE2, HP48


title: sample =Healthy3 treatment=Stimulated time=360 (min)


title: sample =Healthy4 treatment=Control time=0 (min)


title: sample =Healthy4 treatment=Stimulated time=360 (min)


title: sample =Healthy4 treatment=Stimulated time=90 (min)


title: sample =Healthy3 treatment=Stimulated time=180 (min)


title: sample =XCGD1 treatment=Control time=180 (min)


title: sample =Healthy4 treatment=Control time=360 (min)


title: sample =Healthy4 treatment=Stimulated time=180 (min)


title: sample =Healthy3 treatment=Control time=0 (min)

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, XCGD6). "time" indicates time at which transcript levels were analyzed. "treatment" indicates whether the polymorphonuclear leukocytes were resting (Control) or activated by phagocytosis (Stimulated)
Sample_PMN_treatment = Control
Affymetrix MAS version = MAS4
GeneSpring (version 5.0)normalization protocol:
1.  Data Transformation:  Set measurements less than 0.0 to 0.0
2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
3.  Per Gene:  Normalize to median
Keywords = GENE PROFILING IN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS


title: sample =XCGD1 treatment=Control time=360 (min)


title: sample =Healthy3 treatment=Control time=90 (min)


title: sample =Healthy3 treatment=Control time=360 (min)


title: sample =Healthy3 treatment=Control time=180 (min)


title: sample =Healthy2 treatment=Stimulated time=360 (min)


title: sample =Healthy2 treatment=Stimulated time=90 (min)


title: sample =Healthy2 treatment=Stimulated time=180 (min)


title: sample =Healthy2 treatment=Control time=180 (min)


title: sample =Healthy2 treatment=Control time=90 (min)


title: sample =Healthy2 treatment=Control time=0 (min)


title: sample =Healthy1 treatment=Control time=90 (min)


title: sample =Healthy1 treatment=Stimulated time=360 (min)


title: sample =Healthy1 treatment=Stimulated time=180 (min)


title: sample =Healthy1 treatment=Control time=180 (min)


title: sample =Healthy1 treatment=Control time=360 (min)


title: sample =Healthy1 treatment=Control time=0 (min)


title: sample =Healthy1 treatment=Stimulated time=90 (min)


title: T172

status: Public on Dec 10 2003

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

description: standard Affymetrix protocol, MAS 5.0

source_name: skeletal muscle


title: T289

description: standard Affymetrix protocol, MAS 5.0


title: T181

description: standard Affymetrix protocol, MAS 5.0


title: T256

description: standard Affymetrix protocol, MAS 5.0


title: T179

description: standard Affymetrix protocol, MAS 5.0


title: T170

description: standard Affymetrix protocol, MAS 5.0


title: 1783 CP24_23

description:
Primary optic nerve head astrocytes (00-1LC5) passage 4 were grown in P 100 dish to 75% confluence at ambient pressure, exposed 24 h to ambient pressure (CP24) and harvested with cells exposed for 24 h to hydrostatic pressure, pressure experiment # 2 (PE2).
Keywords = astrocytes
Keywords = optic nerve
Keywords = hydrostatic pressure


title: T146

description: standard Affymetrix protocol, MAS 5.0


title: T147

description: standard Affymetrix protocol, MAS 5.0


title: T177

description: standard Affymetrix protocol, MAS 5.0


title: Normal Pancreas Array A number N037

status: Public on Nov 07 2003

city: Rehovot

first: Orit

last: Shmueli

state: Israel

address: Rehovot

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: PolyA+ RNA samples from the twelve healthy human tissues were purchased from Clontech (Palo Alto, CA). Each RNA sample is typically composed of a pool of 10-25 individuals.

source_name: Normal Pancreas


title: Normal Spinal cord Array A number N010

source_name: Normal Spinal cord


title: T149

description: standard Affymetrix protocol, MAS 5.0


title: T142

description: standard Affymetrix protocol, MAS 5.0


title: T178

description: standard Affymetrix protocol, MAS 5.0


title: sample =Healthy2 treatment=Control time=360 (min)


title: T160

description: standard Affymetrix protocol, MAS 5.0


title: Normal Pancreas Array A number N035


title: Normal Bone marrow Array A number N021

source_name: Normal Bone marrow


title: Normal Kidney Array A number N026

source_name: Normal Kidney


title: Normal Liver Array A number N020

source_name: Normal Liver


title: Normal Prostate Array A number N034

source_name: Normal Prostate


title: Normal Prostate Array A number N036


title: Normal Brain Array A number N018

source_name: Normal Brain


title: Normal Thymus Array A number N011

source_name: Normal Thymus


title: sample =XCGD1 treatment=Stimulated time=360 (min)


title: Normal Lung Array A number N014

source_name: Normal Lung


title: Normal Thymus Array A number N019


title: Normal Spinal cord Array A number N016


title: Normal Liver Array A number N002


title: Normal Lung Array A number N005


title: Normal Bone marrow Array A number N001


title: T180

description: standard Affymetrix protocol, MAS 5.0


title: Normal Heart Array A number N007

source_name: Normal Heart


title: Normal Skeletal muscle Array A number N013

source_name: Normal Skeletal muscle


title: Normal Spleen Array A number N004

source_name: Normal Spleen


title: Experiment 5 Control

status: Public on Nov 01 2003

city: Natick

first: Larry

middle: Allen

last: Sonna

address: 42 Kansas Street

department: Thermal and Mountain Medicine Division

institute: USARIEM

description: CaCo cells exposed to control conditions or Vitamin D for 24 hours

source_name: CaCo


title: Normal Kidney Array A number N006


title: Normal Heart Array A number N003


title: Experiment 5 + Vitamin D


title: Experiment 3 Control


title: Normal Skeletal muscle Array A number N009


title: Normal Spleen Array A number N008


title: Experiment 3 + Vitamin D


title: Experiment 2 + Vitamin D


title: Experiment 1 Control


title: tet-3

status: Public on Oct 23 2003

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

description: Rheumatoid arthritis synovial fibroblasts (RASF) were transected with an adenovirus (Ad) expressing a dominant negative (DN) form of Ik-B stimulated 18 hours later with TNF-a. Controls were RASF transfected with Adtet then treated with TNF-a 18 hours later. RNA was extracted 3 hours after TNF-a application.

source_name: RASF


title: Experiment 4 Control


title: tet-2


title: Normal Brain Array A number N012


title: Tet-1


title: Experiment 2 Control


title: Experiment 1 + Vitamin D

source_name: CaCO


title: RASF + IKBDB + TNFa

description: Rheumatoid arthritis synovial fibroblasts (RASF) were transected with an adenovirus (As) expressing a dominant negative (DN) form of Ik-B stimulated 18 hours later with TNF-a. Controls were RASF transfected with Adtet then treated with TNF-a 18 hours later.


title: ikb-3


title: IMR32 GeneChip 8

status: Public on Oct 22 2003

city: Madison

first: Jiang

last: Li

state: WI

address: 777 Highland Ave.

department: School of Pharmacy

institute: University of Wisconsin Madison

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with tert-butylhydroquinone (10µM) for 24 hours and harvested on Jan 26, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells

source_name: human neuroblastoma cells, IMR-32


title: Ikb-2


title: CTX066 GeneChip 6

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with tert-butylhydroquinone (20µM) for 24 hours and harvested on Feb. 20 2002.

Keywords = human neural stem cell
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element

source_name: Human neural stem cells


title: IMR32 GeneChip 4

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with tert-butylhydroquinone (10µM) for 24 hours and harvested on April 17, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: CTX066 GeneChip 2

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with tert-butylhydroquinone (20µM) for 24 hours and harvested on Jan. 16 2002
Keywords = human neural stem cell
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element


title: IMR32 GeneChip 1

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with EtOH (0.01%) for 24 hours and harvested on March 15, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: CTX066 GeneChip 4

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with tert-butylhydroquinone (20µM) for 24 hours and harvested on Jan. 24 2002

Keywords = human neural stem cell
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element


title: CTX066 GeneChip 3

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with EtOH (0.01%) for 24 hours and harvested on Jan. 24 2002

Keywords = human neural stem cell
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element


title: CTX066 GeneChip 1

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with EtOH (0.01%) for 24 hours and harvested on Jan 16, 2002.
Keywords = human neural stem cells
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element

source_name: human neural stem cells


title: IMR32 GeneChip 3

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with EtOH (0.01%) for 24 hours and harvested on April 17, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: IMR32 GeneChip 6

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with tert-butylhydroquinone (10µM) for 24 hours and harvested on Feb 21, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: CTX066 GeneChip 5

description:
Human neural stem cells (CTX066), provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human embryonic cortical tissue (8 weeks post conception). The neurospheres were passaged every 14 days by sectioning into 150 µM section, which then were reseeded into fresh growth medium containing 70% DMEM, 30% Hams F12, 1% penicillin/streptomycin/amphotericin B supplemented with 20 µg/ml EGF, 10 ng/ml LIF and 1% v/v N2 at a density equivalent to 200,000 cells per ml. Half the growth medium was replenished every four days. The cells were treated with EtOH (0.01%) for 24 hours and harvested on Feb. 20 2002

Keywords = human neural stem cell
Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element


title: IMR32 GeneChip 5

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with EtOH (0.01%) for 24 hours and harvested on Feb,21, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: IMR32 GeneChip 7

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with EtOH (0.01%) for 24 hours and harvested on Jan 26, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: CVB3_V-9h

status: Public on Oct 09 2003

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.

source_name: HeLa cell lysate infected with CVB3


title: IMR32 GeneChip 2

description:
Human neuroblastoma cells, IMR-32, were grown in Dulbecco's modified eagle's medium (DMEM) supplemented with fetal calf serum (10%), 100 I.U./ml penicillin, and 100 mg/ml streptomycin. Cultures were maintained at 37 C in a humidified 10% CO2 atmosphere. The cells were treated with tBHQ (10µM) for 24 hours and harvested on March 15, 2001 for microarray analysis.

Keywords = tert-butylhydroquinone
Keywords = antioxidant responsive element
Keywords = IMR-32 cells


title: CVB3_S-5h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 5 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.

source_name: HeLa cell lysate


title: CVB3_V-5h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 5 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_S-7h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 7 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_V-7h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 7 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_S-9h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_V-3h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_S-1h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 1 hour following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_S-3h

description:
Human cervical carcinoma cells (HeLa cells; American-Type Culture
Collection) were cultured in a 10 cm tissue culture plate. Cells were serum starved overnight and infected with phosphate buffered saline for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 3 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed and hybridized to Affymetrix U95A arrays.


title: CVB3_VU-9h-4

status: Public on Oct 04 2003

description: Human cervical carcinoma cells (HeLa cells; American-Type Culture Collection) were cultured in a 10 cm tissue culture plate. Cells were exposed to DMSO + U0126 (10μM) overnight and infected with coxsackievirus B3 (multiplicity of infection=10) for 45 min under serum-free conditions. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 9 hours following infection, cells were scraped into 1ml ice cold PBS and spun at 1000 rpm for 10 minutes. Supernatant was removed and cells lysates were flash frozen in liquid nitrogen. Subsequently, RNA was isolated, processed, and hybridized to Affymetrix U95A arrays.