title: CCFAlmasan_CaP1_0C

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, control: no irradiation, Affymetrix HGU-95C GeneChip(R).
DESIGN: The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  This sample was not irradiated.
EXTRACTION:  PolyA+ mRNA was prepared from total RNA by using QIAGEN Oligotex kits.
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from the PolyA+ mRNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented. A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HGU-95C GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, FlexGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:1066, Count:32
Corner-  Avg:44318, Count:32
Background  Avg:482.21, Stdev:5.29, Max:493.5, Min:470.1
Noise  Avg:13.88, Stdev:0.36, Max:14.8, Min:12.6
RawQ  19.61
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  2.138551
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip (A-E) was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: CCFAlmasan_CaP1_6A

status: Public on Jun 01 2004

type: RNA

city: Cleveland

first: John

middle: Gilmary

last: Hissong

state: OH

address: 9500 Euclid Ave.

department: Cancer Biology

country: USA

institute: Lerner Research Institute Cleveland Clinic Foundation

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, harvested 6 hr after irradiation to a dose of 10 Sv, Affymetrix HGU-95Av1 GeneChip(R).
DESIGN: The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line.  PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.)  The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  Harvested 6 hr after irradiation to a dose of 10 Sv from a J.L. Shepherd and Associates (San Fernando, CA) Irradiator containing a Cesium 137 source.  The dose was delivered at a rate of 2.8 Sv/min.  Cesium 137 is a mixed beta/gamma emmitter; the gamma ray emitted has an energy of 661.657 keV.  For details see, for example, www.bnl.gov/ton.
EXTRACTION:  PolyA+ mRNA was prepared from total RNA by using QIAGEN Oligotex kits.
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from the PolyA+ mRNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented. A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HGU-95Av1 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, FlexGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:1181, Count:32
Corner-  Avg:44344, Count:32
Background  Avg:502.39, Stdev:4.67, Max:521.6, Min:493.8
Noise  Avg:14.88, Stdev:0.54, Max:17.3, Min:13.7
RawQ  19.60
Alpha1  0.04
Alpha2  0.06
Tau  0.015
Gamma1H  0.0025
Gamma1L  0.0025
Gamma2H  0.003
Gamma2L  0.003
Perturbation  1.1
TGT  300
NF  1.000000
SF  0.963883
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip (A-E) was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.  Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray

molecule: total RNA

organism: Homo sapiens

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


title: CCFAlmasan_CaP1_0A

description:
SUMMARY: Response to radiation in prostate adenocarcinoma.
LNCaP C4-2 cells, polyA+ mRNA extracted, control: no irradiation, Affymetrix HGU-95Av1 GeneChip(R).
DESIGN: The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv(Gy) from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
BIOLOGICAL SAMPLE: Cultured LNCaP C4-2 human prostate adenocarcinoma cells.  The parent LNCaP cell lines were obtained from ATCC (Manassas, VA).  The derived LNCaP cell lines are described in Thalmann, GN, et.al., Cancer Res., 54:2577-2581, 1994, PMID: 8168083.  (See also Ray, S and Almasan, A, Cancer Res, 63:4713-4723, 2003, PMID: 1290765.) The C4-2 derivative of the LNCaP cell line is androgen independent.
IRRADIATION:  This sample was not irradiated.
EXTRACTION:  PolyA+ mRNA was prepared from total RNA by using QIAGEN Oligotex kits.
PROCESSING:  Sample processing proceeded as recommended in the Affymetrix GeneChip(R) Expression Analysis Manual.  Double-stranded cDNA was prepared from the PolyA+ mRNA using the GIBCO BRL SuperScript Choice system.  An in vitro transcription reaction was used to produce biotin-labeled cRNA using the Enzo BioArray High Yield RNA Transcript Labeling Kit.  The sample was then purified using the QIAGEN RNA MiniKit and then fragmented. A hybridization mixture was prepared including the fragmented cRNA, the Affymetrix recommended control cocktail and herring sperm DNA.
MICROARRAY:  Affymetrix HGU-95Av1 GeneChip(R).
HYBRIDIZATION: Affymetrix Hybridization Oven 640, Time: 16 hr, Temp: 45 C, Carousel Rotation Speed: 60 rpm.
WASHING AND STAINING:  Affymetrix Fluidics Station 400, FlexGE:WS2v3 Protocol.
SCANNING: Affymetrix Agilent 2500 Scanner, Pixel Size: 3 microns, Filter: 570 nm, Scans: 2.  Original calibration.  The source of the data recorded below is the scan before the final antibody stain. (See the Affymetrix technical note, GeneArray(R) Scanner Update, Part 700575 Revision 2.)
DEVICE SPECIFIC ANALYSIS: Affymetrix Microarray Suite 5.0
Algorithm:  Statistical
Corner+  Avg:928, Count:32
Corner-  Avg:33681, Count:32
Background  Avg:447.32, Stdev:2.84, Max:455.8, Min:440.0
Noise  Avg:14.31, Stdev:0.38, Max:15.4, Min:13.3
RawQ  18.78
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  0.795181
SFGene  All
DEVICE INDEPENDENT ANALYSIS: Silicon Genetics' GeneSpring(R) version 6, build 1333.  The Microarray Suite 5 output data was further processed with GeneSpring(R).  Each chip (A-E) was normalized separately.  Each measurement on the chip was divided by the 50th percentile of all measurements (the median) in that sample.  The percentile was calculated with all normalized measurements above 0.    Values below 0.0 were set to 0.0.
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray


title: IgG1c-2

status: Public on May 27 2004

city: Baltimore

first: Myriam

last: Gorospe

state: MD

address: 5600 Nathan Shock Drive

institute: NIA

description: RNA from IP reactions using untreated cells and anti-IgG1 antibody. Biological repeat 2.

source_name: RKO cells


title: Tuv-2

description: RNA from IP reactions using UVC-treated cells and anti-TIAR antibody. Biological repeat 2.


title: Tuv-3

description: RNA from IP reactions using UVC-treated cells and anti-TIAR antibody. Biological repeat 3.


title: IgG1uv-1

description: RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody. Biological repeat 1.


title: IgG1c-3

description: RNA from IP reactions using untreated cells and anti-IgG1 antibody. Biological repeat 3.


title: IgG1c-1

description: RNA from IP reactions using untreated cells and anti-IgG1 antibody. Biological repeat 1.


title: IgG1uv-2

description: RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody. Biological repeat 2.


title: IgG1uv-3

description: RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody. Biological repeat 3.


title: Tc-3

description: RNA from IP reactions using untreated cells and anti-TIAR antibody. Biological repeat 3.


title: Tuv-1

description: RNA from IP reactions using UVC-treated cells and anti-TIAR antibody. Biological repeat 1.


title: Tc-1

description: RNA from IP reactions using untreated cells and anti-TIAR antibody. Biological repeat 1.


title: liver, 48h starved, chip 22

city: Karlsruhe

first: Michael

middle: J.

last: Pankratz

department: Institute of Genetics

country: Germany

institute: Forschungszentrum Karlsruhe

description:
Mice used in this study were 129/sv males, 8-15 weeks of age, which were housed individually and received water ad libitum. Total RNA and polyA RNA were prepared for each animal separately, and equal amounts of polyA RNA from each batch were pooled. Pool2 normal = 3 animals (No. N4, N5 and N6) fed during and before the 48h experiment with standard food, ad libitum; pool2 starved = 3 animals (No. St4, St5 and St6) fed before the experiment with standard food, ad libitum, starved during the 48h experiment.
The microarray was scanned 3 times: low scan (suffix _L in data table) with a low amplification / intensity to avoid saturated spots for proper data analysis, high scan (suffix _H in data table) with a high amplification / intensity to detect also weak fluorescent spots which are missed in the low scan and medium scan which lies between high and low intensity and gives additional data points for subsequent calculations. For additional information see publication and web link.
Keywords = nutrient response
Keywords = starvation
Keywords = liver
Keywords = anti-aging
Keywords = longevity
Lot batch = mp7_033

organism: Mus musculus

source_name: pool2, normal

source_name: pool2, starved


title: Tc-2

description: RNA from IP reactions using untreated cells and anti-TIAR antibody. Biological repeat 2.


title: Injured 30 day Rat Retina 3

status: Public on May 26 2004

city: Memphis

first: Eldon

middle: E

last: Geisert

state: TN

address: 855 Monroe Avenue

department: Ophthalmology

institute: University of Tennesse

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG093

organism: Rattus norvegicus

source_name: Sprague-Dawley Rat retina (male); 30d post injury


title: Injured 30 day Rat Retina 2

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG019


title: Injured 7 day Rat Retina 3

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG077

source_name: Sprague-Dawley Rat retina (male); 7d post injury


title: Injured 1 day Rat Retina 3

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0080

source_name: Sprague-Dawley Rat retina (male); 1d post injury


title: Injured 3 day Rat Retina 2

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG070

source_name: Sprague-Dawley Rat retina (male); 3d post injury


title: Injured 7 day Rat Retina 1

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG011


title: Injured 1 day Rat Retina 2

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0079


title: Injured 30 day Rat Retina 1

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG018


title: Injured 3 day Rat Retina 1

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG069


title: Injured 7 day Rat Retina 2

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG012


title: Injured 1 day Rat Retina 1

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0076


title: Injured 4h Rat Retina

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape or Retina.  Retinas from two animas were pooled.

Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0078

source_name: Sprague-Dawley Rat retina (male); 4h post injury


title: Injured 4h Rat Retina 3

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of Retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0082


title: Injured 3 day Rat Retina 3

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG075


title: Injured 4h Rat Retina 2

description:
Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape or Retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG0081


title: WT_30C_3

status: Public on May 25 2004

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: RNA extracted from 5 male and 5 female dU2AF50 wild-type flies grown at the restrictive temperature (25C)

organism: Drosophila melanogaster

source_name: Whole flies


title: S284Y_30C_2

description: RNA extracted from 5 male and 5 female dU2AF50 S284Y mutant flies grown at the restrictive temperature (30C)


title: P-c-7-A

status: Public on Jun 02 2004

description: RNA from polysomal fraction #7 collected from untreated cells. Biological repeat 1.


title: S284Y_30C_3


title: WT_30C_2


title: WT_25C_1

description: RNA extracted from 5 male and 5 female dU2AF50 wild-type flies grown at the permisive temperature (25C)


title: P-c-8-A

description: RNA from polysomal fraction #8 collected from untreated cells. Biological repeat 1.


title: imanitib8

status: Public on May 24 2004

city: Heidelberg

first: Benedikt

last: Brors

address: INF 280

department: Theor. Bioinformatics

institute: German Cancer Research Center (DKFZ)

description:
CD34+ cells from imanitib-treated patients
Keywords = CD34+
Keywords = bone marrow
Keywords = Imatinib
Lot batch = 3001955

source_name: bone marrow


title: S284Y_30C_1


title: WT_30C_1


title: S284Y_25C_3

description: RNA extracted from 5 male and 5 female dU2AF50 S284Y mutant flies grown at the permisive temperature (25C)


title: WT_25C_2


title: S284Y_25C_1


title: WT_25C_3


title: S284Y_25C_2


title: imanitib6


title: imanitib5


title: imanitib4


title: control3

description:
Normal CD34+ cells
Keywords = CD34+
Keywords = bone marrow
Keywords = Imatinib
Lot batch = 3001955


title: imanitib3


title: control5


title: control4


title: imanitib1

description:
CD34+ cells from imanitib-treated patients
Keywords = CD34+
Keywords = bone marrow
Keywords = Imatinib
Lot batch = 3001789


title: imanitib2


title: control2


title: control6


title: control1

description:
Normal CD34+ cells
Keywords = CD34+
Keywords = bone marrow
Keywords = Imatinib
Lot batch = 3001789


title: non-branching region of E11.5 lung-S3

status: Public on May 23 2004

city: Boston

first: Jining

last: Lu

state: MA

institute: Boston University School of Medicine

description: The non-branching region include both main bronchi and part of trachea

source_name: from dissected tissue


title: non-branching region of e11.5 lung-S1


title: non-branching region of E11.5 lung-S2


title: branching region of E11.5 lung-S1

description: Both right and left lungs were included for the analysis of the branching region


title: Branching region of E11.5 lung-S2


title: Branching region of e11.5 lung-S3


title: B chip Version2: time 15 day Replicate 4

status: Public on May 21 2004

city: Portland

first: Yuan

last: Fang

state: OR

address: 3375 SW Terwilliger Blvd

department: Ophthalmology, Casey Eye Institute

institute: Oregon Health & Science University

description:
Examine the effect of stimulation stress produced by chemical burn to the mice cornea in the lacrimal gland over a time course (0.5 - 360 hours) in comparison with the non-stimulated control animals.
Using silver nitrate applicator (silver nitrate 37.5 mg and potassium nitrate 12.5 mg,  Graham-Field,Inc.,) do two burns per eye, each with a separate applicator.
For animals observed for more than 24 hours, eyes were then treted with gentamicin ointment to minimize infection.
Total RNA were extracted from both burn and control eyes and were covalently coupled separately with Cy5 and Cy3 monoreactive fluors. The Cy5 and Cy3 labelled RNA were hybridized to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with ScanArray 4000XL and image intensity data were extracted and analyzed with Imagene analysis software.
Keywords = Cornea burn

source_name: Cornea burn eyes, 15 day Replicate 4

source_name: Matched control, non burn eyes


title: B chip Version2: time 15 day Replicate 1

source_name: Cornea burn eyes, 15 day Replicate 1


title: B chip Version2: time 15 day Replicate 6

source_name: Cornea burn eyes, 15 day Replicate 6


title: B chip Version2: time 15 day Replicate 2

source_name: Cornea burn eyes, 15 day Replicate 2


title: B chip Version2: time 15 day Replicate 3

source_name: Cornea burn eyes, 15 day Replicate 3


title: B chip Version2: time 5 day Replicate 6

source_name: Cornea burn eyes, 5 day Replicate 6


title: B chip Version2: time 5 day Replicate 5

source_name: Cornea burn eyes, 5 day Replicate 5


title: B chip Version2: time 3 day Replicate 6

source_name: Cornea burn eyes, 3 day Replicate 6


title: B chip Version2: time 5 day Replicate 1

source_name: Cornea burn eyes, 5 day Replicate 1


title: B chip Version2: time 5 day Replicate 3

source_name: Cornea burn eyes, 5 day Replicate 3


title: B chip Version2: time 5 day Replicate 2

source_name: Cornea burn eyes, 5 day Replicate 2


title: B chip Version2: time 5 day Replicate 4

source_name: Cornea burn eyes, 5 day Replicate 4


title: B chip Version2: time 8 hour Replicate 1

source_name: Cornea burn eyes, 8 hour Replicate 1


title: B chip Version2: time 3 hour Replicate 4

source_name: Cornea burn eyes, 3 hour Replicate 4


title: B chip Version2: time 3 day Replicate 5

source_name: Cornea burn eyes, 3 day Replicate 5


title: B chip Version2: time 8 hour Replicate 2

source_name: Cornea burn eyes, 8 hour Replicate 2


title: B chip Version2: time 3 hour Replicate 2

source_name: Cornea burn eyes, 3 hour Replicate 2


title: A chip: time 15 day Replicate 6

source_name: Matched control, non burn eyes


title: A chip: time 15 day Replicate 5

source_name: Cornea burn eyes, 15 day Replicate 5


title: B chip Version2: time 3 hour Replicate 5

source_name: Cornea burn eyes, 3 hour Replicate 5


title: A chip: time 15 day Replicate 4

source_name: Cornea burn eyes, 15 day Replicate 4


title: B chip Version2: time 3 day Replicate 2

source_name: Cornea burn eyes, 3 day Replicate 2


title: B chip Version2: time 3 day Replicate 1

source_name: Cornea burn eyes, 3 day Replicate 1


title: B chip Version2: time 24 hour Replicate 2

source_name: Cornea burn eyes, 24 hour Replicate 2


title: B chip Version2: time 3 day Replicate 4

source_name: Cornea burn eyes, 3 day Replicate 4


title: B chip Version2: time 3 day Replicate 3

source_name: Cornea burn eyes, 3 day Replicate 3


title: B chip Version2: time 24 hour Replicate 1

source_name: Cornea burn eyes, 24 hour Replicate 1


title: A chip: time 15 day Replicate 3

source_name: Cornea burn eyes, 15 day Replicate 3


title: B chip Version2: time 3 hour Replicate 1

source_name: Cornea burn eyes, 3 hour Replicate 1


title: B chip Version2: time 1 hour Replicate 2

source_name: Cornea burn eyes, 1 hour Replicate 2


title: B chip Version2: time 1 hour Replicate 1

source_name: Cornea burn eyes, 1 hour Replicate 1


title: B chip Version2: time 3 hour Replicate 3

source_name: Cornea burn eyes, 3 hour Replicate 3


title: imanitib7

source_name: bone marrow


title: B chip Version2: time 15 day Replicate 5


title: dt40sage

status: Public on Oct 06 2004

type: SAGE

anchor: NlaIII

city: Neuherberg

first: Randolph

middle: B

last: Caldwell

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute for Molecular Radiobiology

institute: GSF-National Reseearch Center

description:
This library represents total RNA from DT40 Cre1 cells
This work was supported by the EU grants 'Genetics in a cell line' and 'Mechanisms of gene integration'
Library constructed in the laboratory of Jean-Marie Buerstedde, M.D.
submitted for publication with the title: Evaluation of the chicken transcriptome by SAGE of B cell and the DT40 cell line
Organ: bursa of Fabricius
Lab host: E. coli
Vector: pZErO-1
Vector type: plasmid
Library treatment: non-normalized
Keywords = chicken transcriptome SAGE Bursal cell DT40
Lot batch =

organism: Gallus gallus

source_name: ALV induced bursal cell line


title: A chip: time 15 day Replicate 1

source_name: Cornea burn eyes, 15 day Replicate 1

source_name: Matched control, non burn eyes


title: A chip: time 3 day Replicate 5

source_name: Cornea burn eyes, 3 day Replicate 5


title: A chip: time 5 day Replicate 5

source_name: Cornea burn eyes, 5 day Replicate 5


title: A chip: time 3 day Replicate 6

source_name: Cornea burn eyes, 3 day Replicate 6


title: A chip: time 24 hour Replicate 5

source_name: Cornea burn eyes, 24 hour Replicate 5


title: A chip: time 5 day Replicate 6

source_name: Cornea burn eyes, 5 day Replicate 6


title: A chip: time 5 day Replicate 1

source_name: Cornea burn eyes, 5 day Replicate 1


title: A chip: time 15 day Replicate 2

source_name: Cornea burn eyes, 15 day Replicate 2


title: A chip: time 5 day Replicate 4

source_name: Cornea burn eyes, 5 day Replicate 4


title: A chip: time 24 hour Replicate 1

source_name: Cornea burn eyes, 24 hour Replicate 1


title: A chip: time 8 hour Replicate 5

source_name: Cornea burn eyes, 8 hour Replicate 5


title: A chip: time 3 day Replicate 2

source_name: Cornea burn eyes, 3 day Replicate 2


title: A chip: time 3 day Replicate 1

source_name: Cornea burn eyes, 3 day Replicate 1


title: A chip: time 8 hour Replicate 3

source_name: Cornea burn eyes, 8 hour Replicate 3


title: A chip: time 8 hour Replicate 2

source_name: Cornea burn eyes, 8 hour Replicate 2


title: A chip: time 8 hour Replicate 6

source_name: Cornea burn eyes, 8 hour Replicate 6


title: A chip: time 24 hour Replicate 2

source_name: Cornea burn eyes, 24 hour Replicate 2


title: A chip: time 5 day Replicate 2

source_name: Cornea burn eyes, 5 day Replicate 2

source_name: Matched control, non burn eyes


title: A chip: time 24 hour Replicate 3

source_name: Cornea burn eyes, 24 hour Replicate 3


title: A chip: time 8 hour Replicate 4

source_name: Cornea burn eyes, 8 hour Replicate 4


title: A chip: time 3 day Replicate 4

source_name: Cornea burn eyes, 3 day Replicate 4


title: A chip: time 3 day Replicate 3

source_name: Cornea burn eyes, 3 day Replicate 3


title: A chip: time 5 day Replicate 3

source_name: Cornea burn eyes, 5 day Replicate 3


title: A chip: time 8 hour Replicate 1

source_name: Cornea burn eyes, 8 hour Replicate 1


title: A chip: time 24 hour Replicate 4

source_name: Cornea burn eyes, 24 hour Replicate 4


title: A chip: time 3 hour Replicate 5

source_name: Cornea burn eyes, 3 hour Replicate 5


title: A chip: time 3 hour Replicate 6

source_name: Cornea burn eyes, 3 hour Replicate 6


title: B chip Version1: time 24 hour Replicate 5

source_name: Cornea burn eyes, 24 hour Replicate 5


title: B chip Version1: time 24 hour Replicate 6

source_name: Cornea burn eyes, 24 hour Replicate 6


title: A chip: time 3 hour Replicate 4

source_name: Cornea burn eyes, 3 hour Replicate 4


title: A chip: time 3 hour Replicate 3

source_name: Cornea burn eyes, 3 hour Replicate 3


title: A chip: time 3 hour Replicate 1

source_name: Cornea burn eyes, 3 hour Replicate 1


title: B chip Version1: time 8 hour Replicate 6

source_name: Cornea burn eyes, 8 hour Replicate 6


title: B chip Version1: time 24 hour Replicate 3


title: A chip: time 30 min Replicate 6

source_name: Cornea burn eyes, 30 min Replicate 6


title: A chip: time 3 hour Replicate 2

source_name: Cornea burn eyes, 3 hour Replicate 2

source_name: Matched control, non burn eyes


title: B chip Version1: time 24 hour Replicate 4


title: A chip: time 1 hour Replicate 5

source_name: Cornea burn eyes, 1 hour Replicate 5


title: A chip: time 1 hour Replicate 2

source_name: Cornea burn eyes, 1 hour Replicate 2


title: B chip Version1: time 8 hour Replicate 4

source_name: Cornea burn eyes, 8 hour Replicate 4


title: B chip Version1: time 8 hour Replicate 5

source_name: Cornea burn eyes, 8 hour Replicate 5


title: JC_U74Cv2_WT

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: one week old 129sv-C57BVl-6

source_name: TOtal RNA spermatogonia


title: A chip: time 1 hour Replicate 4

source_name: Cornea burn eyes, 1 hour Replicate 4


title: JC_U74Cv2_Null

description:
one week old 129sv-C57BVl-6
Zfp145 knock out

source_name: total spermatogonia


title: A chip: time 1 hour Replicate 3

source_name: Cornea burn eyes, 1 hour Replicate 3


title: A chip: time 1 hour Replicate 1

source_name: Cornea burn eyes, 1 hour Replicate 1


title: B chip Version1: time 1 hour Replicate 5


title: B chip Version1: time 1 hour Replicate 3


title: JC_U74Bv2_WT

description: one week old 129sv-C57Bl/6

source_name: total RNA spermatogonia


title: JC_U74Bv2_Null

description:
one week old 129sv-C57Bl/6
Zfp145 knock out

source_name: Total RNA spermatogonia


title: A chip: time 30 min Replicate 5

source_name: Cornea burn eyes, 30 min Replicate 5


title: A chip: time 30 min Replicate 3

source_name: Cornea burn eyes, 30 min Replicate 3


title: B chip Version1: time 1 hour Replicate 6

source_name: Cornea burn eyes, 1 hour Replicate 6


title: B chip Version1: time 30 min Replicate 6

source_name: Cornea burn eyes, 30 min Replicate 6


title: JC_U74Av2_Null

description:
one week old 129sv/c57Bl6
Zfp145 knock out


title: B chip Version1: time 30 min Replicate 3


title: B chip Version1: time 30 min Replicate 2

source_name: Cornea burn eyes, 30 min Replicate 2


title: B chip Version1: time 30 min Replicate 5

source_name: Matched control, non burn eyes


title: A chip: time 30 min Replicate 4

source_name: Cornea burn eyes, 30 min Replicate 4


title: A chip: time 30 min Replicate 1

source_name: Cornea burn eyes, 30 min Replicate 1


title: B chip Version1: time 30 min Replicate 4


title: Experiment 1: TIME-KSHV+Ad-RTA T=12h

status: Public on May 18 2004

city: San Francisco

first: Don

last: Ganem

state: CA

institute: University of California, San Francisco

description: Experiment 1: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for 12h

source_name: TIME-KSHV+Ad-RTA T=12h

source_name: TIME (Reference)


title: Experiment 3: TIME+Ad-RTA

description: Experiment 3: TIME cells expressing KSHV RTA alone

source_name: TIME+Ad-RTA

source_name: TIME-MOCK (Reference)


title: Experiment 2: TIME-KSHV+Ad-RTA T=12h

description: Experiment 2: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for  T=12h

source_name: TIME-KSHV+Ad-RTA  T=12h

source_name: TIME-mock (Reference)


title: B chip Version1: time 1 hour Replicate 4

source_name: Cornea burn eyes, 1 hour Replicate 4


title: B chip Version1: time 30 min Replicate 1


title: Camptothecin Treated HeLa Replicate 1 U133A

city: Cambridge

first: Garrett

middle: M

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

description:
Cancer Res. 2004 Mar 15;64(6):2096-104
Keywords = HeLa
Keywords = Camptothecin

source_name: Total RNA from camptothecin treated HeLa cells


title: JC_U74Av2_WT

description: one week old 129sv/c57Bl6

source_name: total RNA spermatogonia


title: Untreated HeLa Replicate 3 U133A

source_name: Total RNA from untreated HeLa cells


title: Camptothecin Treated HeLa Replicate 3 U133A


title: Experiment 2: TIME-vGPCR

description: TIME cells expressing KSHV-vGPCR alone

source_name: TIME-vGPCR


title: Experiment 2: TIME+Ad-RTA

description: Experiment 2: Time cells expressing KSHV RTA alone

source_name: TIME-mock


title: A chip: time 30 min Replicate 2


title: Experiment 2: TIME-KSHV+Ad-RTA T=6h

description: Experiment 2: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for 6h

source_name: TIME-KSHV+Ad-RTA T=6h


title: Experiment 1: TIME-KSHV+Ad-RTA T=6h

description: Experiment 1: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for 6h


title: Experiment 1: KSHV+Ad-RTA T=20h

description: Experiment 1: Time cells infected with KSHV and lytically reactivated for 20h

source_name: TIME-KSHV+Ad-RTA T=20h


title: Experiment 1: TIME+Ad-RTA

description: Experiment 1: TIME cells expressing KSHV RTA alone

source_name: TIME-mock (reference)


title: Experiment 3: TIME-vGPCR

description: Experiment 3: TIME cells expressing KSHV-vGPCR alone

source_name: TIME-MOCK (reference)


title: ASLV infected 293T-TVA cells

status: Public on May 19 2004

city: La Jolla

first: Richard

middle: Steven

last: Mitchell

address: 10010 North Torrey Pines Rd

department: Infectious Disease Laboratory

institute: The Salk Institute

description: 293T cells engineered to express TVA receptor infected with an ASLV vector (see Mitchell et al., PLoS).  RNA isolated 48 hours later.

source_name: ASLV infected 293T-TVA cells


title: ASLV infected 293T-TVA cells #2

description:
293T cells engineered to express TVA receptor infected with an ASLV vector (see Mitchell et al., PLoS).  RNA isolated 48 hours later.
Sample 2.


title: Experiment 3: TIME-KSHV+Ad-RTA  T=6h

description: Experiment 3: TIME cells containing KSHV lytically reactivated with Ad-RTA for 6 hours

source_name: TIME-KSHV+Ad-RTA  T=6h


title: Experiment 1: TIME+Ad-vGPCR

description: Experiment 1: TIME cells expressing KSHV vGPCR alone

source_name: TIME+Ad-vGPCR

source_name: TIME (Reference)


title: Camptothecin Treated HeLa Replicate 2 U133A


title: Untreated HeLa Replicate 4 U133A


title: Experiment 3: TIME-KSHV+Ad-RTA T=20h

description: Experiment 3: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for 20h

source_name: TIME-MOCK (Reference)


title: Untreated HeLa Replicate 2 U133A


title: Untreated HeLa Replicate 1 U133A


title: Experiment 3: TIME-KSHV+Ad-RTA T=12h

description: Experiment 3: TIME cells infected with KSHV and lytically reactivated with Ad-RTA for 12h

source_name: TIME-KSHV+Ad-RTA T=12h


title: WT_RAD001_12hours_6

status: Public on May 17 2004

city: Durham

first: Phillip

middle: George

last: Febbo

state: NC

address: 2175 CIEMAS, 101 Science Drive

department: Medicine, Molecular Genetics and Microbiology

institute: Duke Institute for Genome Sciences and Policy

description:
Murine prostates were isolated from transgenic mice (probasin driven AKT) v. littermate wild-type controls treated with either RAD001 (MTOR inhibition) or placebo. 10 micrograms of total RNA was used to synthesize biotin-labeled cRNA using our standard protocol
Keywords = Prostate AKT RAD001 MTOR
Lot batch = 2

source_name: Murine prostate


title: WT_PLACEBO_12hours_1


title: WT_RAD001_48hours_3


title: WT_RAD001_12hours_5


title: WT_RAD001_12hours_4


title: WT_RAD001_12hours_2


title: WT_PLACEBO_12hours_4


title: WT_RAD001_48hours_4


title: WT_RAD001_48hours_5


title: WT_RAD001_12hours_3


title: WT_PLACEBO_48hours_4


title: WT_RAD001_48hours_2


title: WT_PLACEBO_12hours_2


title: WT_RAD001_48hours_1


title: WT_PLACEBO_12hours_3


title: WT_PLACEBO_48hours_2


title: WT_RAD001_12hours_1


title: WT_PLACEBO_48hours_1


title: AKT_PLACEBO_12hours_1

description:
Murine prostates were isolated from transgenic mice (probasin driven AKT) v. littermate wild-type controls treated with either RAD001 (MTOR inhibition) or placebo. 10 micrograms of total RNA was used to synthesize biotin-labeled cRNA using our standard protocol
Keywords = Prostate AKT RAD001 MTOR
Lot batch = 1


title: WT_PLACEBO_48hours_3


title: AKT_RAD001_12hours_5


title: AKT_PLACEBO_12hours_4


title: AKT_PLACEBO_12hours_3


title: AKT_PLACEBO_12hours_5


title: B chip Version1: time 8 hour Replicate 3

description:
Examine the effect of stimulation stress produced by chemical burn to the mice cornea in the lacrimal gland over a time course (0.5 - 360 hours) in comparison with the non-stimulated control animals.
Using silver nitrate applicator (silver nitrate 37.5 mg and potassium nitrate 12.5 mg,  Graham-Field,Inc.,) do two burns per eye, each with a separate applicator.
For animals observed for more than 24 hours, eyes were then treted with gentamicin ointment to minimize infection.
Total RNA were extracted from both burn and control eyes and were covalently coupled separately with Cy5 and Cy3 monoreactive fluors. The Cy5 and Cy3 labelled RNA were hybridized to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with ScanArray 4000XL and image intensity data were extracted and analyzed with Imagene analysis software.
Keywords = Cornea burn

source_name: Cornea burn eyes, 8 hour Replicate 3

source_name: Matched control, non burn eyes


title: AKT_PLACEBO_12hours_2


title: AKT_RAD001_48hours_1


title: AKT_RAD001_12hours_4


title: AKT_PLACEBO_48hours_3


title: AKT_RAD001_12hours_3


title: AKT_PLACEBO_48hours_2


title: AKT_PLACEBO_48hours_1


title: WT macrophages, E. coli vs. Mock, mouse 4

status: Public on May 15 2004

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

description:
Bone marrow was isolated from 6-8 week old C57BL/6J wild type and MyD88-deficient mice.
Macrophages from these marrows were cultured in DMEM media supplemented with 10% FBS and 15% L929 conditioned media (a source for CSF-1) for 8 days (plated at 3 million cells per 10 cm cell culture dish).
Cells were treated for 2 hours with either 10 ng/mL re-purified LPS (from E. coli O111), live E. coli bacteria (log phase; 1 bacteria per macrophage) or media only as a reference (Mock).
High quality total RNA was purified using a combination of the TRIzol protocol (Invitrogen) and RNeasy columns (Qiagen) according to the manufacturer's instructions.
RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies).
Total RNA samples were reverse transcribed and differentially labeled with Cy3 and Cy5 dyes (Amersham) using the Atlas PowerScript Fluorescent Labeling Kit (BD Biosciences).
Labeled cDNA samples were hybridized over night in a Genomic Solutions hybridization station (Perkin-Elmer).
The hybridization buffer was 3xSSC, 50 mM Hepes buffer, 0.1% SDS, pH 7.0, 30 ng/mL salmon sperm DNA, 30 ng/mL poly-A DNA, 30 ng/mL mouse Cot-1 DNA.
The microarray slides were scanned with a GenePix 4000B microarray scanner and images quantified with the GenePix Pro 3.0 software (Axon Instruments).
All data analysis and statistical analysis was performed with BioArray Software Environment (BASE; Lund University, Sweden) and GeneSpring software (Silicon Genetics).
TIFF images can be downloaded from http://pga.mgh.harvard.edu
Keywords = Mus musculus, LPS, endotoxin, macrophages, MyD88

source_name: Macrophages from wildtype mouse 4 treated with live E. coli (1 bact. per mac.) for 2 hours

source_name: Macrophages from wildtype mouse 4 treated with media only for 2 hours


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 1, dye swap

source_name: Macrophages from MyD88-/- mouse 1 treated with media only for 2 hours

source_name: Macrophages from MyD88-/- mouse 1 treated with live E. coli (1 bact. per mac.) for 2 hours


title: AKT_PLACEBO_48hours_4


title: AKT_RAD001_48hours_4


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 4, dye swap

source_name: Macrophages from MyD88-/- mouse 4 treated with media only for 2 hours

source_name: Macrophages from MyD88-/- mouse 4 treated with live E. coli (1 bact. per mac.) for 2 hours


title: AKT_RAD001_12hours_2


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 1


title: MyD88-/- macrophages, LPS vs. Mock, mouse 4

source_name: Macrophages from MyD88-/- mouse 4 treated with 10 ng/mL LPS for 2 hours


title: WT macrophages, E. coli vs. Mock, mouse 4, dye swap


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 3, dye swap

source_name: Macrophages from MyD88-/- mouse 3 treated with media only for 2 hours

source_name: Macrophages from MyD88-/- mouse 3 treated with live E. coli (1 bact. per mac.) for 2 hours


title: AKT_RAD001_12hours_1


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 3


title: WT macrophages, E. coli vs. Mock, mouse 3

source_name: Macrophages from wildtype mouse 3 treated with live E. coli (1 bact. per mac.) for 2 hours

source_name: Macrophages from wildtype mouse 3 treated with media only for 2 hours


title: AKT_RAD001_48hours_2


title: WT macrophages, E. coli vs. Mock, mouse 3, dye swap


title: MyD88-/- macrophages, LPS vs. Mock, mouse 3

source_name: Macrophages from MyD88-/- mouse 3 treated with 10 ng/mL LPS for 2 hours


title: AKT_PLACEBO_48hours_5


title: AKT_RAD001_48hours_5


title: WT macrophages, E. coli vs. Mock, mouse 2, dye swap

source_name: Macrophages from wildtype mouse 2 treated with media only for 2 hours

source_name: Macrophages from wildtype mouse 2 treated with live E. coli (1 bact. per mac.) for 2 hours


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 4


title: WT macrophages, E. coli vs. Mock, mouse 1

source_name: Macrophages from wildtype mouse 1 treated with live E. coli (1 bact. per mac.) for 2 hours

source_name: Macrophages from wildtype mouse 1 treated with media only for 2 hours


title: WT macrophages, E. coli vs. Mock, mouse 1. dye swap


title: Pig embryo array Filamentous sample 1

status: Public on May 13 2004

city: Ames

first: Christopher

middle: K

last: Tuggle

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description:
A novel porcine cDNA macroarray, containing PCR products selected for embryonic expression, was used for transcriptional profiling during conceptu1 development. Total RNA from quadruplicate samples of small spherical (1-5mm), large spherical (6-11mm), tubular (13-45mm), and filamentous (>100mm) was extracted, amplified, and converted to 32P labeled target and hybridized to membranes.
Keywords = Gene expression
Keywords = porcine conceptus
Keywords = cDNA microarray
Keywords = peri-implantation
Keywords = transcriptional profiling

organism: Sus scrofa

source_name: Amplified RNA from porcine Filamentous embryo


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 2, dye swap

source_name: Macrophages from MyD88-/- mouse 2 treated with media only for 2 hours

source_name: Macrophages from MyD88-/- mouse 2 treated with live E. coli (1 bact. per mac.) for 2 hours


title: Pig embryo array Filamentous sample 2


title: Pig embryo array Tubular sample 4

source_name: Amplified RNA from porcine Tubular embryo


title: WT macrophages, E. coli vs. Mock, mouse 2


title: MyD88-/- macrophages, LPS vs. Mock, mouse 1, dye swap

source_name: Macrophages from MyD88-/- mouse 1 treated with media only for 2 hours

source_name: Macrophages from MyD88-/- mouse 1 treated with 10 ng/mL LPS for 2 hours


title: MyD88-/- macrophages, E. coli vs. Mock, mouse 2


title: Pig embryo array Filamentous sample 3


title: Wildtype macrophages, LPS vs. Mock, mouse 4, dye swap

source_name: Macrophages from wildtype mouse 4 treated with media only for 2 hours

source_name: Macrophages from wildtype mouse 4 treated with 10 ng/mL LPS for 2 hours


title: LPS

status: Public on May 14 2004

city: Philadelphia

first: Colleen

middle: M.

last: Kane

state: PA

address: 3610 Hamilton Walk

department: Department of Pathobiology

institute: University of Pennsylvania

description:
CD11c+ IL10-/-DC incubated for 6 hours with LPS
Lot batch = EXPT1


title: Wildtype macrophages, LPS vs. Mock, mouse 4


title: MyD88-/- macrophages, LPS vs. Mock, mouse 3, dye swap

source_name: Macrophages from MyD88-/- mouse 3 treated with media only for 2 hours


title: MyD88-/- macrophages, LPS vs. Mock, mouse 2, dye swap

source_name: Macrophages from MyD88-/- mouse 2 treated with 10 ng/mL LPS for 2 hours


title: Wildtype macrophages, LPS vs. Mock, mouse 1, dye swap

description:
Bone marrow was isolated from 6-8 week old C57BL/6J wild type and MyD88-deficient mice.
Macrophages from these marrows were cultured in DMEM media supplemented with 10% FBS and 15% L929 conditioned media (a source for CSF-1) for 8 days (plated at 3 million cells per 10 cm cell culture dish).
Cells were treated for 2 hours with either 10 ng/mL re-purified LPS (from E. coli O111), live E. coli bacteria (log phase; 1 bacteria per macrophage) or media only as a reference (Mock).
High quality total RNA was purified using a combination of the TRIzol protocol (Invitrogen) and RNeasy columns (Qiagen) according to the manufacturer's instructions.
RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies).
Total RNA samples were reverse transcribed and differentially labeled with Cy3 and Cy5 dyes (Amersham) using the Atlas PowerScript Fluorescent Labeling Kit (BD Biosciences).
Labeled cDNA samples were hybridized over night in a Genomic Solutions hybridization station (Perkin-Elmer).
The hybridization buffer was 3xSSC, 50 mM Hepes buffer, 0.1% SDS, pH 7.0, 30 ng/mL salmon sperm DNA, 30 ng/mL poly-A DNA, 30 ng/mL mouse Cot-1 DNA.
The microarray slides were scanned with a GenePix 4000B microarray scanner and images quantified with the GenePix Pro 3.0 software (Axon Instruments).
All data analysis and statistical analysis was performed with BioArray Software Environment (BASE; Lund University, Sweden) and GeneSpring software (Silicon Genetics).
Keywords = Mus musculus, LPS, endotoxin, macrophages, MyD88

source_name: Macrophages from mouse 1 treated with media only for 2 hours

source_name: Macrophages from mouse 1 treated with 10 ng/mL LPS for 2 hours


title: Wildtype macrophages, LPS vs. Mock, mouse 2

source_name: Macrophages from wildtype mouse 2 treated with 10 ng/mL LPS for 2 hours


title: MyD88-/- macrophages, LPS vs. Mock, mouse 2


title: Wildtype macrophages, LPS vs. Mock, mouse 3

source_name: Macrophages from wildtype mouse 3 treated with 10 ng/mL LPS for 2 hours

source_name: Macrophages from wildtype mouse 3 treated with media only for 2 hours


title: Pig embryo array Filamentous sample 4


title: Pig embryo array Tubular sample 3


title: MEDIA

description:
CD11c+ IL10-/-DC incubated for 6 hours in media alone
Lot batch = EXPT1


title: SEA/LPS

description:
CD11c+ IL10-/-DC incubated for 6 hours with SEA/LPS
Lot batch = EXPT1


title: MyD88-/- macrophages, LPS vs. Mock, mouse 1


title: SEA

description:
CD11c+ IL10-/-DC incubated for 6 hours with SEA
Lot batch = EXPT1


title: Wildtype macrophages, LPS vs. Mock, mouse 3, dye swap


title: Wildtype macrophages, LPS vs. Mock, mouse 2, dye swap

source_name: Macrophages from wildtype mouse 2 treated with media only for 2 hours


title: Wildtype macrophages, LPS vs. Mock, mouse 1


title: kidney stress, day 5, reverse

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: fish was stressed with netting, samples were collected after 5 days

organism: Oncorhynchus mykiss

source_name: control kidney

source_name: stressed kidney


title: brain stress, day 3, direct

description: fish was stressed with netting, samples were collected after 3 days

source_name: stressed brain

source_name: control brain


title: Pig embryo array Large Spherical sample 1

description:
A novel porcine cDNA macroarray, containing PCR products selected for embryonic expression, was used for transcriptional profiling during conceptus development. Total RNA from quadruplicate samples of small spherical (1-5mm), large spherical (6-11mm), tubular (13-45mm), and filamentous (>100mm) was extracted, amplified, and converted to 32P labeled target and hybridized to membranes.
Keywords = Gene expression
Keywords = porcine conceptus
Keywords = cDNA microarray
Keywords = peri-implantation
Keywords = transcriptional profiling

source_name: Amplified RNA from porcine large spherical embryo


title: Pig embryo array Tubular sample 2

source_name: Amplified RNA from porcine Tubular embryo


title: Pig embryo array Large Spherical sample 4


title: kidney stress, day 5, direct


title: Pig embryo array Large Spherical sample 2


title: Pig embryo array Large Spherical sample 3


title: Pig embryo array Tubular sample 1


title: kidney stress, day 1, reverse

description: fish was stressed with netting, samples were collected after 1 day


title: kidney stress, day 3, direct


title: kidney stress, day 3, reverse


title: Pig embryo array Small Spherical sample 3

source_name: Amplified RNA from porcine small spherical embryo


title: Pig embryo array Small Spherical sample 4


title: kidney stress, day 1, direct


title: 76-psad1_6

status: Public on May 11 2004

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

description: Comparison of the Arabidopsis psad1 mutant lacking Photosystem I protein PSI-D1 versus WT. A. Ihnatowicz et al., Plant J 37 (2004), pp. 839-852

organism: Arabidopsis thaliana

source_name: Arabidopsis psad1 mutant, ecotype Columbia 0


title: 76-WT_4

source_name: WT, ecotype Columbia 0


title: 76-psad1_3


title: 76-psad1_4


title: 76-WT_5


title: Pig embryo array Small Spherical sample 2


title: 76-psad1_5


title: pig embryo array Small Spherical 1

source_name: amplified RNA from Small Spherical embryo


title: 76-WT_3


title: brain stress, day 5, direct


title: brain stress, day 1 reverse


title: 76-WT_2


title: brain stress, day 3, reverse

source_name: stress brain


title: 76-WT_6


title: brain stress, day 1, direct


title: 76-psad1_2


title: 76-psad1_1


title: 76-WT_1


title: GC2_SARB31_LT2_2D623_3

status: Public on May 10 2004

type: genomic

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
genomic comparison SARB31/LT2
User - PCheng
Date_of_Scan = Tue Feb 11 16:39:27 2003

molecule: genomic DNA

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Montevideo

source_name: SARB31 gDNA overnight in LB

source_name: LT2 gDNA overnight in LB


title: GC2_SARB37_LT2_2D624_3

description:
genomic comparison SARB37/LT2
User - PCheng
Date_of_Scan = Tue Feb 11 17:46:31 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Newport

source_name: SARB37 gDNA overnight in LB


title: GC2_SARB16_LT2_2D616_1

description:
genomic comparison SARB16/LT2
User - PCheng
Date_of_Scan = Fri Feb 21 08:45:57 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Enteritidis

source_name: SARB16 gDNA overnight in LB


title: GC2_SARB31_LT2_2D623_1


title: GC2_SARB36_LT2_2D621_1

description:
genomic comparison SARB36/LT2
User - PCheng
Date_of_Scan = Fri Feb 07 12:16:14 2003

source_name: SARB36 gDNA overnight in LB


title: GC2_SARB24_LT2_2D622_1

description:
genomic comparison SARB24/LT2
User - PCheng
Date_of_Scan = Tue Feb 11 15:47:09 2003

organism:
Salmonella enterica subsp. enterica serovar Heidelberg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB24 gDNA overnight in LB


title: GC2_SARB37_LT2_2D624_2


title: GC2_SARB23_LT2_2D617_3

description:
genomic comparison SARB23/LT2
User - PCheng
Date_of_Scan = Fri Feb 07 16:26:46 2003

source_name: SARB23 gDNA overnight in LB


title: GC2_SARB16_LT2_2D616_3


title: GC2_SARB31_LT2_2D623_2


title: GC2_SARB1_LT2_2D610_3

description:
genomic comparison SARB1/LT2
User - PCheng
Date_of_Scan = Tue Feb 04 10:40:39 2003

organism:
Salmonella enterica subsp. enterica serovar Agona
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB1 gDNA overnight in LB


title: GC2_SARB26_LT2_2D631_1

description:
genomic comparison SARB26/LT2
User - PCheng
Date_of_Scan = Thu Feb 13 16:36:14 2003

organism:
Salmonella enterica subsp. enterica serovar Infantis
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB26 gDNA overnight in LB


title: GC2_SARB24_LT2_2D622_3


title: GC2_SARB23_LT2_2D617_1


title: GC2_SARB30_LT2_2D615_3

description:
genomic comparison SARB30/LT2
User - PCheng
Date_of_Scan = Thu Feb 06 17:07:35 2003

source_name: SARB30 gDNA overnight in LB


title: GC2_SARB12_LT2_2D611_3

description:
genomic comparison SARB12/LT2
User - PCheng
Date_of_Scan = Tue Feb 04 11:46:52 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Dublin

source_name: SARB12 gDNA overnight in LB


title: GC2_SARB37_LT2_2D624_1


title: GC2_SARB36_LT2_2D621_2


title: GC2_SARB30_LT2_2D615_1


title: GC2_SARB1_LT2_2D610_1


title: GC2_SARB23_LT2_2D617_2


title: GC2_SARB24_LT2_2D622_2


title: GC2_SARB1_LT2_2D610_2


title: GC2_SARB12_LT2_2D611_2


title: GC2_SARB36_LT2_2D621_3


title: GC2_SARB12_LT2_2D611_1


title: GC2_SARB16_LT2_2D616_2


title: GC2_SARB30_LT2_2D615_2


title: GC2_SARB42_LT2_2D467_3

description:
genomic comparison SARB42/LT2
User - PCheng
Date_of_Scan = Mon Nov 18 10:23:49 2002

organism:
Salmonella enterica subsp. enterica serovar Paratyphi A
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB42 gDNA overnight in LB


title: GC2_SARB42_LT2_2D467_2


title: GC2_SARB42_LT2_2D467_1


title: GC2_CT18_LT2_2D186_1

description:
genomic comparison CT18/LT2
User - PCheng
Date_of_Scan = Mon Oct 07 14:59:21 2002

organism:
Salmonella enterica subsp. enterica serovar Typhi
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: CT18 gDNA overnight in LB


title: GC2_LT2_Mitomycin C_T180_2d782_1

description:
LT2 exposed to 2ug/mL Mitomycin C for 180 min compared to untreated log phase gDNA.
User - PCheng
Date_of_Scan = Fri May 23 09:59:37 2003

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: LT2 T180 Mitomycin C gDNA

source_name: LT2 log phase gDNA


title: GC2_CT18_LT2_2D186_3


title: RRE2_LT2_MitomycinC_20min_2d783_1

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 20min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Thu May 29 15:15:28 2003
Keywords = Salmonella

source_name: LT2 20 min post treatment

source_name: LT2 pretreatment


title: RRE2_LT2_MitomycinC_10min_2d785_1

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 10min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Thu May 29 15:53:32 2003
Keywords = Salmonella

source_name: LT2 10 min post treatment


title: RRE2_LT2_MitomycinC_10min_2d785_2


title: RRE2_LT2_MitomycinC_10min_2d785_3


title: GC2_LT2_H2O2_T180_2d781_3

description:
LT2 exposed to 2mM H2O2 for 180 min and compared to untreated overnight culture of LT2
User - PCheng
Date_of_Scan = Fri May 23 09:13:18 2003

source_name: LT2 T180 H2O2 gDNA

source_name: LT2 untreated overnight gDNA


title: GC2_LT2_Mitomycin C_T180_2d782_2


title: GC2_Ty2b log vs overnight gDNA_2d536_3

description:
Ty2b log gDNA compared to overnight gDNA
User - Fblackmer
Date_of_Scan = Thu Jan 02 11:32:12 2003

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: Ty2b log gDNA

source_name: Ty2b overnight gDNA


title: GC2_Ty2b log vs overnight gDNA_2d536_2


title: GC2_CT18_LT2_2D186_2

source_name: LT2 gDNA overnight in LB


title: GC2_Ty2b log vs overnight gDNA_2d536_1


title: GC2_Ty2b 3hr H2O2_2d532_2

description:
Ty2b exposed to 2mM H2O2 for 3 hrs compared to untreated overnight Ty2b gDNA.
User - FBlackmer
Date_of_Scan = Thu Jan 02 09:06:30 2003

source_name: Ty2b 3hr H2O2 gDNA

source_name: Ty2b untreated overnight gDNA


title: GC2_LT2_Mitomycin C_T180_2d782_3


title: GC2_LT2_H2O2_T180_2d781_2


title: RRE2_LT2_MitomycinC_20min_2d783_3


title: RRE2_LT2_MitomycinC_20min_2d783_2


title: GC2_Ty2b 3hr H2O2_2d532_3


title: GC3_Ty2b rifampicin_2d501_3

description:
Ty2b grown to 0.5 OD600 and exposed to 125ug/mL rifampicin for 30 min compared to overnight untreated Ty2b gDNA and 0.5 OD untreated log pahse Ty2b gDNA. Alexa labeled log phase is weak.
User - Fblackmer
Date_of_Scan = Wed Dec 18 12:31:35 2002
Sample_target_source3: Ty2b log gDNA

source_name: Ty2b rifampicin gDNA


title: RRE2_LT2_MitomycinC_5min_2d693_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C afor 5min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Tue Jun 03 11:02:02 2003
Keywords = Salmonella

source_name: LT2 5 min post treatment


title: RRE2_LT2_MitomycinC_5min_2d693_1


title: GC2_LT2_H2O2_T180_2d781_1


title: GC2_Ty2b 3hr H2O2_2d532_1


title: RRE2_LT2_MitomycinC_5min_2d693_2


title: GC3_Ty2b rifampicin_2d501_1


title: GC3_Ty2b rifampicin_2d501_2


title: RE3_Ty2b_Chloramphenicol_2d499_2

description:
Ty2b grown to 0.5 OD600 and exposed to 300ug/mL Chloramphenicol for 30 mintues compared to overnight untreated Ty2b gDNA and log phase (0.5 OD) untreated Ty2b gDNA. Alexa labeled log gDNA is weak.
User - Fblackmer
Date_of_Scan = Wed Dec 18 10:33:04 2002
Sample_target_source3: Ty2b log gDNA

source_name: Ty2b Chloramphenicol gDNA


title: RE3_Ty2b_Chloramphenicol_2d499_1


title: RE3_Ty2b_Chloramphenicol_2d499_3


title: GC2_TAQ100F2_5hr H2O2_2d573_3

description:
TAQ100F2 exposed to 2mM H2O2 for 5hrs and compared to untreated 5hr TAQ100F2 gDNA
User - Fblackmer
Date_of_Scan = Fri Jan 31 10:09:18 2003

source_name: TAQ100F2 5hr H2O2

source_name: TAQ100F2 untreated gDNA


title: GC2_TAQ100F1_3hr H2O2_2d664_3

description:
TAQ100F1 was exposed to 2mM H2O2 for 3hr and compared to 3hr untreated TAQ100F1 gDNA. Treated sample was labled with Cy3.
User-Fblackmer
Date_of_Scan = Thu Feb 06 15:14:29 2003

source_name: TAQ100F1 3hr H2O2

source_name: TAQ100F1 3hr untreated gDNA


title: RRE2_TAQ100F2_3hr H2O2_2d671_3

description:
TAQ100F2 exposed to 2mM H2O2 for 3hr compared to untreated 3hr TAQ100F2 RNA
User - FBlackmer
Date_of_Scan = Fri Feb 14 11:32:22 2003
Keywords = Salmonella

source_name: TAQ100F2 3hr H2O2 RNA

source_name: TAQ100F2 untreated 3hr RNA


title: GC2_TAQ100F2_3hr Mitomycin C_2d669_1

description:
TAQ100F2 exposed to 2ug/mL Mitomycin C for 3hrs compared to untreated 3hr TAQ100F2 gDNA. Treated sample labeled with Cy3.
User - FBlackmer
Date_of_Scan = Wed Feb 12 11:25:23 2003

source_name: TAQ100F2 3hr Mitomycin C gDNA

source_name: TAQ100F2 3hr untreated gDNA


title: GC2_TAQ100F2_5hr H2O2_2d573_1


title: GC2_TAQ100F2_3hr_H2O2_2d660_2

description:
TAQ100F2 exposed to 2mM H2O2 for 3hrs compared to untreated 3hr TA100F2 gDNA
User - Fblackmer
Date_of_Scan = Fri Jan 31 12:30:06 2003

source_name: TAQ100F2 3hr H2O2

source_name: TAQ100F2 untreated 3hr gDNA


title: GC2_TAQ100F2_3hr Mitomycin C_2d669_3


title: GC2_TAQ100F2_3hr Mitomycin C_2d668_3

description:
TAQ100F2 treated with 2ug/mL Mitomycin C for 3hrs compared to 3hr untreated TAQ100F2 gDNA.
User - FBlackmer
Date_of_Scan = Wed Feb 12 10:57:24 2003


title: GC2_TAQ100F1_3hr H2O2_2d664_2


title: GC2_TAQ100F1_3hr H2O2_2d665_3

description:
TAQ100F1 was exposed to 2mM H2O2 for 3hr and compared to untreated 3hr TAQ100F1. Treated sample labeled with Cy5.
User - FBlackmer
Date_of_Scan = Thu Feb 06 15:36:47 2003


title: GC2_TAQ100F1_3hr H2O2_2d665_2


title: GC2_TAQ100F1_3hr H2O2_2d665_1


title: GC2_TAQ100F2_3hr_H2O2_2d660_1


title: GC2_TAQ100F2_3hr Mitomycin C_2d668_2


title: GC2_TAQ100F2_3hr Mitomycin C_2d669_2


title: GC2_TAQ100F2_3hr_H2O2_2d660_3


title: RRE2_TAQ100F2_3hr H2O2_2d671_1


title: RRE2_TA100_3hr H2O2 _2d667_3

description:
TA100 was exposed to 2mM H2O2 for 3hrs and compared to untreated 3hr TA100 RNA. Treated sample labeled with Cy3.
User - Fblackmer
Date_of_Scan = Tue Feb 11 12:54:34 2003

source_name: TA100 3hr H2O2 RNA

source_name: TA100 untreated 3hr RNA


title: GC2_TAQ100F2_3hr Mitomycin C_2d668_1


title: RRE2_TAQ100F2_3hr H2O2_2d671_2


title: GC2_TAQ100F1_3hr H2O2_2d664_1


title: GC2_TAQ100F2_5hr H2O2_2d573_2


title: RRE2_TA100_3hr H2O2 _2d667_2


title: RRE2_TA100_3hr H2O2 _2d667_1


title: RRE2_TA100_3hr H2O2 RNA_2d666_2

description:
TA100 eposed to 2mM H2O2 for 3hr and compared to untreated 3hr TA100
User - FBlackmer
Date_of_Scan = Tue Feb 11 12:33:02 2003

source_name: TA100 3hr H2O2

source_name: TA100 3hr untreated


title: GC2_DT104_3hr H2O2_2d663_2

description:
DT104 exposed to 2mM H2O2 for 3hr compared to DT104 untreated log phase gDNA. Treated sample labeled with Cy3.
User - Fblackmer
Date_of_Scan = Tue Feb 04 13:56:30 2003
Keywords = Salmonella

source_name: DT104 2hr H2O2 gDNA

source_name: DT104 log phase gDNA


title: GC2_TA100_3hr H2O2_2d661_2

description:
TA100 exposed to 2mM H2O2 for 3hr compared to untreated 3hr TA100 gDNA.
User - FBlackmer
Date_of_Scan = Fri Jan 31 12:54:17 2003

source_name: TA100 untreated 3hr H2O2


title: GC2_CT18_log vs overnight gDNA_2d533_3

description:
genomic comparison of CT18 log phase gDNA versus overnight gDNA
User - FBlackmer
Date_of_Scan = Thu Jan 02 09:43:50 2003
Keywords = Salmonella

source_name: CT18 log phase gDNA

source_name: CT18 overnight gDNA


title: GC2_TA100_5hr_H2O2_2d572_3

description:
TA100 exposed to 2mM H2O2 for 5 hours caompared to 5hr untreated TA100 gDNA.
User - FBlackmer
Date_of_Scan = Fri Jan 31 09:37:04 2003

source_name: TA100 5hr H2O2

source_name: TA100 5hr untreated


title: GC2_SARB48_5hr H2O2 gDNA_2d607_2

description:
SARB48 was exposed to 2mM H2O2 for 5hours and then copmared against a 5hr untreated sample of SARB48 gDNA.
User - FBlackmer
Date_of_Scan = Fri Jan 31 10:42:22 2003
Keywords = Salmonella

organism: Salmonella enterica subsp. enterica serovar Paratyphi C

source_name: SARB48 5hr H2O2 treated gDNA

source_name: SARB48 5hr H2O2 untreated gDNA


title: GC2_DT104_3hr H2O2 gDNA_2d662_2

description:
DT104 exposed to 2mM H2O2 for 3hr compasre to untreated log phase DT104 gDNA. Treated sample labeled with Cy5.
User - Fblackmer
Date_of_Scan = Tue Feb 04 13:17:28 2003
Keywords = Salmonella

source_name: DT104 3hr H2O2 gDNA


title: GC2_CT18_log vs overnight gDNA_2d533_1


title: GC2_CT18_3hr Mitomycin C gDNA_2d534_1

description:
CT18 exposed to 2ug/mL Mitomycin C for 3hrs compared to untreated log phase CT18 gDNA. Treated sample labeled with Cy3.
User - Fblackmer
Date_of_Scan = Thu Jan 02 10:10:03 2003
Keywords = Salmonella

source_name: CT18 3hr Mitomycin C gDNA


title: GC3_CT18 rifampicin vs log and overnight gDNA_2d500_3

description:
CT18 grown to 0.5 OD600 and then exposed to 125ug/mL Rifampicin for 30min compared to log phase (0.5 OD600) labeled with Alexa (weak signal) and overnight gDNA (labeled with Cy5).
User - FBlackmer
Date_of_Scan = Wed Dec 18 11:36:55 2002
Sample_target_source3: CT18 log phase gDNA
Keywords = Salmonella

source_name: CT18 rifampicin gDNA


title: GC2_DT104_3hr H2O2 gDNA_2d662_3


title: RRE2_TA100_3hr H2O2 RNA_2d666_1


title: RRE2_TA100_3hr H2O2 RNA_2d666_3


title: GC2_TA100_3hr H2O2_2d661_1


title: GC3_CT18 rifampicin vs log and overnight gDNA_2d500_1


title: GC2_DT104_3hr H2O2_2d663_3


title: GC2_CT18_3hr Mitomycin C gDNA_2d534_2


title: GC2_DT104_3hr H2O2 gDNA_2d662_1


title: GC2_SARB48_5hr H2O2 gDNA_2d607_3


title: GC2_TA100_3hr H2O2_2d661_3


title: GC3_CT18 rifampicin vs log and overnight gDNA_2d500_2


title: GC2_DT104_3hr H2O2_2d663_1


title: GC2_TA100_5hr_H2O2_2d572_2


title: GC2_TA100_5hr_H2O2_2d572_1


title: GC2_CT18_log vs overnight gDNA_2d533_2


title: GC2_CT18_3hr Mitomycin C gDNA_2d534_3


title: GC2_SARB48_5hr H2O2 gDNA_2d607_1


title: GC2_CT18_3hr Mitomycin C gDNA_2d608_3

description:
CT18 exposed to 2ug/mL of Mitomycin C for 3hrs copmared to untreated log phase CT18 gDNA. Treated samples labeled with Cy5.
User - FBlackmer
Date_of_Scan = Fri Jan 31 11:08:59 2003
Keywords = Salmonella

source_name: CT18 log gDNA


title: GC2_14028s_3hr H2O2 gDNA_2d541_3

description:
14028s exposed to 2mM H2O2 for 3hr compared to untreated overnight 14028s gDNA.
User - Fblackmer
Date_of_Scan = Wed Jan 08 13:23:31 2003

source_name: 14028s overnight gDNA


title: GC2_14028s 2hr H2O2_2d680_2

description:
14028s exposed to 2mM H2O2 for 2hrs compared to untreated log phase 14028s gDNA.
User - FBlackmer
Date_of_Scan = Thu Mar 13 11:41:17 2003
Keywords = Salmonella

source_name: 14028s 2hr H2O2 gDNA

source_name: 14028s log gDNA


title: GC2_14028s 2hr H2O2_2d680_1


title: GC2_14028s 2hr H2O2_2d680_3


title: GC2_LT2 log gDNA vs overnight gDNA_2d535_2

description:
genomic comparison LT2 log vs overnight gDNA
User - FBlackmer
Date_of_Scan = Thu Jan 02 10:41:21 2003

source_name: LT2 log gDNA

source_name: LT2 overnight gDNA


title: GC2_14028s_3hr H2O2 gDNA_2d541_1


title: GC2_CT18_3hr Mitomycin C gDNA_2d608_1


title: GC2_14028s_3hr H2O2 gDNA_2d541_2


title: GC3_LT2_MitomycinC_3hr_2d571_2

description:
LT2 exposed to 2ug/mL Mitomycin C for 3hrs compared to untreated log gDNA and untreated overnight gDNA
User - Fblackmer
Date_of_Scan = Sat Jan 25 15:12:03 2003
Sample_target_source3: LT2 overnight gDNA

source_name: LT2 3hr MitomycinC gDNA


title: GC3_LT2_MitomycinC_3hr_2d571_3


title: RRE2_LT2_MitomycinC_3hr_2d670_1

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C
User - Fblackmer
Date_of_Scan = Wed Feb 12 14:23:02 2003
Keywords = Salmonella

source_name: LT2 3hr post treatment

source_name: LT2 log pretreatment


title: RRE2_LT2_MitomycinC_3hr_2d670_3


title: RRE2_LT2_MitomycinC_3hr_2d670_2


title: GC2_LT2_3hr Mitomycin C gDNA vs overnight gDNA_2d540_3

description:
LT2 exposed to 2ug/mL Mitomycin C for 3h compared to overnight unexposed culture of LT2
User - FBlackmer
Date_of_Scan = Wed Jan 08 13:51:41 2003
Keywords = Salmonella

source_name: 3hr Mitomycin C LT2 gDNA


title: GC3_LT2_MitomycinC_3hr_2d571_1


title: GC2_LT2 log gDNA vs overnight gDNA_2d535_3


title: GC2_LT2_3hr Mitomycin C gDNA vs overnight gDNA_2d540_2


title: GC2_LT2 log gDNA vs overnight gDNA_2d535_1


title: RRE2_LT2_MitomycinC_30min_2D784_2

description:
Salmonella Typhimurium LT2 gene expression post treatment with 2ug/ml Mitomycin C.
Keywords = Salmonella

source_name: LT2 30min post treatment with 2ug/ml Mitomycin C.

source_name: LT2 pretreatment


title: RRE2_LT2_MitomycinC_30min_2D784_3


title: GC2_LT2_3hr Mitomycin C gDNA vs overnight gDNA_2d540_1


title: GC2_SL1344_3hr H2O2 gDNA_2d542_2

description:
SL1344 was exposed to 2mM H2O2 for 3hrs and compared to an untreated overnight culture of SL1344. The treated sample was labeled with Cy3.
User - Fblackmer
Date_of_Scan = Wed Jan 08 14:15:34 2003
Keywords = Salmonella

source_name: SL1344 3hr H2O2 gDNA

source_name: SL1344 overnight gDNA


title: GC2_SL1344_3hr H2O2 gDNA_2d542_3


title: RRE2_LT2_MitomycinC_30min_2D784_1


title: GC2_SL1344_3hr H2O2 gDNA_2d570_2

description:
SL1344 was exposed to 2mM H2O2 for 3hrs and compared to an untreated overnight culture of SL1344. Treated sample was labeled with Cy5.
User - Fblackmer
Date_of_Scan =Fri Jan 24 09:36:36 2003
Keywords = Salmonella


title: GC2_LT2 2hr H202_2d539_3

description:
LT2 exposed to 2mM H2O2 for 2hrs labeled with Cy3 and compared to untreated overnight culture of LT2
User - FBlackmer
Date_of_Scan = Fri Jan 03 11:40:13 2003
Keywords = Salmonella

source_name: LT2 2hr H2O2 gDNA

source_name: LT2 untreated overnight gDNA


title: RRE2_LT2_H2O2_3hr_2d677_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2mM H2O2
User - Fblackmer
Date_of_Scan = Thu Mar 06 14:29:20 2003
Keywords = Salmonella


title: GC2_LT2_3hr H2O2 gDNA_2d527_2

description:
LT2 exposed to 2mM H2O2 for 3hr compared to untreated overnight LT2 gDNA. Treated sample labeled with Cy5.
User - FBlackmer
Date_of_Scan = Mon Jan 13 09:44:18 2003
Keywords = Salmonella

source_name: LT2 3hr H2O2 gDNA


title: GC2_LT2 2hr H202_2d539_1


title: GC2_LT2_3hr H2O2_2d537_1

description:
LT2 exposed to 2mM H2O2 for 3hr compared to untreated overnight culture. 3hr sample labeled with Cy3.
User - FBlackmer
Date_of_Scan = Thu Jan 02 12:10:00 2003
Keywords = Salmonella


title: GC2_SL1344_3hr H2O2 gDNA_2d542_1


title: GC2_LT2_3hr H2O2 gDNA_2d527_1


title: RRE2_LT2_H2O2_2hr_2d678_1

description:
Salmonella typhimurium LT2 Expression after tratment with 2mM H2O2
User - Fblackmer
Date_of_Scan = Thu Mar 13 12:09:31 2003
Keywords = Salmonella

source_name: LT2 2hr post treatment


title: RRE2_LT2_H2O2_2hr_2d678_3


title: GC2_LT2_3hr H2O2_2d537_2


title: GC2_SL1344_3hr H2O2 gDNA_2d570_1


title: GC2_CT18_3hr Mitomycin C gDNA_2d608_2

source_name: CT18 3hr Mitomycin C gDNA

source_name: CT18 log gDNA


title: GC2_LT2_2hr H2O2 gDNA_2d530_1

description:
LT2 exposed to 2mM H2O2 for 2hr compared to untreated LT2 overnight gDNA. Treated sample labeled with Cy5.
User - Fblackmer
Date_of_Scan = Mon Jan 13 10:30:32 2003
Keywords = Salmonella


title: GC2_LT2 2hr H202_2d539_2


title: GC2_LT2_3hr H2O2 gDNA_2d527_3


title: RRE2_LT2_H2O2_3hr_2d677_1


title: GC2_LT2_3hr H2O2_2d537_3


title: GC2_LT2_2hr H2O2 gDNA_2d530_2


title: RRE2_LT2_H2O2_2hr_2d678_2


title: RRE2_LT2_H2O2_3hr_2d677_2


title: GC2_LT2_1hr H2O2_2d538_2

description:
LT2 exposed to 2mM H2O2 for 1hour compared to untreated overnight culture. 1hr sample labeled with Cy3
User - Fblackmer
Date_of_Scan = Fri Jan 03 11:05:30 2003
Keywords = Salmonella

source_name: LT2 1hr H2O2 gDNA


title: GC2_SL1344_3hr H2O2 gDNA_2d570_3


title: GC2_LT2_1hr H2O2_2d531_2

description:
LT2 exposed to 2mM H2O2 for 1hour compared to untreated overnight gDNA. Treated sample labeled with Cy5.
User - Fblackmer
Date_of_Scan = Mon Jan 13 11:15:41 2003
Keywords = Salmonella


title: GC2_LT2_1hr H2O2_2d531_3


title: GC2_LT2_1hr H2O2_2d538_1


title: RRE2_LT2_MitomycinC_60min_2d692_2

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 60 min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Fri May 30 11:20:48 2003
Keywords = Salmonella

source_name: LT2 60 min post treatment


title: RRE2_LT2_MitomycinC_5min_2d786_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 5min and compared to untreated log phase RNA
User - PCheng
Date_of_Scan =Thu May 29 16:19:27 2003
Keywords = Salmonella

source_name: LT2 5 min post treatment


title: GC2_LT2_2hr H2O2 gDNA_2d530_3

source_name: LT2 overnight gDNA


title: RRE2_LT2_MitomycinC_40min_2d695_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 40min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Tue Jun 03 12:26:28 2003
Keywords = Salmonella

source_name: LT2 40 min post treatment


title: RRE2_LT2_MitomycinC_5min_2d786_1


title: RRE2_LT2_MitomycinC_40min_2d695_1


title: GC2_LT2_1hr H2O2_2d531_1


title: RRE2_14028s_H2O2_2hr_2d679_1

description:
Salmonella typhimurium 14028s Expression after treatment with 2mM H2O2
User - FBlackmer
Date_of_Scan =Thu Mar 13 11:21:25 2003
Keywords = Salmonella

source_name: 14028s 2hr post treatment

source_name: 14028s log pretreatment


title: RRE2_LT2_MitomycinC_10min_2d694_2

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 10min compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Tue Jun 03 11:48:24 2003
Keywords = Salmonella

source_name: LT2 10 min post treatment


title: RRE2_LT2_MitomycinC_60min_2d692_3

source_name: LT2 pretreatment


title: GC2_14028s_3h H2O2 gDNA_2d683_2

description:
14028s exposed to 2mM H2O2 for 3hr compared to untreated log phase 14028s gDNA.
User - FBlackmer
Date_of_Scan = Thu Mar 20 10:13:33 2003
Keywords = Salmonella

source_name: 14028s 3hr H2O2 gDNA

source_name: 14028s log phase gDNA


title: RRE2_LT2_MitomycinC_5min_2d786_2


title: GC2_LT2_1hr H2O2_2d538_3


title: RRE2_LT2_MitomycinC_10min_2d694_1


title: Sample 19 Kidney Normal Mouse - Control Diet

city: Charlotte

first: Ralph

middle: A.

last: Meyer

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

description:
This is a study of the change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 5 days.  RNA from 3 mice were pooled for each microarray.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia

organism: Mus musculus

source_name: C57BL/6J Mouse Male Kidney


title: RRE2_14028s_H2O2_3hr_2d676_1

description:
Salmonella typhimurium 14028s Expression after treatment with 2mM H2O2.
User -Fblackmer
Date_of_Scan = Thu Mar 06 14:05:54 2003
Keywords = Salmonella

source_name: 14028s 3hr post treatment


title: RRE2_14028s_H2O2_2hr_2d679_3


title: RH_RRE2_14028_cheB_2h on plate_2D_1

status: Public on Sep 02 2004

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

description:
Salmonella typhimurium 14028 on plate vs cheB on plate for 2h
User - TWang
Date_of_Scan = 2003/03/11 11:14:58

source_name: cheB 2h on plate

source_name: 14028 2h on plate


title: RRE2_14028s_H2O2_3hr_2d676_2


title: Sample 17 Kidney Hyp Mouse - Control Diet

description:
This is a study of the change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 3 days.  RNA from 3 mice were pooled for each microarray.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia

source_name: C57BL/6J Mouse Female Kidney


title: RRE2_LT2_MitomycinC_40min_2d695_2


title: Sample 18 Kidney Hyp Mouse - Low Phosphate Diet


title: RRE2_LT2_MitomycinC_60min_2d692_1


title: RRE2_14028s_H2O2_3hr_2d676_3


title: GC2_14028s_3h H2O2 gDNA_2d683_3


title: GC2_14028s_3h H2O2 gDNA_2d683_1


title: Sample 16 Kidney Normal Mouse - Low Phosphate Diet


title: Sample 20 Kidney Normal Mouse - Low Phosphate Diet


title: Sample 14 Kidney Hyp Mouse - Low Phosphate Diet

description:
Study of change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 3 days.  RNA from 3 mice is pooled for each sample.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia


title: Sample 15 Kidney Normal Mouse - Control Diet


title: GC2_PbA3_LT2_2D698_3

description:
genomic comparison PbA3/LT2
User - Fblackmer
Date_of_Scan = Fri Feb 28 11:36:22 2003

organism:
Salmonella enterica subsp. enterica serovar Paratyphi B
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: PbA3 gDNA overnight in LB

source_name: LT2 gDNA overnight in LB


title: GC2_PbA3_LT2_2D698_2


title: RRE2_14028s_H2O2_2hr_2d679_2


title: RRE2_LT2_MitomycinC_10min_2d694_3


title: Sample 11 Kidney Normal Mouse - Control Diet


title: Sample 13 Kidney Hyp Mouse - Control Diet


title: Sample 12 Kidney Normal Mouse - Low Phosphate Diet


title: GC2_PbA3_LT2_2D698_1


title: Sample 10 Kidney Hyp Mouse - Low Phosphate Diet

description:
Study of change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 5 days.  RNA from 3 mice is pooled for each sample.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia


title: Sample 09 Kidney Hyp Mouse - Control Diet


title: Sample 07 Kidney Hyp Mouse - Control Diet


title: GC2_PbA1_LT2_2D697_1

description:
genomic comparison PbA1/LT2
User - Fblackmer
Date_of_Scan = Fri Feb 28 11:14:19 2003

source_name: PbA1 gDNA overnight in LB


title: GC2_PbA1_LT2_2D697_2


title: Sample 08 Kidney Hyp Mouse - Low Phosphate Diet


title: GC2_SPPB7_LT2_2D696_3

description:
genomic comparison SPPB7/LT2
User - Fblackmer
Date_of_Scan = Fri Feb 28 10:28:39 2003

source_name: SPPB7 gDNA overnight in LB


title: Sample 04 Kidney Mouse Hyp - Low Phosphate Diet


title: GC2_SPPB7_LT2_2D696_1


title: GC2_020150_LT2_2D655b_3

description:
genomic comparison 020150/LT2
User - PCheng
Date_of_Scan = Sat Mar 15 13:34:45 2003

organism:
Salmonella enterica subsp. enterica serovar Oranienburg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 020150 gDNA overnight in LB


title: GC2_SPPB7_LT2_2D696_2


title: RH_RRE2_swarmer ref_timecourse on hard agar plate (1.5%) with glucose_0.5h_2D_3

description:
Salmonella typhimurium swarmer ref_broth timecourse with glucose_0.5h
User - TWang
Date_of_Scan = 2003/01/10 11:38:11

source_name: swarmer ref_0.5h with glucose

source_name: swarmer ref


title: GC2_020150_LT2_2D655b_2


title: GC2_002693_LT2_2D774_3

description:
genomic comparison 002693/LT2
User - PCheng
Date_of_Scan = Tue Jul 01 11:33:53 2003

source_name: 002693 gDNA overnight in LB


title: GC2_002693_LT2_2D774_2


title: Sample 02 Kidney Normal Mouse - Low Phosphate Diet

description:
Study of change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 5 days.  RNA from 3 mice is pooled for each sample.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = hyp
Keywords = phex
Keywords = x-linked hypophosphatemia


title: Sample 06 Kidney Normal Mouse - Low Phosphate Diet


title: GC2_002693_LT2_2D774_1


title: Sample 01 Kidney Normal mouse - Control diet

source_name: Mouse male kidney C57BL/6J


title: Sample 03 Kidney Hyp Mouse - Control Diet


title: Sample 05 Kidney Normal Mouse - Control Diet


title: GC2_020150_LT2_2D655b_1


title: GC2_011277_LT2_2D740_3

description:
genomic comparison 011277/LT2
User - PCheng
Date_of_Scan = Wed May 28 12:07:20 2003

source_name: 011277 gDNA overnight in LB


title: GC2_PbA1_LT2_2D697_3


title: GC2_011277_LT2_2D740_2


title: GC2_011650_LT2_2D741_2

description:
genomic comparison 011650/LT2
User - PCheng
Date_of_Scan = Wed May 28 11:26:09 2003

source_name: 011650 gDNA overnight in LB


title: GC2_011650_LT2_2D741_1


title: GC2_SARB63_LT2_2D753_719_3

description:
genomic comparison SARB63/LT2
User - PCheng
Date_of_Scan = Wed Apr 09 10:34:50 2003

source_name: SARB63 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_40min_3D691_3

description:
Salmonella typhimurium LT2 Expression after tratment with 2 ug/ml Mitomycin C for 40min and compared to untreated log phase RNA
User - PCheng
Date_of_Scan = Fri May 30 10:05:24 2003
Keywords = Salmonella

source_name: LT2 40 min post treatment

source_name: LT2 pretreatment


title: GC2_SARB58_LT2_3D155_2

description:
genomic comparison SARB58/LT2
User - PCheng
Date_of_Scan = Fri Apr 25 12:43:48 2003

organism:
Salmonella enterica
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB58 gDNA overnight in LB


title: GC2_011277_LT2_2D740_1


title: GC2_011650_LT2_2D741_3


title: GC2_SARB58_LT2_3D155_3


title: GC2_SARB58_LT2_3D155_1


title: GC2_SARB63_LT2_2D753_719_1


title: GC2_SARB33_LT2_2D725_719_3

description:
genomic comparison SARB33/LT2
User - PCheng
Date_of_Scan = Thu Apr 24 15:11:15 2003

organism:
Salmonella enterica subsp. enterica serovar Muenchen
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB33 gDNA overnight in LB


title: RRE2_LT2_MitomycinC_40min_3D691_1


title: GC2_SARB33_LT2_2D725_719_1


title: GC2_SARB63_LT2_2D753_719_2


title: GC2_LT2_H2O2_T120_gDNA_3D137_3

description:
LT2 exposed to 2mM H2O2 for 120min and compared to untreated gDNA
User - PCheng
Date_of_Scan = Thu Jul 17 09:30:00 2003

source_name: LT2 H2O2 120min gDNA

source_name: LT2 log phase gDNA


title: GC2_024513_LT2_2D723_71_2

description:
genomic comparison 024513/LT2
User - PCheng
Date_of_Scan = Wed Apr 23 15:24:40 2003

source_name: 024513 gDNA overnight in LB

source_name: LT2 gDNA overnight in LB


title: GC2_LT2_H2O2_T120_gDNA_3D137_1


title: GC2_LT2_H2O2_T240_gDNA_3D136_3

description:
genomic comparison CT18/LT2
User - PCheng
Date_of_Scan = Thu Jul 17 10:40:13 2003

source_name: LT2 H2O2 240min gDNA

source_name: LT2 untreated gDNA


title: RRE2_LT2_MitomycinC_40min_3D691_2


title: GC2_SARB33_LT2_2D725_719_2


title: GC2_024513_LT2_2D723_71_1


title: GC2_SARB38_LT2_2D721_71_3

description:
genomic comparison SARB38/LT2
User - PCheng
Date_of_Scan = Tue Apr 22 14:44:02 2003

source_name: SARB38 gDNA overnight in LB


title: GC2_024513_LT2_2D723_71_3


title: GC2_SARB38_LT2_2D721_71_2


title: GC2_LT2_H2O2_T120_gDNA_3D137_2


title: GC2_SARB38_LT2_2D721_71_1


title: GC2_LT2_H2O2_T240_gDNA_3D136_2


title: GC2_LT2_H2O2_T240_3D131_3

description:
LT2 exposed to 2mM H2O2 for 240min compared to a overnight cultue for untreated LT2.
User - PCheng
Date_of_Scan = Thu Jul 10 10:38:36 2003

source_name: LT2 untreated overnight gDNA


title: GC2_LT2_H2O2_T240_3D131_2


title: GC2_SARB6_LT2_2D720_719_1

description:
genomic comparison SARB6/LT2
User - PCheng
Date_of_Scan = Tue Apr 22 14:27:03 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Choleraesuis

source_name: SARB6 gDNA overnight in LB


title: RE3_SL1344_HS_42C_30 min_3D295_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 42C
User - PCheng
Date_of_Scan = Thu Aug 14 16:32:01 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 30 min post treatment

source_name: SL1344 pretreatment


title: GC2_LT2_H2O2_T240_gDNA_3D136_1


title: RE3_SL1344_HS_42C_30 min_3D295_2


title: GC2_LT2_H2O2_T60_gDNA_3D135_3

description:
LT2 exposed to 2mM H2O2 for 60min and compared to untreated gDNA
User - PCheng
Date_of_Scan = Wed Jul 16 11:15:37 2003

source_name: LT2 H2O2 60min gDNA


title: GC2_LT2_H2O2_T60_gDNA_3D135_2


title: GC2_LT2_H2O2_T240_3D131_1


title: GC2_LT2_H2O2_T60_gDNA_3D135_1


title: GC2_SARB65_LT2_2D716_713_3

description:
genomic comparison SARB65/LT2
User - PCheng
Date_of_Scan = Tue Apr 15 18:13:17 2003

source_name: SARB65 gDNA overnight in LB


title: GC2_SARB65_LT2_2D716_713_2


title: GC2_SARB6_LT2_2D720_719_3


title: GC2_SARB65_LT2_2D716_713_1


title: GC2_SARB6_LT2_2D720_719_2


title: GC2_SARB59_LT2_2D716_713_3

description:
genomic comparison SARB59/LT2
User - PCheng
Date_of_Scan = Tue Apr 15 12:52:47 2003

organism:
Salmonella enterica subsp. enterica serovar Senftenberg
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB59 gDNA overnight in LB


title: RE3_SL1344_HS_42C_30 min_3D295_1


title: RE3_SL1344_HS_42C_10 min_3D294_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 42C
User - PCheng
Date_of_Scan = Thu Aug 14 15:52:43 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 10 min post treatment


title: RE3_SL1344_HS_42C_10 min_3D294_2


title: GC2_024358q_LT2_2D657_2

description:
genomic comparison 024358q/LT2
User - PCheng
Date_of_Scan = Mon Mar 17 09:48:39 2003

source_name: 024358q gDNA overnight in LB


title: GC2_SARB59_LT2_2D716_713_1


title: GC2_024358q_LT2_2D657_3


title: GC2_SARB59_LT2_2D716_713_2


title: RE3_SL1344_HS_42C_5 min_3D293_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 42C
User - PCheng
Date_of_Scan = Thu Aug 14 15:15:14 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 5 min post treatment


title: GC2_024358q_LT2_2D657_1


title: GC2_022481_LT2_2D656_1

description:
genomic comparison 022481/LT2
User - PCheng
Date_of_Scan = Mon Mar 17 09:01:00 2003

source_name: 022481 gDNA overnight in LB


title: RE3_SL1344_HS_37C_180 min_3D173_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Aug 01 12:43:35 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 180 min post treatment


title: RE3_SL1344_HS_42C_5 min_3D293_1


title: RE3_SL1344_HS_42C_5 min_3D293_2


title: RE3_SL1344_HS_37C_180 min_3D173_2


title: GC2_022481_LT2_2D656_3


title: GC2_SARB64_LT2_2D684_719_3

description:
genomic comparison SARB64/LT2
User - PCheng
Date_of_Scan = Tue Mar 25 10:15:50 2003

source_name: SARB64 gDNA overnight in LB


title: RE3_SL1344_HS_42C_30 min_3D172_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Aug 01 12:02:16 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 150 min post treatment


title: RE3_SL1344_HS_42C_10 min_3D294_1


title: GC2_SARB64_LT2_2D684_719_2

source_name: LT2 gDNA overnight in LB


title: RE3_SL1344_HS_42C_30 min_3D172_2


title: GC2_Ty2_LT2_2D180_189_3

description:
genomic comparison Ty2/LT2
User - PCheng
Date_of_Scan = Thu Oct 10 17:51:38 2002

source_name: Ty2 gDNA overnight in LB


title: RE3_SL1344_HS_37C_120 min_3D171_2

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Wed Jul 30 11:43:39 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 120 min post treatment


title: GC2_Ty2_LT2_2D180_189_1


title: GC2_Ty2_LT2_2D180_189_2


title: RE3_SL1344_HS_37C_120 min_3D171_3


title: RE3_SL1344_HS_42C_30 min_3D172_1


title: GC2_SARB64_LT2_2D684_719_1


title: RE3_SL1344_HS_37C_120 min_3D171_1


title: RE3_SL1344_HS_37C_180 min_3D173_1


title: GC2_022481_LT2_2D656_2


title: RE3_SL1344_HS_37C_90 min_3D170_3

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Thu Jul 31 09:27:25 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 90 min post treatment


title: GC2_SARC11_LT2_2D688_3

description:
genomic comparison SARC11/LT2
User - PCheng
Date_of_Scan = Fri Mar 28 12:07:19 2003

organism:
Salmonella bongori
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARC11 gDNA overnight in LB


title: RE3_SL1344_HS_37C_90 min_3D170_2


title: RE3_SL1344_HS_37C_90 min_3D170_1


title: RE3_SL1344_HS_37C_60 min_3D141_1

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Jul 18 12:58:08 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 60 min post treatment


title: GC2_022382_LT2_2D772_3

description:
genomic comparison 022382/LT2
User - PCheng
Date_of_Scan = Tue Jul 01 12:20:00 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Paratyphi B var. L(+) tartrate +

source_name: 022382 gDNA overnight in LB


title: RE3_SL1344_HS_37C_10 min_3D140_2

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Jul 18 12:29:33 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 pretreatment


title: GC2_SARC11_LT2_2D688_2


title: GC2_001186_LT2_2D773_1

description:
genomic comparison 001186/LT2
User - PCheng
Date_of_Scan = Tue Jul 01 11:56:08 2003

organism:
Salmonella enterica subsp. enterica serovar Muenster
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 001186 gDNA overnight in LB


title: RE3_SL1344_HS_37C_10 min_3D140_3


title: GC2_001186_LT2_2D773_3


title: RE3_SL1344_HS_37C_30 min_3D142_1

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Jul 18 13:21:54 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 30 min post treatment


title: RE3_SL1344_HS_37C_30 min_3D142_3


title: GC2_SARB56_LT2_2D771_3

description:
genomic comparison SARB56/LT2
User - PCheng
Date_of_Scan = Wed Jun 25 13:42:06 2003

organism:
Salmonella enterica subsp. enterica serovar Saintpaul
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB56 gDNA overnight in LB


title: RE3_SL1344_HS_37C_60 min_3D141_2


title: GC2_022382_LT2_2D772_2


title: RE3_SL1344_HS_37C_10 min_3D140_1

source_name: SL1344 10 min post treatment


title: RE3_SL1344_HS_37C_60 min_3D141_3


title: GC2_SARB13_LT2_2D770_3

description:
genomic comparison SARB13/LT2
User - PCheng
Date_of_Scan = Wed Jun 25 13:10:09 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Dublin

source_name: SARB13 gDNA overnight in LB


title: GC2_SARB13_LT2_2D770_1


title: GC2_022382_LT2_2D772_1


title: GC2_SARC11_LT2_2D688_1


title: GC2_001186_LT2_2D773_2


title: RE3_SL1344_HS_37C_30 min_3D142_2


title: GC2_SARB56_LT2_2D771_2


title: GC2_SARB13_LT2_2D770_2


title: RE3_SL1344_HS_37C_5 min_3D139_1

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Jul 18 11:45:46 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 5 min post treatment


title: RE3_SL1344_HS_37C_5 min_3D139_3


title: GC2_SARB56_LT2_2D771_1


title: GC2_SARB19_LT2_2D768_3

description:
genomic comparison SARB19/LT2
User - PCheng
Date_of_Scan = Thu Jun 19 13:19:52 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Emek

source_name: SARB19 gDNA overnight in LB


title: RE3_SL1344_HS_37C_10 min_3D134_2

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Fri Jul 11 08:43:36 2003
Sample_target_source3: SL1344 genomic DNA


title: GC2_SARC14_LT2_2D747_2

description:
genomic comparison SARC14/LT2
User - PCheng
Date_of_Scan = Wed Jun 11 14:40:54 2003

organism:
Salmonella enterica subsp. indica
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARC14 gDNA overnight in LB


title: GC2_SARC14_LT2_2D747_1


title: GC2_SARB18_LT2_2D748_3

description:
genomic comparison SARB18/LT2
User - PCheng
Date_of_Scan = Thu Jun 12 11:03:06 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Enteritidis

source_name: SARB18 gDNA overnight in LB


title: RE3_SL1344_HS_37C_10 min_3D134_1

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: GC2_SARB19_LT2_2D768_1

source_name: LT2 gDNA overnight in LB


title: GC2_SARB19_LT2_2D768_2


title: GC2_SARC14_LT2_2D747_3


title: RE3_SL1344_HS_37C_10 min_3D134_3


title: RE3_SL1344_HS_37C_5 min_3D139_2


title: RE3_SL1344_HS_37C_10 min_3D133_2

description:
Salmonella typhimurium SL1344 Expression after heatshock with 37C
User - PCheng
Date_of_Scan = Wed Jul 09 14:23:01 2003
Sample_target_source3: SL1344 genomic DNA


title: RE3_SL1344_HS_37C_5 min_3D127_3

description:
Salmonella typhimurium SL1344 Expression after heatshock at 37C for 5 min
User - PCheng
Date_of_Scan = Thu Jun 19 08:48:58 2003
Sample_target_source3: SL1344 genomic DNA

source_name: SL1344 30C pretreatment


title: GC2_SARB18_LT2_2D748_2


title: RE3_LT2_H2O2_30 min_3D251_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 30min
User - PCheng
Date_of_Scan = Wed Aug 13 16:16:47 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 30 min post treatment

source_name: LT2 pretreatment


title: GC2_SARB50_LT2_2D738_3

description:
genomic comparison SARB50/LT2
User - PCheng
Date_of_Scan = Fri May 16 16:38:40 2003

organism:
Salmonella enterica subsp. enterica serovar Paratyphi C
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB50 gDNA overnight in LB


title: RE3_LT2_H2O2_30 min_3D251_2


title: RE3_LT2_H2O2_30 min_3D251_1


title: RE3_SL1344_HS_37C_10 min_3D133_3


title: GC2_SARB50_LT2_2D738_1


title: GC2_SARB69_LT2_2D736_3

description:
genomic comparison SARB69/LT2
User - PCheng
Date_of_Scan = Thu May 15 11:42:58 2003

organism:
Salmonella enterica subsp. enterica serovar Typhisuis
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB69 gDNA overnight in LB


title: GC2_SARB69_LT2_2D736_1


title: RE3_LT2_H2O2_60 min_3D252_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 60min
User - PCheng
Date_of_Scan = Tue Aug 12 15:59:54 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 60 min post treatment


title: RE3_SL1344_HS_37C_5 min_3D127_2


title: RE3_LT2_H2O2_60 min_3D252_3


title: GC2_SARB18_LT2_2D748_1


title: GC2_SARB69_LT2_2D736_2


title: GC2_SARB50_LT2_2D738_2


title: RE3_LT2_H2O2_240 min_3D299_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 240min
User - PCheng
Date_of_Scan = Wed Aug 20 11:07:28 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 240 min post treatment


title: RE3_LT2_H2O2_60 min_3D252_1


title: RE3_SL1344_HS_37C_10 min_3D133_1

source_name: SL1344 pretreatment


title: RE3_LT2_H2O2_240 min_3D299_1


title: RE3_LT2_H2O2_240 min_3D299_3


title: GC2_SARB49_LT2_2D735_3

description:
genomic comparison SARB49/LT2
User - PCheng
Date_of_Scan = Tue May 13 12:34:08 2003

source_name: SARB49 gDNA overnight in LB


title: GC2_SARB21_LT2_2D734_2

description:
genomic comparison SARB21/LT2
User - PCheng
Date_of_Scan = Tue May 13 12:03:11 2003

organism:
Salmonella enterica subsp. enterica serovar Gallinarum
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: SARB21 gDNA overnight in LB


title: RE3_SL1344_HS_37C_5 min_3D127_1

source_name: SL1344 30 min post treatment


title: RE3_LT2_H2O2_120 min_3D297_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 120min
User - PCheng
Date_of_Scan = Wed Aug 20 11:59:25 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 120 min post treatment


title: GC2_SARB49_LT2_2D735_1


title: GC2_SARB49_LT2_2D735_2


title: GC2_000175_LT2_2D733_3

description:
genomic comparison 000175/LT2
User - PCheng
Date_of_Scan = Tue May 13 11:17:11 2003

organism:
Salmonella enterica subsp. enterica serovar Typhi
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 000175 gDNA overnight in LB


title: RE3_LT2_H2O2_120 min_3D297_2


title: GC2_SARB21_LT2_2D734_3


title: GC2_000175_LT2_2D733_1


title: RE3_LT2_H2O2_40 min_3D287_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 40min
User - PCheng
Date_of_Scan = Mon Aug 18 10:25:44 2003
Sample_target_source3: LT2 cy5 labeled genomic DNA

source_name: LT2 40 min post treatment


title: GC2_996933_LT2_2D732_2

description:
genomic comparison 996933/LT2
User - PCheng
Date_of_Scan = Thu May 08 12:05:38 2003

source_name: 996933 gDNA overnight in LB


title: RE3_LT2_H2O2_120 min_3D297_1


title: RE3_LT2_H2O2_180 min_3D298_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 180min.
User - PCheng
Date_of_Scan = Wed Aug 20 10:10:53 2003
Sample_target_source3: LT2 Cy5 lableled genomic DNA

source_name: LT2 180 min post treatment


title: GC2_SARB21_LT2_2D734_1

source_name: LT2 gDNA overnight in LB


title: GC2_996933_LT2_2D732_1


title: GC2_000175_LT2_2D733_2


title: RE3_LT2_H2O2_180 min_3D298_1


title: RE3_LT2_H2O2_180 min_3D298_2


title: GC2_996933_LT2_2D732_3


title: RE3_LT2_H2O2_40 min_3D287_2


title: RE3_LT2_H2O2_20 min_3D286_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 20min
User - PCheng
Date_of_Scan = Mon Aug 18 09:25:03 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 20 min post treatment


title: RE3_LT2_H2O2_20 min_3D286_2


title: GC2_022621_LT2_2D731_3

description:
genomic comparison 022621/LT2
User - PCheng
Date_of_Scan = Thu May 01 15:45:55 2003

source_name: 022621 gDNA overnight in LB


title: GC2_022621_LT2_2D731_1


title: GC2_994730_LT2_2D730_3

description:
genomic comparison 994730/LT2
User - PCheng
Date_of_Scan = Thu May 01 15:26:37 2003

organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Newport

source_name: 994730 gDNA overnight in LB


title: RE3_LT2_H2O2_5 min_3D275_2

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 5min
User - PCheng
Date_of_Scan = Mon Aug 25 09:05:20 2003
Sample_target_source3: LT2 Cy5 labeled genomic DNA

source_name: LT2 5 min post treatment

source_name: LT2 pretreatment


title: RE3_LT2_H2O2_5 min_3D275_3


title: GC2_022621_LT2_2D731_2


title: RE3_LT2_H2O2_40 min_3D287_1


title: GC2_994730_LT2_2D730_1


title: RE3_LT2_H2O2_5 min_3D275_1


title: GC2_994730_LT2_2D730_2


title: GC2_SARB68_LT2_2D728_3

description:
genomic comparison SARB68/LT2
User - PCheng
Date_of_Scan = Wed Apr 30 13:52:35 2003

source_name: SARB68 gDNA overnight in LB


title: GC2_SARB67_LT2_2D729_3

description:
genomic comparison SARB67/LT2
User - PCheng
Date_of_Scan = Wed Apr 30 14:12:37 2003

source_name: SARB67 gDNA overnight in LB


title: RE3_LT2_H2O2_20 min_3D148_3

description:
Salmonella typhimurium LT2 Expression after exposure to 2mM H2O2 for 20min
User - PCheng
Date_of_Scan = Tue Jul 29 13:17:28 2003
Sample_target_source3: LT2 genomic DNA


title: GC2_SARB68_LT2_2D728_2