title: GSG26

description: Genepix


title: GSG23

status: Public on Feb 01 2006

type: RNA

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Genepix

hyb_protocol: SSC/SDS 55C

scan_protocol: Agilent

data_processing: VSN

molecule: total RNA

organism: Mus musculus

source_name: GSG - 6

label_protocol: Aminoallyl-UTP labeled cRNA

tag: Gamma-SG deficient

tag: Male

tag: 6 wk

tag: Hindlimb muscle

source_name: GSG - 4

tag: 4 wk


title: GSG25

description: Genepix

source_name: GSG - 10

tag: 10 wk

source_name: GSG - 8

tag: 8 wk


title: SNU-387 vs. Universal control 4

status: Public on Jan 26 2006

city: Daejeon

first: Heun-Sik

last: Lee

address: 52 Eoeun-dong, Yuseong-gu

country: South Korea

institute: Korea Reaearch Institute of Bioscience and Biotechnology

description: Pro v4.0 (Axon Instruments, Whipple Road Union City, CA)

hyb_protocol: Genisphere 3DNA Expression Array Detection Kit (Genisphere, Hatfield, PA)

scan_protocol: Scannarray 5000 (Packard, Billerica, MA)

data_processing: braju.com, BRB-ArrayTools

organism: Homo sapiens

extract_protocol: RNeasy midi-prep (Qiagen, Chatsworth, CA)

tag: Hepatoma cell line

source_name: Universal control

tag: Pooled total RNA from 9 cancer cells (SNU-16, Raji, CaSki, Y-79, MCF7, A431, HCT116, Ovk-4 and Jurkat)


title: BSG1

description: Genepix

label_protocol: Aminoallyl-UTP labelled cRNA

tag: Beta-SG deficient

source_name: BSG - 1

extract_protocol: Aminoallyl-UTP labelled cRNA

tag: 1 wk


title: SNU-368 vs. Universal control 4

label_protocol: Genisphere 3DNA Expression Array Detection Kit (Genisphere, Hatfield, PA)


title: SNU-449 vs. Universal control 3


title: BSG4

description: Genepix

source_name: BSG - 8

source_name: BSG - 6


title: BSG8

description: Genepix

source_name: BSG - 20

tag: 20 wk

source_name: BSG - 14

tag: 14 wk


title: BSG2

description: Genepix

source_name: BSG - 4


title: BSG14

description: Genepix


title: BSG11

description: Genepix


title: BSG7

description: Genepix

source_name: BSG - 12

tag: 12 wk


title: SNU-368 vs. Universal control 3


title: BSG12

description: Genepix


title: BSG9

description: Genepix


title: BSG6

description: Genepix

source_name: BSG - 10


title: SNU-354 vs. Universal control 3


title: BSG5

description: Genepix


title: BSG15

description: Genepix


title: SNU-475 vs. Universal control 4


title: NIH 3T3 epsilon3

city: Los Angeles

first: sigal

last: gery

state: CA

country: USA

institute: Cedars-Sinai Medical Center

description: The zinc-inducible C/EBP expression vectors pMTa, pMTb, pMTd and pMTe were constructed by cloning the human C/EBPa, C/EBPb, C/EBPd and C/EBPe cDNAs, respectively, into the pMTCB6+ vector (pMT, a kind gift from F.J. Rauscher, III, The Wistar Institute, Philadelphia, PA).  NIH 3T3 cells were transfected with zinc-inducible C/EBP vectors as well as control empty vector using the GenePORTER™ transfection Reagent (GTS Inc.). Multiple polyclonal clones were obtained by selection with G418 (700 mg/ml). Clones were screened by Western blot analysis for C/EBP protein expression following induction for 16 h with ZnSO4 (100 mM). Oligonucleotide array hybridization and data analysis. Triplicate clones of NIH 3T3 cells were induced by addition of ZnSO4 (100 mM) for 16 h to the medium. Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA). Biotinylated cRNAs were prepared and hybridized to murine MG_74Av2 microarrays (Affymetrix, Santa Clara, CA, USA), which contains >12 000 genes. The probed arrays were scanned with a Hewlett Packard Gene Array scanner. The scanned output image files were analyzed using Affymetrix Microarray Suite version 5.0. To identify genes that were differently expressed between the five-sample sets (empty vector, C/EBPa, C/EBPb, C/EBPd and C/EBPe) class compression analysis were performed using BRBArray Tools (developed by Richard Simon and Amy Peng Lam; http://linus.nci.nih.gov/BRB-ArrayTools.html). Medium normalization was applied to the arrays and the percent absent filter was set at 80% to exclude probe sets that were unreliable. A list of 158 genes with probability of 95% that contain no more then 10% false discoveries was generated. Of these genes, 117 were significant at the 0.001 level of univariate F-test used and the remaining 41 were significant at the 0.027 level.

source_name: NIH 3T3


title: BSG13

description: Genepix


title: BSG3

description: Genepix


title: SNU-449 vs. Universal control 4


title: SNU-387 vs. Universal control 3


title: PLC/PRF/5 vs. Universal control 4


title: SNU-475 vs. Universal control 3


title: PLC/PRF/5 vs. Universal control 3


title: NIH 3T3 beta3


title: SNU-182 vs. Universal control 4


title: SNU-182 vs. Universal control 3


title: NIH 3T3 alpha3


title: NIH 3T3 epsilon


title: SNU-354 vs. Universal control 4


title: NIH 3T3 delta2


title: NIH 3T3 delta


title: NIH 3T3 epsilon2


title: NIH 3T3 delta3


title: NIH 3T3 beta


title: NIH 3T3 alpha2


title: NIH 3T3 beta2


title: Hep3B vs. Universal control 3


title: Hep3B vs. Universal control 4


title: NIH 3T3 alpha


title: HepG2 vs. Universal control 4


title: S1(Cy3)-C1(Cy5) comparison

status: Public on Jan 21 2006

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description: resistance to IBDV was determined according to viral-load in the bursa of infected chicks 3 days post-challenge, so that low viral-load indicates resistance (R) and high viral-load indicates susceptibility (S).

hyb_protocol: the array was incubated with preheated blocking solution (containing final concentration of 100 ug BSA per 1 ml solution) at 42ºC for 1 hour. After blocking, the slide was washed with DDW and with Isopropanol and immediately dried by centrifugation. The labelled cDNA samples were combined and cleaned using QIAquick PCR purification kit (QIAGEN) and filtered in a 0.45um-pores spin column. Next, the combined sample was added 10% SDS, heated at 99.9ºC for 2 minutes and then let to cool down to room temperature. The sample was then loaded on the array area of the slide and covered with a coverslip. Slide was placed in hybridization chamber which was then sealed and incubated at 63ºC for 16 hours. After hybridization, the slide was washed once with SDS, 3 more times with decreasing concentrations of SSC, and then dried.

scan_protocol: scanning was performed using ScanArray 5000 and its corresponding software (PerkinElmer Life Sciences). The microarray was scanned twice – once with 543 nm HeNe laser for excitation of Cy3 and once with 633 nm HeNe laser for excitation of Cy5. Scanning resolution was 10 um. Images were quantified using ImaGene 5 software (BioDiscoveries).

data_processing: the Signal mean (i.e., the average signal of all measurements inside the borders of a spot) and the Background median (i.e., the median of all measurements in the proximate surroundings of a spot, outside its borders) of each spot on the array were used for analysis. Data of both channels were normalized using the locally weighted scatterplot smoothing (LOWESS) method, implemented in the statistical software package R. The output of the normalization is a natural logarithmic (ln) value of the normalized background-subtracted signal for each probe. The value obtained from channel 2 was subtracted from the value obtained from channel 1. The result of this subtraction is the natural logarithmic (ln) value of the ratio between the normalized values of the two dyes. These values are given in the “VALUE” column of the data file.

organism: Gallus gallus

source_name: S1 – a spleen of IBDV-susceptible chick (group: S; subgroup: 1).

label_protocol: total RNA was amplified (MessageAmp II kit; Ambion) using oligo(dT) primer to produce antisense-RNA in high yields. aRNA was reverse-transcribed using SuperScript III (Invitrogen), incorporating aminoallyl-dUTP into the newly synthesized cDNA. After cleaning, cDNA sample was coupled with Cy3 dye and then quenched.

growth_protocol: chicks were grown under routine management conditions until the age of 13d, when they were housed in isolators.

extract_protocol: total RNA was extracted from preserved spleen tissue with TRIzol (Gibco BRL, Paisley, UK) according to manufacturer’s instructions.

treatment_protocol: spleen was harvested at age 24d (3d post-challenge). A small and thin slice (about 200 mg, 3-5 mm thick) was cut and soaked in 1 ml of RNAlater buffer (Ambion). According to the manufacturer instructions, the tissue was kept 24 hours at 4ºC and then stored at -20ºC until RNA extraction.

tag: Gender

value: female; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-susceptible; Tissue:spleen.

source_name: C1 – spleens of two non-challenged chicks (group: C; subgroup: 1).

label_protocol: total RNA was amplified (MessageAmp II kit; Ambion) using oligo(dT) primer to produce antisense-RNA in high yields. aRNA was reverse-transcribed using SuperScript III (Invitrogen), incorporating aminoallyl-dUTP into the newly synthesized cDNA. After cleaning, cDNA sample was coupled with Cy5 dye and then quenched.

treatment_protocol: spleens were harvested at age 24d (3d post-challenge). A small and thin slice (about 200 mg, 3-5 mm thick) was cut and soaked in 1 ml of RNAlater buffer (Ambion). According to the manufacturer instructions, the tissue was kept 24 hours at 4ºC and then stored at -20ºC until RNA extraction.

value: one male and one female; Age:24 days; non-challenged; Tissue:spleen.


title: NIH 3T3 vector3


title: R4(Cy3)-C4(Cy5) comparison

source_name: R4 – spleens of two IBDV-resistant chicks (group: R; subgroup: 4).

value: two males; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-resistant; Tissue:spleen.

source_name: C4 – spleens of two non-challenged chicks (group: C; subgroup: 4).

value: two males; Age:24 days; non-challenged; Tissue:spleen.


title: HepG2 vs. Universal control 3


title: R2(Cy3)-C2(Cy5) comparison

source_name: R2 – spleens of two IBDV-resistant chicks (group: R; subgroup: 2).

value: one male and one female; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-resistant; Tissue:spleen.

source_name: C2 – spleens of two non-challenged chicks (group: C; subgroup: 2).


title: MM253 Control

status: Public on Jan 20 2006

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

description: MM253 Control

data_processing: LOWESS, background subtracted

source_name: MM253 Control

tag: Cell Line

value: MM253 melanoma cell line

tag: Treatment

value: Control

tag: Time

source_name: MM329 Reference

value: MM329 melanoma cell line

value: Reference RNA


title: NIH 3T3 vector2


title: MM253 24 h PEP005

description: MM253 24 h PEP005


title: S3(Cy3)-C3(Cy5) comparison

source_name: S3 – spleens of two IBDV-susceptible chicks (group: S; subgroup: 3).

value: two males; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-susceptible; Tissue:spleen.

source_name: C3 – spleens of two non-challenged chicks (group: C; subgroup: 3).


title: S2(Cy5)-C2(Cy3) comparison

source_name: S2 – spleens of two IBDV-susceptible chicks (group: S; subgroup: 2).


title: MM455 Control

description: MM455 Control

source_name: MM455 Control

value: MM455 melanoma cell line


title: NIH 3T3 vector


title: MM127 Control

description: MM127 Control

source_name: MM127 Control

value: MM127 melanoma cell line


title: MM127 24 h TPA

description: MM127 24 h TPA

source_name: MM127 24 h TPA

value: TPA


title: S4(Cy5)-C4(Cy3) comparison

source_name: S4 – spleens of two IBDV-susceptible chicks (group: S; subgroup: 4).

value: one male and one female; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-susceptible; Tissue:spleen.


title: R1(Cy5)-C1(Cy3) comparison

source_name: R1 – a spleen of IBDV-resistant chick (group: R; subgroup: 1).

value: female; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-resistant; Tissue:spleen.


title: R3(Cy5)-C3(Cy3) comparison

source_name: R3 – spleens of two IBDV-resistant chicks (group: R; subgroup: 3).

value: two females; Age:24 days; non-challenged; Tissue:spleen.


title: R3(Cy3)-S3(Cy5) comparison

value: two females; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-susceptible; Tissue:spleen.


title: R1(Cy3)-S1(Cy5) comparison

source_name: R1 – a spleen of one IBDV-resistant chick (group: R; subgroup: 1).

source_name: S1 – a spleen of one IBDV-susceptible chick (group: S; subgroup: 1).

value: female; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-susceptible; Tissue:spleen.


title: R2(Cy5)-S2(Cy3) comparison


title: MM455 24 h TPA

description: MM455 24 h TPA

source_name: MM455 24 h TPA


title: LSPM2 Control

description: LSPM2 Control

source_name: LSPM2 Control

value: LSPM2 melanoma cell line


title: MM455 24 h PEP005

description: MM455 24 h PEP005


title: LSPM2 Control Recovery

description: LSPM2 Control Recovery

source_name: LSPM2 Control Recovery


title: MM253 24 h TPA

description: MM253 24 h TPA

source_name: MM253 24 h TPA


title: MM127 6 h TPA

description: MM127 6 h TPA

source_name: MM127 6 h TPA

value: 6 h


title: D24 24 h PEP005

description: D24 24 h PEP005

value: D24 melanoma cell line

source_name: MM329 Reference


title: D24 Control

description: D24 Control

source_name: D24 Control


title: D24 24 h TPA

description: D24 24 h TPA

source_name: D24 24 h TPA


title: D23 24 h TPA

description: D23 24 h TPA

source_name: D23 24 h TPA

value: D23 melanoma cell line


title: D23 24 h PEP005

description: D23 24 h PEP005


title: MM127 24 h TPA + 24 h

description: MM127 24 h TPA + 24 h

value: 24 h + 24 h Recovery


title: D04 Control

description: D04 Control

source_name: D04 Control

value: D04 melanoma cell line

value: Control


title: MM127 Control Recovery

description: MM127 Control Recovery

source_name: MM127 Control Recovery

value: MM329 melanoma cell line

value: Reference RNA


title: R4(Cy5)-S4(Cy3) comparison

source_name: R4 – spleens of two IBDV-resistant chicks (group: R; subgroup: 4).

value: two males; Age:24 days; challenged with IBDV at 21 days of age; Phenotype:IBDV-resistant; Tissue:spleen.


title: D23 Control

description: D23 Control

source_name: D23 Control


title: D04 24 h PEP005

description: D04 24 h PEP005


title: LSPM2 24 h TPA

description: LSPM2 24 h TPA

source_name: LSPM2 24 h TPA


title: LSPM2 24 h TPA + 24 h

description: LSPM2 24 h TPA + 24 h

source_name: LSPM2 24 h TPA + 24 h

value: 24 h with 24 h recovery


title: MM127 24 h PEP005

description: MM127 24 h PEP005

value: MM127 melanoma cell line


title: A07RM 24 h PEP005

description: A07RM 24 h PEP005

source_name: A07RM 24 h PEP005

value: A07RM melanoma cell line


title: LSPM2 6 h TPA

description: LSPM2 6 h TPA

source_name: LSPM2 6 h TPA

value: TPA


title: LSPM2 24 h PEP005

description: LSPM2 24 h PEP005

source_name: LSPM2 24 h PEP005


title: D04 24 h TPA

description: D04 24 h TPA

source_name: D04 24 h TPA


title: SNU-475 vs. Universal control 2

status: Public on Jan 13 2006

source_name: Universal control


title: SNU-387 vs. Universal control 1


title: A07RM 24 h TPA

description: A07RM 24 h TPA

source_name: A07RM 24 h TPA


title: SNU-368 vs. Universal control 1

tag: Hepatoma cell


title: A07RM Control

description: A07RM Control

source_name: A07RM Control


title: PLC/PRF/5 vs. Universal control 1


title: SNU-475 vs. Universal control 1


title: SNU-387 vs. Universal control 2


title: SNU-182 vs. Universal control 1


title: SNU-449 vs. Universal control 1


title: SNU-449 vs. Universal control 2


title: SNU-368 vs. Universal control 2


title: SNU-182 vs. Universal control 2


title: SNU-354 vs. Universal control 2


title: SNU-354 vs. Universal control 1


title: PLC/PRF/5 vs. Universal control 2


title: unc-43(n1186) Sample 1

status: Public on Jan 02 2006

city: Boston

first: Michael

last: Dybbs

state: MA

department: Molecular Biology

institute: Mass General Hopital

description:
Samples were prepared as follows. Animals were first synchronized by hypochlorite treatment and arrested at the first larval stage by incubation for 22 hours in M9. Animals were then grown at 20°C on 15 cm NG HB101 plates until the fourth larval stage (approximately 46 hours). Animals were washed, harvested in M9 and the flash frozen in liquid N2 and stored at -80° C. Total RNA was prepared by Trizol extraction.

Targets were prepared and hybridized at the Harvard Medical School Biopolymer Facility. Starting with 10 ug of total RNA first strand cDNA was synthesized as described in the Affymetrix expression technical manual.

Raw image files were converted to probe set data (.cel files) in Microarray Suite (MAS 5.0). The 9 probe set data files were normalized together, and expression values were determined, using the Robust Multi-chip Average (RMA) method as implemented in RMAExpress (Bolstad/Berkeley).

organism: Caenorhabditis elegans

source_name: Whole animal, fourth larval stage


title: HepG2 vs. Universal control 1


title: Hep3B vs. Universal control 1


title: Hep3B vs. Universal control 2


title: HepG2 vs. Universal control 2

tag: Pooled RNA from 9 cancer cells (SNU-16, Raji, CaSki, Y-79, MCF7, A431, HCT116, Ovk-4 and Jurkat)


title: unc-43(n1186) Sample 3


title: tom-1(nu468) Sample 1


title: unc-43(n1186) Sample 2


title: Wild type Sample 2


title: Wild type Sample 4


title: T6.3_60hpi_BiolRep3

status: Public on Jan 01 2006

city: Stillwater

first: Margaret

last: Essenberg

state: OK

address: 246 NRC, OSU

department: Biochemistry & Mol. Biol.

institute: Oklahoma State University

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 60hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

data_processing: Log (base 2) normalization feature normalized ratio (647/546) of background corrected means

organism: Gossypium hirsutum

source_name: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 60hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 60hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: Wild type Sample 1


title: tom-1(nu468) Sample 2


title: volunteer 90 in vitro Control Neutrophils

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCRMA

label: biotin

source_name: Neutrophil

label_protocol: Approximately 3 ?g of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

extract_protocol: Approximately 20 million airspace or peripheral blood neutrophils, previously stabilized in RNAlater (Ambion), were lysed in Trizol (Life Technologies) and total RNA isolated with Rneasy MinElute columns (Qiagen).


title: T4.3_30hpi_BiolRep3

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 30hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 30hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 30hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: T6.1_60hpi_BiolRep1

source_name: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 60hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 60hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: volunteer 89 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 88 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 90 Pre-Endotoxin Instillation Circulating Neutrophils


title: Wild type Sample 3


title: volunteer 89 Post-Endotoxin Instillation Circulating Neutrophils


title: T4.2_30hpi_BiolRep2

source_name: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2)

tag: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 30hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 30hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: T6.2_60hpi_BiolRep2

source_name: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2)

tag: 60hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 60hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 60hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: volunteer 90 Post-Endotoxin Instillation Circulating Neutrophils


title: T3.2_20hpi_BiolRep2

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 20hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2)

tag: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 20hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 20hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: T5.3_45hpi_BiolRep3

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 45hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 45hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 45hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: volunteer 90 Airspace Neutrophils

description: volunteer 90 Airspace Neutrophils

tag: volunteer 90 Airspace Neutrophils


title: volunteer 87 in vitro Control Neutrophils


title: volunteer 90 in vitro Endotoxin Neutrophils


title: volunteer 88 in vitro Control Neutrophils


title: volunteer 88 Post-Endotoxin Instillation Circulating Neutrophils


title: T3.3_20hpi_BiolRep3

source_name: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 20hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 20hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: volunteer 88 in vitro Endotoxin Neutrophils


title: volunteer 87 in vitro Endotoxin Neutrophils


title: T2.3_14hpi_BiolRep3

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 14hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 14hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 14hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: volunteer 87 Post-Endotoxin Instillation Circulating Neutrophils

source_name: Neutrophil


title: T5.2_45hpi_BiolRep2

source_name: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2)

tag: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 45hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 45hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: T4.1_30hpi_BiolRep1

source_name: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 30hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 30hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 30hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: T2.2_14hpi_BiolRep2

source_name: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2)

tag: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 14hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 14hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: T5.1_45hpi_BiolRep1

source_name: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 45hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 45hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 45hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: T3.1_20hpi_BiolRep1

source_name: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 20hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 20hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 20hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: volunteer 88 Airspace Neutrophils

description: volunteer 88 Airspace Neutrophils

tag: volunteer 88 Airspace Neutrophils


title: volunteer 84 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 80 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 84 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 84 in vitro Control Neutrophils


title: volunteer 87 Airspace Neutrophils

description: volunteer 87 Airspace Neutrophils

tag: volunteer 87 Airspace Neutrophils


title: volunteer 84 Airspace Neutrophils

description: volunteer 84 Airspace Neutrophils

tag: volunteer 84 Airspace Neutrophils


title: volunteer 89 Airspace Neutrophils

description: volunteer 89 Airspace Neutrophils

tag: volunteer 89 Airspace Neutrophils


title: volunteer 84 in vitro Endotoxin Neutrophils


title: volunteer 70 Pre-Endotoxin Instillation Circulating Neutrophils


title: T2.1_14hpi_BiolRep1

source_name: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 14hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 14hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 14hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: volunteer 80 Airspace Neutrophils

description: volunteer 80 Airspace Neutrophils

tag: volunteer 80 Airspace Neutrophils


title: volunteer 75 in vitro Endotoxin Neutrophils


title: volunteer 75 Post-Endotoxin Instillation Circulating Neutrophils


title: T1.3_8hpi_BiolRep3

description: Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated. Samples consisting of one leaf were harvested at 8hpi. Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere). Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments). Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 3)

tag: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)

source_name: 8hpi Non-inoculated Im216 leaves (Biological Replicate 3)

tag: 8hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 3)


title: volunteer 75 in vitro Control Neutrophils


title: volunteer 75 Airspace Neutrophils

description: volunteer 75 Airspace Neutrophils

tag: volunteer 75 Airspace Neutrophils


title: T1.2_8hpi_BiolRep2

source_name: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 2

tag: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)

source_name: 8hpi Non-inoculated Im216 leaves (Biological Replicate 2)

tag: 8hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 2)


title: volunteer 70 Airspace Neutrophils

description: volunteer 70 Airspace Neutrophils

source_name: Neutrophil

tag: volunteer 70 Airspace Neutrophils


title: volunteer 70 Post-Endotoxin Instillation Circulating Neutrophils


title: T1.1_8hpi_BiolRep1

description:
Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1.
Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated.  Samples consisting of one leaf were harvested at 8hpi.  Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere).  Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments).  Normalized log ratio VALUES were determined using the R-project statistical environment (http://www.r-project.org/), Bioconductor (http://www.bioconductor.org/) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/) website (H. Weng and P. Ayoubi, unpublished).

source_name: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Im216 leaves (Biological Replicate 1)

tag: 8hpi Xanthomonas campestris pv. malvacearum race 1-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)

source_name: 8hpi Non-inoculated Im216 leaves (Biological Replicate 1)

tag: 8hpi Non-inoculated Gossypium hirsutum L. line Im216 leaves (Biological Replicate 1)


title: volunteer 59 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 60 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 53 Airspace Neutrophils

description: volunteer 53 Airspace Neutrophils

tag: volunteer 53 Airspace Neutrophils


title: volunteer 59 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 59 Airspace Neutrophils

description: volunteer 59 Airspace Neutrophils

tag: volunteer 59 Airspace Neutrophils


title: volunteer 60 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 53 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 37 Pre-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 48 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 49 Pre-Endotoxin Instillation Circulating Neutrophils


title: volunteer 48 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 53 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 32 Airspace Neutrophils

description: Circulating Neutrophil

tag: volunteer 32 Airspace Neutrophils


title: volunteer 48 Airspace Neutrophils

description: Circulating Neutrophil

tag: volunteer 48 Airspace Neutrophils


title: volunteer 49 Airspace Neutrophils

description: volunteer 49 Airspace Neutrophils

tag: volunteer 49 Airspace Neutrophils


title: volunteer 21 Pre-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 21 Post-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 32 Post-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 09 Post-Endotoxin Instillation Circulating Neutrophils

description: Airspace Neutrophil


title: volunteer 32 Pre-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 37 Post-Endotoxin Instillation Circulating Neutrophils

description: Circulating Neutrophil


title: volunteer 49 Post-Endotoxin Instillation Circulating Neutrophils


title: volunteer 09 Airspace Neutrophils

description: Airspace Neutrophil

tag: volunteer 09 Airspace Neutrophils


title: volunteer 16 Airspace Neutrophils

description: Airspace Neutrophil

tag: volunteer 16 Airspace Neutrophils


title: fibroblast_tendon_stimulated_chipB_rep2

city: Sheffield

first: Steve

last: Winder

address: Western Bank

department: Department of Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Primary fibroblast from the cornea of the fetal mouse, mechanically stimulated by fluid flow

data_processing: Robust Multichip Average (RMA, module Affy 1.4.32 of Bioconductor)

label_protocol: Standard Affymetrix GeneChip Eukaryotic Two-Cycle Target Labeling

extract_protocol: RNA extractions were carried out with the Absolutely RNA RT-PCR Miniprep kit (Stratagene, La Jolla, CA, USA) according to the manufacturer's instructions. Contaminating RNases were inactivated in solutions upon treatment with 0.1% (v/v) DEPC, while RNaseZap was used according to the manufacturer's instructions to eliminate RNase contamination on work surfaces and pipettes.

treatment_protocol: Embryos used for fibroblast isolation were obtained from a time mated CD1 mouse. At 19-days post conception, the pregnant mouse was euthanized by CO2 asphyxiation and immediately swabbed with 70% ethanol in a sterile hood. Tendon, corneal and skin fibroblasts were isolated according to Spector et al {Spector, Goldman Robert D, et al. 1998 381 /id}.  Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% FCS in a 5% CO2 humidified atmosphere at 37 °C, and were subcultured when they reached approximately 80% confluence.  Cells were cultured until five population doublings, at which point they were seeded onto a gelatin-coated (1% w/v) glass plate (7cm x 10cm) and allowed to adhere for approximately seven hours prior to stimulation. STIMULATION: Fluid flow was applied to cells using a parallel plate flow chamber described previously {Ohtsuka, Ando, et al. 1993 341 /id}. Wall shear stress (tw) was calculated according to the equation tw = 6mQ/(bh2), where m is the fluid viscosity (0.001 Pa s), Q is the fluid flow rate (ml/s), and b and h are the width (5.5 cm) and height (0.04 cm) of the flow channel, respectively. The assembled system was maintained at 37 °C in a 5% CO2 humidified incubator. In this study, tendon, corneal and skin fibroblasts were subjected to a shear stress of 0.1 dynes/cm2 for 14 hours, with a flow perfusate of DMEM supplemented with 2% FCS and 1% penicillin/streptomycin.

tag: Primary fibroblast, fetal mouse tendon, mechanically stimulated


title: volunteer 21 Airspace Neutrophils

description: Airspace Neutrophil

tag: volunteer 21 Airspace Neutrophils


title: fibroblast_skin_stimulated_chipB_rep2

description: Primary fibroblast from the skin of the fetal mouse, mechanically stimulated by fluid flow

tag: Primary fibroblast, fetal mouse skin, mechanically stimulated


title: fibroblast_skin_stimulated_chipB_rep1


title: fibroblast_tendon_stimulated_chipB_rep1


title: fibroblast_tendon_control_chipB_rep3

description: Primary fibroblast from the tendon of the fetal mouse, not mechanically stimulated

treatment_protocol: Embryos used for fibroblast isolation were obtained from a time mated CD1 mouse. At 19-days post conception, the pregnant mouse was euthanized by CO2 asphyxiation and immediately swabbed with 70% ethanol in a sterile hood. Tendon, corneal and skin fibroblasts were isolated according to Spector et al {Spector, Goldman Robert D, et al. 1998 381 /id}.  Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% FCS in a 5% CO2 humidified atmosphere at 37 °C, and were subcultured when they reached approximately 80% confluence.  Cells were cultured until five population doublings, at which point they were seeded onto a gelatin-coated (1% w/v) glass plate (7cm x 10cm) and allowed to adhere for approximately seven hours. STATIC CONTROL: The fibroblast-seeded glass plate was transferred to a single-well plate and overlaid with DMEM supplemented with 2% FCS and 1% penicillin/streptomycin. Fibroblasts remained under these conditions for the duration of the 14 hour experiment

tag: Primary fibroblast, fetal mouse tendon, unstimulated control


title: fibroblast_skin_control_chipB_rep3

description: Primary fibroblast from the skin of the fetal mouse, not mechanically stimulated

tag: Primary fibroblast, fetal mouse skin, unstimulated control


title: fibroblast_cornea_stimulated_chipB_rep3

tag: Primary fibroblast, fetal mouse cornea, mechanically stimulated


title: fibroblast_skin_control_chipB_rep2


title: fibroblast_skin_stimulated_chipB_rep3


title: fibroblast_tendon_control_chipB_rep2


title: fibroblast_tendon_stimulated_chipB_rep3


title: fibroblast_cornea_control_chipB_rep3

description: Primary fibroblast from the cornea of the fetal mouse, not mechanically stimulated

tag: Primary fibroblast, fetal mouse cornea, unstimulated control


title: volunteer 37 Airspace Neutrophils

description: Circulating Neutrophil

tag: volunteer 37 Airspace Neutrophils


title: fibroblast_cornea_stimulated_chipB_rep1


title: fibroblast_cornea_stimulated_chipB_rep2


title: fibroblast_tendon_control_chipB_rep1


title: fibroblast_skin_control_chipB_rep1


title: volunteer 16 Post-Endotoxin Instillation Circulating Neutrophils

description: Airspace Neutrophil


title: fibroblast_cornea_control_chipB_rep1


title: Human5VSRef41

city: New Haven

first: Yoav

last: Gilad

state: CT

address: 333 Cedar St.

department: Genetics

institute: Yale

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 5 vs Reference slide 41
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF

source_name: polyA RNA

source_name: total RNA


title: fibroblast_cornea_control_chipB_rep2


title: Human5VSRef49b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 5 vs Reference slide 49b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human5VSRef11b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 5 vs Reference slide 11b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human4VSRef48b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 4 vs Reference slide 48b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human5VSRef51

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 5 vs Reference slide 51
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human4VSRef47b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 4 vs Reference slide 47b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human4VSRef15

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 4 vs Reference slide 15
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human4VSRef16

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 4 vs Reference slide 16
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human5VSRef50b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 5 vs Reference slide 50b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human3VSRef84

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 3 vs Reference slide 84
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human3VSRef14b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 3 vs Reference slide 14b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human3VSRef29

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 3 vs Reference slide 29
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human2VSRef22

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 2 vs Reference slide 22
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human3VSRef22b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 3 vs Reference slide 22b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp5VSRef94

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 5 vs Reference slide 94
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF

organism:
Pan troglodytes
Homo sapiens


title: Human1VSRef17b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 1 vs Reference slide 17b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus5VSRef90

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 5 vs Reference slide 90
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF

organism:
Macaca mulatta
Homo sapiens


title: Human2VSRef215b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 2 vs Reference slide 21b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Human1VSRef24

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 1 vs Reference slide 24
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp5VSRef93

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 5 vs Reference slide 93
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Human2VSRef15b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 2 vs Reference slide 15b
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus5VSRef60b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 5 vs Reference slide 60b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus5VSRef59

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 5 vs Reference slide 59
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp5VSRef54b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 5 vs Reference slide 54b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Human2VSRef25

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 2 vs Reference slide 25
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus4VSRef48

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 4 vs Reference slide 48
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus4VSRef47

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 4 vs Reference slide 47
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Human1VSRef28

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Human 1 vs Reference slide 28
characteristics_ch2: human
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus5VSRef11

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 5 vs Reference slide 11
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus4VSRef29b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 4 vs Reference slide 29b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus4VSRef28b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 4 vs Reference slide 28b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus3VSRef43

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 3 vs Reference slide 43
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus3VSRef32b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 3 vs Reference slide 32b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus3VSRef32

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 3 vs Reference slide 32
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus2VSRef16b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 2 vs Reference slide 16b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus1VSRef19

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 1 vs Reference slide 19
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus2VSRef38

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 2 vs Reference slide 38
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus3VSRef31b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 3 vs Reference slide 31b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus1VSRef56b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 1 vs Reference slide 56b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus1VSRef55b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 1 vs Reference slide 55b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan5VSRef57b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 5 vs Reference slide 57b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF

organism:
Pongo pygmaeus
Homo sapiens


title: Orangutan5VSRef13

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 5 vs Reference slide 13
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus1VSRef17

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 1 vs Reference slide 17
characteristics_ch2: rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus2VSRef20b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 2 vs Reference slide 20b
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan4VSRef45

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 4 vs Reference slide 45
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: adult 091504 Cr6 3-10

status: Public on Mar 31 2006

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

description: liver from adult male Fundulus heteroclitus

hyb_protocol: Probes are heated to 100C for 10 minutes, and then chilled on ice. Arrays are prehybridized with 5 mL of ExpressHyb Hybridization Solution (Clontech, Palo Alto, CA) and 1 mg sheared salmon sperm (denatured at 95C for 10 minutes then chilled on ice) at 68C for greater than 4 hours. Arrays were hybridized overnight at 68C. The blots were washed four times for 15 minutes at 64C using 2x SSC/0.5% SDS, then four times for 15 minutes at 64C using 0.5x SSC/0.5% SDS.

scan_protocol: Blots are wrapped in plastic wrap and exposed to a phosphoscreen at room temperature, visualized on BioRad FX Imager (Hercules, CA), and quantified with Invitrogen ResGen Pathways software (Carlsbad, CA).

data_processing: Data normalized to immediate background using ResGen Pathways software.

label: radioactive phosphorus 33 - [33P] dATP

organism: Fundulus heteroclitus

source_name: Fundulus heteroclitus adult male liver

label_protocol: 2 ug RNA is diluted into 10 uL of DEPC water. 10 uL of 0.5 uM poly T primers are added and incubated at 65C for 5 minutes and cooled to room temperature for two minutes. Radiolabelled cDNA is made by adding 30 uL of a mix containing 10 uL 5x reverse transcription buffer, 6 uL 10 mM dNTPs (without dATP), 10 uCi [33P]dATP, and 200 units MMLV-RT and incubating for 2 hours at 37C. Probes are cleaned of short nucleotide sequences through ProbeQuant G-50 Micro Columns (Amersham Biosciences, Piscataway, NJ) and counted on scintillation counter.

extract_protocol: RNA isolation performed by TriReagent according to manufacture’s protocols, followed by DNAse treatment.

treatment_protocol: Laboratory acclimated fish were exposed in individual tanks to potassium chromate at 3.0 mg/L Cr(VI) for 7 days with water exchanges every other day. Fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish were fed daily Tetramin flake fish food. At the conclusion of the exposure, livers were excised and frozen at -80C.

tag: Adult (>4cm in length) male liver excised immediately upon euthanasia


title: Orangutan3VSRef46b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 3 vs Reference slide 46b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan3VSRef46

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 3 vs Reference slide 46
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan4VSRef43b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 4 vs Reference slide 43b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan2VSRef35

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 2 vs Reference slide 35
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan2VSRef34b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 2 vs Reference slide 34b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Rhesus2VSRef20

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Rhesus 2 vs Reference slide 20
characteristics_ch2: Rhesus
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan2VSRef33b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 2 vs Reference slide 33b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan1VSRef39

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 1 vs Reference slide 39
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan3VSRef35b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 3 vs Reference slide 35b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan1VSRef21

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 1 vs Reference slide 21
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan1VSRef24b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 1 vs Reference slide 24b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan2VSRef26

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 2 vs Reference slide 26
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp5VSRef52b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 5 vs Reference slide 52b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp4VSRef59

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 4 vs Reference slide 59
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan5VSRef33

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 5 vs Reference slide 33
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan5VSRef44b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 5 vs Reference slide 44b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp4VSRef37

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 4 vs Reference slide 37
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan1VSRef13b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 1 vs Reference slide 13b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp4VSRef42b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 4 vs Reference slide 42b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp3VSRef42

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 3 vs Reference slide 42
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp4VSRef51b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 4 vs Reference slide 51b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp3VSRef36b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 3 vs Reference slide 36b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan3VSRef58

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 3 vs Reference slide 58
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan4VSRef44

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 4 vs Reference slide 44
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp3VSRef37b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 3 vs Reference slide 37b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp2VSRef40

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 2 vs Reference slide 40
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Orangutan4VSRef45b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 4 vs Reference slide 45b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp3VSRef49

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 3 vs Reference slide 49
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: fibroblast_tendon_stimulated_chipA_rep3

description: Primary fibroblast from the cornea of the fetal mouse, mechanically stimulated by fluid flow


title: Chimp1VSRef25b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 1 vs Reference slide 25b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp1VSRef23b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee vs Reference slide 23b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp2VSRef39b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 2 vs Reference slide 39b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp1VSRef

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee vs Reference
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp2VSRef27

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 2 vs Reference slide 27
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: Chimp2VSRef38b

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 2 vs Reference slide 38b
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: fibroblast_tendon_stimulated_chipA_rep1


title: fibroblast_tendon_stimulated_chipA_rep2


title: Chimp1VSRef34

description:
data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 1 vs Reference slide 34
characteristics_ch2: Chimp
source_name_ch2: EXP
source_name_ch1: REF


title: fibroblast_tendon_control_chipA_rep3

description: Primary fibroblast from the tendon of the fetal mouse, not mechanically stimulated


title: fibroblast_skin_stimulated_chipA_rep2

description: Primary fibroblast from the skin of the fetal mouse, mechanically stimulated by fluid flow


title: fibroblast_skin_stimulated_chipA_rep1


title: fibroblast_skin_control_chipA_rep3

description: Primary fibroblast from the skin of the fetal mouse, not mechanically stimulated


title: fibroblast_tendon_control_chipA_rep2


title: fibroblast_skin_control_chipA_rep2


title: fibroblast_skin_stimulated_chipA_rep3


title: fibroblast_cornea_control_chipA_rep3

description: Primary fibroblast from the cornea of the fetal mouse, not mechanically stimulated


title: fibroblast_skin_control_chipA_rep1


title: fibroblast_cornea_stimulated_chipA_rep1


title: fibroblast_cornea_control_chipA_rep1


title: fibroblast_cornea_stimulated_chipA_rep2


title: fibroblast_cornea_stimulated_chipA_rep3


title: fibroblast_cornea_control_chipA_rep2


title: fibroblast_tendon_control_chipA_rep1


title: soc1-101D_Experiment 3

city: Seoul

first: Horim

address: San56-1, Seoul National University, Shillim-dong, Kwanak-gu

department: Biological Sciences

institute: Seoul National University

description: This data is compared to Col_Experiment 3

data_processing: Scaling factor: 500

label: Biotin

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: soc1-101D was grown in long days (16L:8D) for 7 days after germination at 21 degree Celcius

tag: Basal Strain

value: Col, soc1-101D is an early flowering mutant


title: 5 week bitransgenic Ker86

city: Cleveland

first: Melissa

last: Landis

state: OH

address: 2109 Adelbert

department: Pharmacology

institute: Case Western Reserve School of Medicine

description: 5 week female Bitransgenic (LH crossed with MMTV-neu)

data_processing: Normalized Affymetrix signal intensities

label: UTP-biotin

source_name: Bitransgenic mouse 5week mammary gland


title: soc1-2_Experiment 3

growth_protocol: soc1-2 was grown in long days (16L:8D) for 7 days after germination at 21 degree Celcius

value: Col, soc12 is a knock-out mutant. This mutant displays late flowering phenotype


title: soc1-101D_Experiment 1

description: This data is compared to Col_Experiment 1


title: Col_Experiment 2

description: This data is used as a baseline to compare with data of soc1-101D_Experiment 2

growth_protocol: Col was grown in long days (16L:8D) for 7 days after germination at 21 degree Celcius

tag: Strain

value: Col, vegetative stage


title: 10week bitransgenic Ker4

description: 10 week female Bitransgenic (LH crossed with MMTV-neu)

source_name: Bitransgenic mouse 10week mammary gland


title: soc1-101D_Experiment 2

description: This data is compared to Col_Experiment 2


title: 5 week bitransgenic Ker87

tag: 5 week female Bitransgenic (LH crossed with MMTV-neu)


title: ALS: SOD1 mouse model, hybridisation 5

status: Public on Dec 31 2005

city: Göttingen

first: Bettina

last: Spielbauer

address: Humboldtallee 23

department: Neuro and Sensory Physiology

country: Germany

institute: University of Goettingen

description:
hSOD1(G93A) transgenic mice: transgenic mice expressing the human SOD1 gene with a G93A mutation (Gurney et al., 1994 [PMID: 8209258]), purchased from The Jackson Laboratory (B6SJL-Tg(SOD1-G93A)1Gur/J, stock no. 002726 [http://www.jax.org/]); fALS (familial amyotrophic lateral sclerosis) mouse model. Control mice: non-transgenic littermates. Timepoint: 17 week-old mice; transgenic mice showed severe signs of paralysis.
RNA preparation: isolation of total RNA from spinal cords using RNeasy Maxi Kit (Qiagen) followed by DNase I digestion.
RNA processing: RNA amplification (BD Atlas SMART Fluorescent Probe Amplification Kit, starting material: 1000 ng of total RNA, optimised amplification for each sample, stopped at PCR-cycle 18, 19 or 20 within the exponential amplification phase), labeling of amplified cDNA with cy3-/cy5-dCTP (Qiagen LabelStar Array Kit, per array and dye, 1000 ng of amplified cDNA were labeled using two labeling-reactions from the kit).
Microarray hybridisation and washing: according to the slide manufacturer´s recommendations (cf. GLP1800); microarray scanning: GMS 428 Microarray Scanner (AffyMetrix).
Microarray raw data: software package AIM (Katzer et al., 2003 [PMID: 15376910]). Signals with low quality were excluded from data analysis. Normalisation: pin-wise lowess-regression based normalisation (Yang et al., 2002 [PMID: 11842121]).
Keywords = amyotrophic lateral sclerosis, ALS, SOD1 mouse model

source_name: hSOD1(G93A) transgenic mouse, animal 394 (cy3 labeling)

source_name: Non-transgenic control mouse, animal 390 (cy5 labeling)


title: 10week bitransgenic Ker82

tag: 10 week female Bitransgenic (LH crossed with MMTV-neu)


title: Col_Experiment 1

description: This data is used as a baseline to compare with data of soc1-101D_Experiment 1


title: Col_Experiment 3

description: This data is used as a baseline to compare with data of soc1-101D_Experiment 3 or soc1-2_Experiment 3

tag: Strain:Col, vegetative stage


title: TRH -arg12

city: Providence

first: Xianne

last: Leong

state: RI

department: Medical Oncology

institute: Rhode Island Hospital; Brown University

description:
Biosource strain/age/gender/disease state:
neoplastically transformed cells derived from clonal subpopulations of derivation cell lines that were produced  by 11 brief repeated exposures of normal diploid hepatic epithelial line WB-F344 cells to 5 ug/ml of N-methyl-N-Nitro-N-nitrosoguanidine

Growth protocol:
Cells were routinely cultured in  modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS.

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum without L-Arginine HCl  for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Labeling/Scanning/Hybrization/Quantification protocol:
Target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix). Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner. Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). Data obtained was analyzed with GeneSpring 6.0.

Keywords = arginine, hepatocyte, cancer, rat, amino acid, gene regulation, microarray

organism: Rattus norvegicus

source_name: GP7TB transformed rat hepatic cells cultured in arginine-deficient media for 18 hours


title: 10week bitransgenic Ker83


title: 5 week bitransgenic Ker85


title: ALS: SOD1 mouse model, hybridisation 2

source_name: Non-transgenic control mouse, animal 304 (cy3 labeling)

source_name: hSOD1(G93A) transgenic mouse, animal 287 (cy5 labeling)


title: ALS: SOD1 mouse model, hybridisation 3

source_name: hSOD1(G93A) transgenic mouse, animal 287 (cy3 labeling)

source_name: Non-transgenic control mouse, animal 294 (cy5 labeling)


title: Control replicate 6

city: Okazaki

first: Hajime

last: Watanabe

state: Aichi

address: 5-1, Higashiyama

department: Center for Integrative Bioscience

country: Japan

institute: National Institutes of Natural Sciences

description: Wild type neonate (<24h)

scan_protocol: standard GenePix procedures

data_processing: GeneSpring version7.2

organism: Daphnia magna

source_name: Daphnia magna neonate

label_protocol: Approximately 0.5ug of total RNA was processed to produce cRNA targets.

extract_protocol: Approximately 10 neonates were lysed in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

treatment_protocol: Control

tag: Wild type, female, neonate, whole body


title: ALS: SOD1 mouse model, hybridisation 6

source_name: Non-transgenic control mouse, animal 390 (cy3 labeling)

source_name: hSOD1(G93A) transgenic mouse, animal 303 (cy5 labeling)


title: Control replicate 3

description: Wild type neonate (<24h)


title: Control replicate 5

description: Wild type neonate (<24h)


title: Control replicate 4

description: Wild type neonate (<24h)


title: TRH -arg10


title: TRH+arg11

description:
Biosource strain/age/gender/disease state:
neoplastically transformed cells derived from clonal subpopulations of derivation cell lines that were produced  by 11 brief repeated exposures of normal diploid hepatic epithelial line WB-F344 cells to 5 ug/ml of N-methyl-N-Nitro-N-nitrosoguanidine

Growth protocol:
Cells were routinely cultured in  modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS.

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum with L-Arginine HCl at 0.168 gm/liter for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Labeling/Scanning/Hybrization/Quantification protocol:
Target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix). Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner. Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). Data obtained was analyzed with GeneSpring 6.0.

Keywords = arginine, hepatocyte, cancer, rat, amino acid, gene regulation, microarray

source_name: GP7TB transformed rat hepatic cells cultured in high levels of arginine for 18 hours


title: ALS: SOD1 mouse model, hybridisation 4

source_name: Non-transgenic control mouse, animal 294 (cy3 labeling)

source_name: hSOD1(G93A) transgenic mouse, animal 394 (cy5 labeling)


title: ALS: SOD1 mouse model, hybridisation 1

source_name: hSOD1(G93A) transgenic mouse, animal 303 (cy3 labeling)

source_name: Non-transgenic control mouse, animal 304 (cy5 labeling)


title: TRH+arg7


title: Control replicate 1

description: Wild type neonate (<24h)


title: Control replicate 2

description: Wild type neonate (<24h)


title: PCP low replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 75 ug/l of pentachlorophenol for 24 h.


title: TRH+arg9


title: NRH -arg6

description:
Biosource strain/age/gender/disease state:
normal diploid hepatic epithelial cell line WB-F344 isolated from liver of an adult male Fischer-344 rat

Growth protocol:
Cells were routinely cultured in  modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS. Cells used in experiments were of low passage (<15)

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum without L-Arginine HCl  for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Labeling/Scanning/Hybrization/Quantification protocol:
Target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix). Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner. Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). Data obtained was analyzed with GeneSpring 6.0.

Keywords = arginine, hepatocyte, cancer, rat, amino acid, gene regulation, microarray

source_name: WB normal rat hepatic cells cultured in arginine-deficient media for 18 hours


title: NRH+arg5

description:
Biosource strain/age/gender/disease state:
normal diploid hepatic epithelial cell line WB-F344 isolated from liver of an adult male Fischer-344 rat

Growth protocol:
Cells were routinely cultured in  modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS. Cells used in experiments were of low passage (<15)

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum with L-Arginine HCl at 0.168 gm/liter for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Labeling/Scanning/Hybrization/Quantification protocol:
Target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix). Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner. Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). Data obtained was analyzed with GeneSpring 6.0.
Keywords = arginine
Keywords = hepatocyte
Keywords = cancer
Keywords = rat
Keywords = amino acid
Keywords = gene regulation
Keywords = microarray

source_name: WB normal rat hepatic cells cultured in high levels of arginine for 18 hours


title: TRH -arg8


title: PCP high replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 150 ug/l of pentachlorophenol for 24 h.


title: NRH+arg3


title: CuSO4 low replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 5 ug/l of copper sulphate for 24 h.


title: CuSO4 high replicate 2

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 10 ug/l of copper sulphate for 24 h.


title: PCP high replicate 2

description: Wild type neonate (<24h)


title: PCP low replicate 1

description: Wild type neonate (<24h)


title: PCP high replicate 1

description: Wild type neonate (<24h)


title: CuSO4 high replicate 3

description: Wild type neonate (<24h)


title: CuSO4 low replicate 2

description: Wild type neonate (<24h)


title: Staphylococcus aureus_no treatment_20min_replicate1

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: No treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_no treatment

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.

extract_protocol: Total RNA was isolated at 20 min after OD600 reached 0.8 using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: No treatment

tag: NCTC 8325 Wild type


title: CuSO4 low replicate 1

description: Wild type neonate (<24h)


title: bNF low replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 0.5 mg/l of beta-naphthoflavone for 24 h.


title: Staphylococcus aureus_no treatment_20min_replicate2

description: No treatment


title: Staphylococcus aureus_no treatment_10min_replicate3

description: No treatment

extract_protocol: Total RNA was isolated at 10 min after OD600 reached 0.8 using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: Staphylococcus aureus_no treatment_20min_replicate3

description: No treatment


title: CuSO4 high replicate 1

description: Wild type neonate (<24h)


title: bNF low replicate 2

description: Wild type neonate (<24h)


title: Staphylococcus aureus_hydrogen peroxide_20min_replicate3

description: Hydrogen peroxide treatment

source_name: Staphylococcus aureus_hydrogen peroxide

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 10mM hydrogen peroxide immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 20 min incubation with hydrogen peroxide using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: Hydrogen peroxide (10mM)


title: Staphylococcus aureus_hydrogen peroxide_20min_replicate1

description: Hydrogen peroxide treatment


title: Staphylococcus aureus_hydrogen peroxide_20min_replicate2

description: Hydrogen peroxide treatment


title: Staphylococcus aureus_no treatment_10min_replicate2

description: No treatment


title: bNF low replicate 1

description: Wild type neonate (<24h)


title: bNF high replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 1mg/l of beta-naphthoflavone for 24 h.


title: Staphylococcus aureus_no treatment_10min_replicate1

description: No treatment


title: NRH+arg1


title: Staphylococcus aureus_hydrogen peroxide_10min_replicate2

description: Hydrogen peroxide treatment

extract_protocol: Total RNA was isolated after 10 min incubation with hydrogen peroxide using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: NRH -arg2


title: Staphylococcus aureus_hydrogen peroxide_10min_replicate1

description: Hydrogen peroxide treatment


title: bNF high replicate 2

description: Wild type neonate (<24h)


title: bNF high replicate 1

description: Wild type neonate (<24h)


title: Staphylococcus aureus_hydrogen peroxide_10min_replicate3

description: Hydrogen peroxide treatment


title: H2O2 low replicate 1

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 1.2 mg/l of hydrogen peroxide for 24 h.


title: H2O2 high replicate 3

description: Wild type neonate (<24h)

treatment_protocol: Exposed to 2.4 mg/l of hydrogen peroxide for 24 h.


title: H2O2 high replicate 2

description: Wild type neonate (<24h)


title: H2O2 low replicate 2

description: Wild type neonate (<24h)


title: H2O2 low replicate 3

description: Wild type neonate (<24h)


title: H2O2 high replicate 1

description: Wild type neonate (<24h)


title: SKOV3

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

institute: Hiroshima University

description: Expression profiles of exponentially growing ovarian cancer cell lines were compared with their drug sensitivity.

hyb_protocol: Each cRNA sample was fragmented, and hybridized with a CodeLink UniSet Human 20K I Bioarray™ using Parallel Processing Kit™ (CodeLink) for 18 h at 37°C in an Innova™ 4080 incubator (New Brunswick Scientific) shaking at 300 rpm. The hybridized arrays were rinsed with 0.75 x TNT buffer at 46°C for 1 h, labeled with Streptavidin-Cy5 at room temperature for 30 min, rinsed with TNT buffer and 0.05% Tween 20, and dried by centrifugation.

scan_protocol: The arrays were scanned using Agilent DNA Microarray Scanner™ (Agilent, PaloAlto, CA, USA).

data_processing: Tiff file was analyzed with CodeLink Expression Analysis Software (Ver. 2.3).

source_name: ovarian cancer cell line

label_protocol: Biotin-labeled cRNA was synthesized from 1-µg total RNA using CodeLink Expressioin Assay Reagent Kit (Amersham) and Biotin-11-UTP (PerkinElmer) according to the manufacturers’ protocols.

growth_protocol: Cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) at 37°C in a humidified atmosphere of 5% CO2 and passaged every 3 days.

extract_protocol: Total RNA was prepared using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA). The quality of RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: serous adenoarcinoma


title: OVTOKO

tag: clear cell adenocarcinoma


title: RMG1


title: KF28


title: Leptin treated mouse gallbladder 8

city: Indianapolis

first: Henry

last: Pitt

state: IN

address: 535 Barnhill Dr. RT130D

institute: Indiana University School of Medicine

description: Female B6.V-lepob obese mice (n=24) aged 7 weeks were obtained from The Jackson Laboratory (Bar Harbor, ME).  Upon arrival, mice were placed on a standard chow diet and were allowed to acclimate fro 1 week before starting the experiment.  For leptin treatments, mice received daily intraperitoneal injections of either recombinant mouse leptin (R&D Systems, Minneapolis, MN) (n=12) at a dose of 5 µg/g body weight or with saline as a control (n=12) for 4 weeks.  At 12 weeks of age, mice were fasted overnight with free access to water.  The following morning the mice underwent cholecystectomy. Three gallbladders were pooled and total RNA was isolated.

data_processing: Data were generated using MAS 5.0 and normalized using global scaling.

label: biotinylated UTP and CTP

source_name: Gallbladder-leptin treated

value: B6.V-lep ob

tag: Gender

value: Female

tag: Age

value: 12 weeks

tag: Tissue

value: Gallbladder


title: KFr13Tx

tag: TXL/CDDP-resistant variant of KF28


title: Leptin treated mouse gallbladder 6

source_name: Gallbladder- leptin treated

value: B6.V-Lep ob


title: KK


title: WF Sample5

status: Public on Dec 30 2005

city: Seattle

first: Xuefeng

last: Ren

state: WA

institute: Fred Hutchinson Cancer Research Center

description:
Normal mammary gland
Sample_characteristics: WF Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures

source_name: Mammary gland


title: WF Sample4


title: KF


title: Leptin treated mouse gallbladder 7


title: SHIN3


title: WF Sample2


title: WF Sample3


title: Saline treated mouse gallbladder 4

source_name: gallbladder-saline treated

value: female

value: gallbladder


title: OVISE


title: Leptin treated mouse gallbladder 5

source_name: Gallbladder - leptin treated


title: Saline treated mouse gallbladder 2

source_name: gallbladder saline treated

tag: strain

tag: gender

tag: age

tag: tissue


title: BUF/N Sample5

description:
Normal mammary gland
Sample_characteristics: BUF/N Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: Saline treated mouse gallbladder 3


title: WF Sample1


title: BUF/N Sample3


title: BUF/N Sample2


title: Saline treated mouse gallbladder 1

source_name: gallbladder -saline treated


title: BUF/N Sample4


title: BUF/N Sample1


title: TAYA


title: ACI Sample4

description:
Normal mammary gland
Sample_characteristics: ACI Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: F344 Sample5

description:
Normal mammary gland
Sample_characteristics: F344 Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: ACI Sample5


title: F344 Sample1


title: Cop Sample1

description:
Normal mammary gland
Sample_characteristics: Cop Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: ACI Sample1


title: Cop Sample4


title: F1(CopXF344)Hybrid Sample3

description:
Normal mammary gland
Sample_characteristics: F1(Cop X F344)Hybrid Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures