title: Kidney Replicate K, Round 3 labeled with dye Cy3

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 3
Keywords = microarray

source_name: reference standard RNA, labeled with Cy5

source_name: Kidney K, type: Round 3,labeled with Cy3


title: Embryo 13,derived from AI, labeled with dye Cy5

status: Public on Nov 30 2005

type: RNA

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

country: USA

institute: University of Connecticut

description:
cDNA from embryo aRNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = AI
Keywords = microarray

scan_protocol: Fluoresecent images for both dye channels were obtained using a GenePix 4000B (Axon Instruments, Inc., CA) dual-laser confocal scanner and images were processed using GenePix Pro 4.0 (Axon Instruments, Inc., CA).

data_processing: microarray image was acquired and analyzed using GenePix Pro 4.0.

molecule: total RNA

organism: Bos taurus

source_name: Embryo 13, type: AI,labeled with Cy5

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent three rounds of linear amplification (Baugh et. al. 2001), the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: Single blastocyst total RNA isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

extract_protocol: RNA isolation was accomplished using Trizol. The RNA underwent two rounds of linear amplification (Baugh et. al. 2001) , the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: reference total RNA isolated by Trizol from EBTr, MDBK, and BL30 cell lines and brain tissue.


title: Kidney Replicate K, Round 1 labeled with dye Cy3

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 1
Keywords = microarray

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labeled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.

source_name: Kidney K, type: Round 1,labeled with Cy3

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent 1, 2 or 3 rounds of linear amplification (Baugh et. al. 2001) round 0 is equal to unamplfied total RNA. The aRNA/total RNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: total RNA isolated by Trizol


title: Kidney Replicate 1 Round 1 labeled with dye Cy3

scan_protocol: Fluoresecent images for both dye channels were obtained using a GenePix 4000B (Axon Instruments, Inc., CA) dual-laser confocal scanner and images were processed using GenePix Pro 4.0 (Axon Instruments, Inc., CA)."

source_name: reference standard RNA, labeled with Cy5"

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labeled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray."

extract_protocol: RNA isolation was accomplished using Trizol. The RNA underwent two rounds of linear amplification (Baugh et. al. 2001) , the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column."

tag: reference total RNA isolated by Trizol from EBTr, MDBK, and BL30 cell lines and brain tissue. "

source_name: Kidney 1, type: Round 1,labeled with Cy3"

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent 1, 2 or 3 rounds of linear amplification (Baugh et. al. 2001) round 0 is equal to unamplfied total RNA. The aRNA/total RNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column."


title: Embryo 8,derived from AI, labeled with dye Cy5

source_name: Embryo 8, type: AI,labeled with Cy5


title: Kidney Replicate K, Round 3, labeled with dye Cy5

source_name: Kidney K, type: Round 3,labeled with Cy5

extract_protocol: RNA isolation was accomplished using Trizol. The RNA uderwent 1, 2 or 3 rounds of linear amplification (Baugh et. al. 2001), round 0 is equal to unamplified total RNA. The aRNA/total RNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.


title: Kidney Replicate K, Round 0 labeled with dye Cy3

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 0
Keywords = microarray

source_name: Kidney K, type: Round 0,labeled with Cy3


title: Kidney Replicate 1, Round 2, labeled with dye Cy5

description:
cDNA from Kidney aRNA/total RNA and the reference standard.
Keywords = Kidney Validation
Keywords = cow
Keywords = Round 2
Keywords = microarray

source_name: Kidney 1, type: Round 2,labeled with Cy5


title: Kidney Replicate K, Round 1, labeled with dye Cy5

source_name: Kidney K, type: Round 1,labeled with Cy5


title: Embryo 13,derived from AI, labeled with dye Cy3

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 0.05 M sodium carbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were purified separately with a QIAquick PCR purification column. Each labelled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, and suspended/combined in 40 µl of ddH2O containing 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 µg T7dT24.  After denaturation for 2 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 0.2% SDS) is added and mixture is hybridized to the microarray.

source_name: Embryo 13, type: AI,labeled with Cy3


title: Embryo 17,derived from AI, labeled with dye Cy3

source_name: Embryo 17, type: AI,labeled with Cy3


title: Kidney Replicate 1, Round 1, labeled with dye Cy5

source_name: Kidney 1, type: Round 1,labeled with Cy5


title: Embryo H3,derived from AI, labeled with dye Cy5

source_name: Embryo H3, type: AI,labeled with Cy5


title: Kidney Replicate 1, Round 3, labeled with dye Cy5

source_name: Kidney 1, type: Round 3,labeled with Cy5


title: Embryo 15,derived from AI, labeled with dye Cy5

source_name: Embryo 15, type: AI,labeled with Cy5


title: Kidney Replicate 1, Round 0, labeled with dye Cy5

source_name: Kidney 1, type: Round 0,labeled with Cy5


title: Embryo 7,derived from AI, labeled with dye Cy5

source_name: Embryo 7, type: AI,labeled with Cy5


title: Embryo 7,derived from AI, labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Embryo 7, type: AI,labelled with Cy3


title: Embryo 16,derived from AI, labeled with dye Cy3

source_name: Embryo 16, type: AI,labeled with Cy3


title: Kidney Replicate 1, Round 2 labeled with dye Cy3

source_name: Kidney 1, type: Round 2,labeled with Cy3


title: Kidney Replicate 1, Round 3 labeled with dye Cy3

source_name: Kidney 1, type: Round 3,labeled with Cy3


title: Embryo 3,derived from AI, labeled with dye Cy5

source_name: Embryo 3, type: AI,labelled with Cy5

source_name: reference standard RNA, labelled with Cy3


title: Embryo 6,derived from AI, labeled with dye Cy5

source_name: Embryo 6, type: AI,labelled with Cy5


title: Embryo 1,derived from AI

source_name: reference standard RNA, labelled with Cy5

source_name: Embryo 1, type: AI,labelled with Cy3


title: IFN-gamma vs IFN-gamma M.tuberculosis 48h

status: Public on Nov 25 2005

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: color swap ratio experiment

hyb_protocol: Before hybridization, 1.25 µg labeled cRNA of each product were fragmented and mixed with control targets and hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were carried out for approximately 17 h at 60°C. The slides were washed according to the manufacturer's manual and scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap dye reversal was performed.

scan_protocol: Features were extracted with an image analysis tool Version A 6.1.1 (Agilent Technologies) using default settings. Data analysis was carried out on the Rosetta Inpharmatics platform Resolver Built 4.0. Ratio profiles were generated from raw scan data by a processing pipeline, which includes pre-processing (Feature Extraction) and post-processing (Rosetta Resolver) of data and error model adjustments to the raw scan data. Ratio profiles were combined in an error-weighted fashion (Rosetta Resolver) to create ratio experiments, and ratio experiments consisted of one or more ratio profiles.

data_processing: Rosetta Resolver 5.1

organism: Mus musculus

source_name: IFN-gamma 48h

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). cDNA was reverse transcribed from 4 µg total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase.

growth_protocol: Bone marrow cells were flushed from femura and tibiae of 8-12 wk old female C57/BL6 mice and differentiated into macrophages by incubation in DMEM supplemented with glutamine, sodium pyruvate, hepes buffer, 10% FCS, 5% horse serum, and 20% L929 fibroblast conditioned medium for 6 d.

extract_protocol: 10exp7 infected cells per condition and time point were lysed in 2 ml Trizol (Gibco). RNA was precipitated and purified with RNeasy (Qiagen). To eliminate DNA contaminations, RNA preparations were treated with DNAse I (Invitrogen) and purified with RNeasy (Qiagen). RNA integrity and quantities were subsequently monitored with a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, US).

treatment_protocol: BMM were treated with 1000 U/ml IFN-gamma for 24 + 48h.

tag: strain

tag: gender

value: female

tag: age

value: 90 days

source_name: IFN-gamma M.tuberculosis 48h

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). cDNA was reverse transcribed from 4 µg total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) and T7 polymerase.

treatment_protocol: BMM were treated with 1000 U/ml IFN-gamma for 24. Subsequently, M. tuberculosis H37Rv was taken from a fresh late-logarithmic culture, washed once in DMEM, and added at an MOI of 10 for 48 h.


title: IFN-gamma vs IFN-gamma M.tuberculosis 4h

description: color swap ratio experiment

source_name: IFN-gamma BMM 4h

treatment_protocol: BMM were treated with 1000 U/ml IFN-gamma for 24 + 4h.

source_name: IFN-gamma M.tuberculosis 4h

treatment_protocol: BMM were treated with 1000 U/ml IFN-gamma for 24. Subsequently, M. tuberculosis H37Rv was taken from a fresh late-logarithmic culture, washed once in DMEM, and added at an MOI of 10 for 4 h.


title: Embryo 5,derived from AI, labeled with dye Cy5

source_name: Embryo 5, type: AI,labelled with Cy5


title: Embryo 8,derived from AI, labeled with dye Cy3

source_name: Embryo 8, type: AI,labeled with Cy3


title: Embryo 3,derived from AI

source_name: Embryo 3, type: AI,labelled with Cy3


title: Embryo 1,derived from AI, labeled with dye Cy5

source_name: Embryo 1, type: AI,labelled with Cy5


title: Embryo 5,derived from AI

source_name: Embryo 5, type: AI,labelled with Cy3


title: Female Wnt4 -/- (Cy3) versus female Wnt4 +/+ (Cy5)

status: Public on Nov 24 2005

city: Durham

first: Douglas

last: Coveney

state: NC

address: Research Drive

department: Cell Biology

institute: Duke University Medical Center

description:
 One of the earliest morphological changes during testicular differentiation is the establishment of an XY specific vasculature. The testis vascular system is derived from mesonephric endothelial cells that migrate into the gonad. In the XX gonad, mesonephric cell migration and testis vascular development is inhibited by WNT4 signaling. In Wnt4
mutant XX gonads, endothelial cells migrate from the mesonephros and form a male-like coelomic vessel. Consequently, the XX Wnt4 mutant mice presented an opportunity to focus a
gene expression screen on the processes of mesonephric cell migration and testicular vascular development. We compared differences in gene expression between XY Wnt4+/+ and XX Wnt4+/+ gonads and between XX Wnt4-/- and XX Wnt4+/+ gonads to identify genes similarly upregulated in wildtype XY gonads and XX mutant gonads. Expression profiling was performed on gonads collected from XY Wnt4+/+, XX Wnt4+/+ and Wnt4-/- embryos at 12.0 days post coitum, using arrays spotted with the Operon Mouse Genome Oligo Set, version 2.0. Competitive dual-color hybridizations with dye-swap controls were performed in duplicate for each of two comparisons: XY Wnt4+/+, versus XX Wnt4+/+, and XX Wnt4-/- versus XX Wnt4+/+. For both comparisons, the wild-type XX sample is used as the reference.

hyb_protocol: Hybridization was performed by the Duke University Microarray Facility, a full protocol is available at: http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc

scan_protocol: Scanning was performed by the Duke University Microarray facility using the Axon GenePix Pro 4000A

data_processing: Per spot and per chip intensity dependent Lowess normalizations were performed on median intensity values.  Normalized values were used to calculated the log base 2 of the ratio (F635/F532), for all spots with a signal above background.

source_name: Female Wnt4 +/+ Cy5

label_protocol: Labeling was performed by the Duke University Microarray Facility, a protocol is available at: http://mgm.duke.edu/genome/dna_micro/core/protocols/dir_labeling.doc

extract_protocol: Gonads from 12.0 dpc XX Wnt4 +/+ embryos were separated from the adjacent mesonephroi, submerged in RNAlater Stabilization Reagent (Qiagen, Cat No. 76104) and stored at -80°C.  Gonads were collected from more than 100 embryos for each sex/genotype of interest, and pooled in multiple groups prior to RNA isolation.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen Cat No. 74104), following manufacturer’s instructions, and given to the Duke University Microarray Facility.

tag: Sex

value: Female (XX)

tag: Genotype

value: Wnt4 +/+ (wild-type)

source_name: Female Wnt4 -/- Cy3

extract_protocol: Gonads from 12.0 dpc XX Wnt4 -/- embryos were separated from the adjacent mesonephroi, submerged in RNAlater Stabilization Reagent (Qiagen, Cat No. 76104) and stored at -80°C.  Gonads were collected from more than 100 embryos for each sex/genotype of interest, and pooled in multiple groups prior to RNA isolation.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen Cat No. 74104), following manufacturer’s instructions, and given to the Duke University Microarray Facility.


title: Mist1KO caerulein rep1

status: Public on Nov 23 2005

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

country: Canada

institute: The University of Western Ontario/CHRI

description: Mist1KO caerulein injected total RNA

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GeneSpring

label: fluorescene

source_name: pancreas

label_protocol: Approximately 10 µg of total RNA was processed to produce fluorescently labeled cRNA targets.

extract_protocol: 2-4 month old male Mist1KO mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate

tag: Wild type, pancreas


title: IL-4 vs IL-4 M.tuberculosis 48h

description: color swap ratio experiment

source_name: IL-4 BMM

treatment_protocol: BMM were treated with 1000 U/ml IL-4 for 24 + 48h.

source_name: IL-4 M.tuberculosis 48h

treatment_protocol: BMM were treated with 1000 U/ml IL-4 for 24. Subsequently, M. tuberculosis H37Rv was taken from a fresh late-logarithmic culture, washed once in DMEM, and added at an MOI of 10 for 48 h.


title: Mist1KO caerulein rep3

description: Mist1KO caerulein injected total RNA

label_protocol: Approximately 10 µg of total RNA was processed to produce fluoresenctly cRNA targets.

tag: Wild type,pancreas


title: Embryo 6,derived from AI

source_name: Embryo 6, type: AI,labelled with Cy3


title: IL-4 vs IFN-gamma 4h

description: color-swap dye reversal ratio experiment

data_processing: Rosetta Resolver V5.1

treatment_protocol: BMM were treated with 1000 U/ml IL-4 for 24 + 4h.

source_name: IFN-gamma BMM

treatment_protocol: BMM were treated with 1000 U/ml IFN-gamma for 24+4h.


title: Male wild-type (Cy5) versus female wild-type (Cy3)

description:
One of the earliest morphological changes during testicular differentiation is the establishment of an XY specific vasculature.  The testis vascular system is derived from mesonephric endothelial cells that migrate into the gonad.  In the XX gonad, mesonephric cell migration and testis vascular development is inhibited by WNT4 signaling.  In Wnt4
mutant XX gonads, endothelial cells migrate from the mesonephros and form a male-like coelomic vessel. Consequently, the XX Wnt4 mutant mice presented an opportunity to focus a
gene expression screen on the processes of mesonephric cell migration and testicular vascular development.  We compared differences in gene expression between XY Wnt4+/+ and XX Wnt4+/+ gonads and between XX Wnt4-/- and XX Wnt4+/+ gonads to identify genes similarly upregulated in wildtype XY gonads and XX mutant gonads.  Expression profiling was performed on gonads collected from XY Wnt4+/+, XX Wnt4+/+ and Wnt4-/- embryos at 12.0 days post coitum, using arrays spotted with the Operon Mouse Genome Oligo Set, version 2.0.  Competitive dual-color hybridizations with dye-swap controls were performed in duplicate for each of two comparisons: XY Wnt4+/+, versus XX Wnt4+/+, and XX Wnt4-/- versus XX Wnt4+/+.  For both comparisons, the wild-type XX sample is used as the reference.

data_processing: Per spot and per chip intensity dependent Lowess normalizations were performed on median intensity values.  Normalized values were used to calculated the log base 2 of the ratio (F635/F532)

source_name: Male wild-type Cy5

label_protocol:
Labeling was performed by the Duke University Microarray Facility, a protocol is available at:
http://mgm.duke.edu/genome/dna_micro/core/protocols/dir_labeling.doc

extract_protocol: Gonads from 12.0 dpc XY +/+ embryos were separated from the adjacent mesonephroi, submerged in RNAlater Stabilization Reagent (Qiagen, Cat No. 76104) and stored at -80°C.  Gonads were collected from more than 100 embryos for each sex/genotype of interest, and pooled in multiple groups prior to RNA isolation.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen Cat No. 74104), following manufacturer’s instructions, and given to the Duke University Microarray Facility.

value: Male (XY)

value: wild-type

source_name: Female wild-type Cy3

extract_protocol: Gonads from 12.0 dpc XX +/+ embryos were separated from the adjacent mesonephroi, submerged in RNAlater Stabilization Reagent (Qiagen, Cat No. 76104) and stored at -80°C.  Gonads were collected from more than 100 embryos for each sex/genotype of interest, and pooled in multiple groups prior to RNA isolation.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen Cat No. 74104), following manufacturer’s instructions, and given to the Duke University Microarray Facility.


title: Mist1KO saline rep2

description: Mist1KO saline injected total RNA

extract_protocol: 2-4 month old male Mist1KO mice were injected once hourly for four hours with saline and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate


title: Female Wnt4 -/- (Cy5) versus female Wnt4 +/+ (Cy3)

description:
One of the earliest morphological changes during testicular differentiation is the establishment of an XY specific vasculature. The testis vascular system is derived from mesonephric endothelial cells that migrate into the gonad. In the XX gonad, mesonephric cell migration and testis vascular development is inhibited by WNT4 signaling. In Wnt4
mutant XX gonads, endothelial cells migrate from the mesonephros and form a male-like coelomic vessel. Consequently, the XX Wnt4 mutant mice presented an opportunity to focus a
gene expression screen on the processes of mesonephric cell migration and testicular vascular development. We compared differences in gene expression between XY Wnt4+/+ and XX Wnt4+/+ gonads and between XX Wnt4-/- and XX Wnt4+/+ gonads to identify genes similarly upregulated in wildtype XY gonads and XX mutant gonads. Expression profiling was performed on gonads collected from XY Wnt4+/+, XX Wnt4+/+ and Wnt4-/- embryos at 12.0 days post coitum, using arrays spotted with the Operon Mouse Genome Oligo Set, version 2.0. Competitive dual-color hybridizations with dye-swap controls were performed in duplicate for each of two comparisons: XY Wnt4+/+, versus XX Wnt4+/+, and XX Wnt4-/- versus XX Wnt4+/+. For both comparisons, the wild-type XX sample is used as the reference.

source_name: Female Wnt4 -/- Cy5

extract_protocol: Gonads from 12.0 dpc Wnt4 -/- embryos were separated from the adjacent mesonephroi, submerged in RNAlater Stabilization Reagent (Qiagen, Cat No. 76104) and stored at -80°C.  Gonads were collected from more than 100 embryos for each sex/genotype of interest, and pooled in multiple groups prior to RNA isolation.  Total RNA was isolated using the RNeasy Mini Kit (Qiagen Cat No. 74104), following manufacturer’s instructions, and given to the Duke University Microarray Facility.

source_name: Female Wnt4 +/+ Cy3

value: wild-type (Wnt4 +/+)


title: Mist1KO caerulein rep2

description: Mist1KO caerulein injected total RNA


title: Wild type caerulein rep3

description: Wild type caerulein injected total RNA

extract_protocol: 2-4 month old male C57BL6 mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate


title: Kidney Replicate 1, Round 0 labeled with dye Cy3

source_name: reference standard RNA, labeled with Cy5

source_name: Kidney 1, type: Round 0,labeled with Cy3


title: Characterization of an arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.

hyb_protocol: Labeled samples were mixed and then hybridized to a microarray for 15 h at 60C. The slides were washed at room temperature in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC for 5 min each with gentle shaking.

scan_protocol: The slides were scanned with a GenePix 4000B Scanner

organism: Arabidopsis thaliana

source_name: WT arabidopsis plants

tag: RNA samples was directly labeled with Cy3-dUTP fluorescent dye using random hexamer primers. Excess nucleotides and primers were removed. The slide was scanned with a GenePix 4000B Scanner. The hybridization intensities were measured using ScanAlyze 4.24. The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria

source_name: GAPN mutant arabidopsis plants

tag: RNA samples was directly labeled with Cy5-dUTP fluorescent dye using random hexamer primers. Excess nucleotides and primers were removed. The slide was scanned with a GenePix 4000B Scanner. The hybridization intensities were measured using ScanAlyze 4.24. The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria


title: Mist1KO saline rep3

description: Mist1KO saline injected total RNA


title: Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.

data_processing: Significance Analysis of Microarrays using the one class response

source_name: GAPN mutant arabidopsis plant

tag: The experimental RNA sample was directly labeled with Cy3-dUTP fluorescent dye

source_name: WT arabidopsis plant

tag: The experimental RNA sample was directly labeled with Cy5-dUTP fluorescent dye


title: Mist1KO saline rep1

description: Mist1KO saline injected total RNA

label_protocol: Approximately10 µg of total RNA was processed to produce fluorescently labeled cRNA targets.


title: Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene-2

description: Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities. The experiments were repeated three times with samples from different experiments, as biological replicates. In dye swapping experiments, the RNA samples from different experiments were labeled reciprocally, both as a biological and technical repetition for comparing the reproducibility of the experiments.The hybridization intensities of each microarray element were measured using ScanAlyze 4.24 (available at http://genome-www4.stanford.edu/MicroArray/SMD /restech.html). The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.

data_processing: Significance Analysis of Microarrays


title: Wild type saline rep1

description: Wild type saline injected total pancreatic tissue

label: fluoroscene

label_protocol: Approximately 10 µg of total RNA was processed to produce fluorescently labeled RNA

extract_protocol: 2-4 month male C57BL6 mice were injected with saline once hourly for 4hours, sacrificed and total RNA isolated using guanadinium isothiocianate

tag: Wild type pancreas


title: wt anaerobic plus NO3  AN rep 3

status: Public on Nov 21 2005

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655. The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO. Test RNA from E.coli K-12 MG1655 fnr- was isolated from three independently anaerobically grown cultures plus nitrite. Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA. An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers' instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

data_processing: Raw, not normalised

organism: Escherichia coli

source_name: wt anaerobic plus NO3

tag: Strain:E.coli K-12 MG1655, Genetic background

value: wt, Growth conditions:anaerobic plus NO3

source_name: anaerobic reference

value: wt, Growth conditions:anaerobic


title: wt anaerobic plus NO3 rep 3

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 wt was isolated from three independently anaerobically grown cultures plus nitrate.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

tag: Strain:E.coli K-12 MG1655

tag: Genetic background

value: wt

tag: Growth conditions

value: anaerobic plus NO3

source_name: aerobic reference

value: aerobic


title: narXLP rep 1

source_name: narXLP anaerobic plus NO2

value: narXLP, Growth conditions:anaerobic plus NO2


title: Wild type caerulein rep2

description: Wild type caerulein injected total RNA

source_name: pancreas

extract_protocol: 2-4 month old male C57BL6 mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadimium isothiocianate


title: Wild type caerulein rep1

description: Wild type caerulein injected total RNA

label_protocol: Approximately 10 µg of total RNA was processed to produce fluorescently cRNA targets.


title: narXLP rep 3


title: Male wild-type (Cy3) versus female wild-type (Cy5)

source_name: Female wild-type Cy5

source_name: Male wild-type Cy3


title: wt anaerobic plus NO3  AN rep 2


title: narXL rep 2

source_name: narXL anaerobic plus NO2

value: narXL, Growth conditions:anaerobic plus NO2


title: narXL rep 4


title: Wild type saline rep2

description: Wild type saline injected total RNA

label_protocol: Approximately 10µg of total RNA was processed to produce fluorescently labeled cRNA targets.

extract_protocol: 2-4 month old male C57BL6 mice were injected once hourly for four hours with saline and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate


title: fnr- anaerobic plus NO3  AN rep 3

source_name: fnr- anaerobic plus NO3

value: fnr-, Growth conditions:anaerobic plus NO3


title: wt anaerobic plus NO2  AN rep 3

source_name: wt anaerobic plus NO2

value: wt, Growth conditions:anaerobic plus NO2


title: Wild type saline replicate3

description: Wild type saline injected total RNA


title: wt anaerobic plus NO3  AN rep 1


title: narXL rep 3


title: narXLP rep 2


title: narXL rep 1


title: fnr- anaerobic plus NO3  AN rep 2


title: fnr- anaerobic plus NO3 rep 3

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 fnr- was isolated from three independently anaerobically grown cultures plus nitrate.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

value: fnr-


title: wt anaerobic plus NO3 rep 2


title: fnr- anaerobic plus NO3  AN rep 1


title: wt anaerobic plus NO2  AN rep 1


title: fnr- anaerobic plus NO2  AN rep 3

source_name: fnr- anaerobic plus NO2

value: fnr-, Growth conditions:anaerobic plus NO2


title: wt anaerobic plus NO2  AN rep 2


title: fnr- anaerobic plus NO3 rep 1


title: wt anaerobic plus NO2 rep 2

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 wt was isolated from three independently anaerobically grown cultures plus nitrite.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

value: anaerobic plus NO2


title: fnr- anaerobic plus NO2  AN rep 2


title: fnr- anaerobic plus NO3 rep 2


title: wt anaerobic plus NO2 rep 3


title: wt anaerobic plus NO3 rep 1


title: wt anaerobic  AN rep 3

source_name: wt anaerobic


title: fnr- anaerobic plus NO2 rep 1

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 fnr- was isolated from three independently anaerobically grown cultures plus nitrite.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).


title: fnr- anaerobic  AN rep 3

source_name: fnr- anaerobic

value: fnr-, Growth conditions:anaerobic


title: fnr- anaerobic plus NO2  AN rep 1


title: wt anaerobic  AN rep 2


title: fnr- anaerobic plus NO2 rep 2


title: wt anaerobic  AN rep 1


title: fnr- anaerobic  AN rep 2


title: fnr- anaerobic  AN rep 1


title: fnr- anaerobic plus NO2 rep 3


title: wt anaerobic plus NO2 rep 1


title: wt aerobic  AN rep 3

source_name: wt aerobic

value: wt, Growth conditions:aerobic


title: wt anaerobic rep 2

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 wt was isolated from three independently anaerobically grown cultures.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).

value: anaerobic


title: wt aerobic  AN rep 1


title: wt aerobic  AN rep 2


title: fnr- aerobic  AN rep 3

source_name: fnr- aerobic

value: fnr-, Growth conditions:aerobic


title: fnr- anaerobic rep 3

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 fnr- was isolated from three independently anaerobically grown cultures.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).


title: fnr- anaerobic rep 1

value: wtGrowth conditions:aerobic


title: fnr- anaerobic rep 2


title: wt anaerobic rep 3

tag: Genetic background:wt


title: wt aerobic rep 1

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 wt was isolated from three independently aerobically grown cultures.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).


title: fnr- aerobic rep 3

description: Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655.  The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO.  Test RNA from E.coli K-12 MG1655 fnr- was isolated from three independently aerobically grown cultures.  Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA.  An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions.  Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd).  The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).


title: Pat22-ALC-TU-1

status: Public on Nov 19 2005

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: Post-cirrhosis Hepatocellular Carcinoma

hyb_protocol: Hybridization of the [α 33P]-labelled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

organism: Homo sapiens

source_name: Tumoral liver

label_protocol: Within each RNA preparation prepared as above the target poly(A) mRNAs were labelled as follows : 10μg total RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg 5'(dT23)VN3' oligonucleotide were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labelled cDNAs were immediately used for hybridization.

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159

tag: 78 years old man with alcoholic liver disease


title: fnr- aerobic  AN rep 1


title: wt aerobic rep 3

value: aaerobic


title: wt anaerobic rep 1


title: Pat21-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 65 years old man with hepatitis C


title: Pat21-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat21-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: wt aerobic rep 2


title: Pat19-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 70 years old man with alcoholic liver disease


title: Pat20-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 73 years old woman with hepatitis C


title: Pat22-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat20-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: fnr- aerobic  AN rep 2

value: wt, Growth conditions:anaerobic


title: Pat22-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat20-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: fnr- aerobic rep 1

value: wt


title: Pat19-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat17-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 69 years old man with hepatitis C


title: fnr- aerobic rep 2


title: Pat18-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat19-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat18-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat16-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 56 years old man with alcoholic liver disease


title: Pat18-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat15-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 70 years old man with hepatitis C


title: Pat16-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat15-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat15-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat17-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat17-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat14-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 63 years old man with hepatitis C


title: Pat14-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat16-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat12-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 64 years old man with alcoholic liver disease


title: Pat13-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 72 years old man with alcoholic liver disease


title: Pat12-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat14-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat11-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 50 years old man with alcoholic liver disease


title: Pat11-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat13-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat12-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat13-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat11-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat10-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 73 years old man with alcoholic liver disease


title: Pat8-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 66 years old man with hepatitis C


title: Pat9-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat8-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat10-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat9-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat9-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat10-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat8-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat5-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.

tag: 79 years old man with alcoholic liver disease


title: Pat5-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat5-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat7-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 49 years old man with alcoholic liver disease


title: Pat7-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat6-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 63 years old man with alcoholic liver disease


title: Pat4-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 72 years old woman with hepatitis C


title: Pat7-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat2-ALC-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 68 years old man with alcoholic liver disease


title: Pat4-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat3-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 67 years old woman with hepatitis C


title: Pat6-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat2-ALC-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat2-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat3-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat22-ALC-CIR-2

description: Cirrhotic liver taken away from a Hepatocellular Carcinoma

source_name: Cirrhotic liver

tag: 78 years old man with alcoholic liver disease


title: Pat4-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat6-ALC-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat1-HCV-TU-1

description: Post-cirrhosis Hepatocellular Carcinoma

tag: 71 years old woman with hepatitis C


title: Pat1-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat1-HCV-TU-3

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat21-HCV-CIR-2

tag: 65 years old man with hepatitis C


title: Pat21-HCV-CIR-3


title: Pat22-ALC-CIR-3


title: Pat21-HCV-CIR-1


title: Pat20-HCV-CIR-3

tag: 73 years old woman with hepatitis C


title: Pat22-ALC-CIR-1


title: Pat3-HCV-TU-2

description: Post-cirrhosis Hepatocellular Carcinoma


title: Pat20-HCV-CIR-2


title: Pat20-HCV-CIR-1


title: Pat19-ALC-CIR-2

tag: 70 years old man with alcoholic liver disease


title: Pat19-ALC-CIR-1


title: Pat18-ALC-CIR-3


title: Pat18-ALC-CIR-2


title: Pat17-HCV-CIR-3

tag: 69 years old man with hepatitis C


title: Pat17-HCV-CIR-2


title: Pat16-ALC-CIR-1

tag: 56 years old man with alcoholic liver disease


title: Pat17-HCV-CIR-1


title: Pat18-ALC-CIR-1


title: Pat16-ALC-CIR-3


title: Pat15-HCV-CIR-3

tag: 70 years old man with hepatitis C


title: Pat19-ALC-CIR-3


title: Pat15-HCV-CIR-2


title: Pat13-ALC-CIR-3

tag: 72 years old man with alcoholic liver disease


title: Pat11-ALC-CIR-1

tag: 50 years old man with alcoholic liver disease


title: Pat12-ALC-CIR-2

tag: 64 years old man with alcoholic liver disease


title: Pat13-ALC-CIR-2


title: Pat15-HCV-CIR-1


title: Pat10-ALC-CIR-2

tag: 73 years old man with alcoholic liver disease


title: Pat14-HCV-CIR-3

tag: 63 years old man with hepatitis C


title: Pat11-ALC-CIR-3


title: Pat13-ALC-CIR-1


title: Pat9-HCV-CIR-3


title: Pat14-HCV-CIR-1


title: Pat10-ALC-CIR-1


title: Pat10-ALC-CIR-3


title: Pat7-ALC-CIR-3

tag: 49 years old man with alcoholic liver disease


title: Pat12-ALC-CIR-1


title: Pat8-HCV-CIR-3

tag: 66 years old man with hepatitis C


title: Pat16-ALC-CIR-2


title: Pat6-ALC-CIR-3

tag: 63 years old man with alcoholic liver disease


title: Pat11-ALC-CIR-2


title: Pat12-ALC-CIR-3


title: Pat7-ALC-CIR-1


title: Pat7-ALC-CIR-2


title: Pat9-HCV-CIR-1


title: Pat8-HCV-CIR-1


title: Pat9-HCV-CIR-2


title: Pat6-ALC-CIR-2


title: Pat8-HCV-CIR-2

tag: 66 yeras old man with hepatitis C


title: Control5-1

description: histologically normal liver taken away from a focal nodular hyperplasia

source_name: liver

tag: 30 years old woman


title: Control4-2

description: histologically normal liver taken away from a benign adenoma and  focal nodular hyperplasia

tag: 43 years old woman


title: Pat6-ALC-CIR-1


title: Control4-1


title: Pat3-HCV-CIR-1

tag: 67 years old woman with hepatitis C


title: Pat4-HCV-CIR-1

tag: 72 years old woman with hepatitis C


title: T4-infected E. coli cult.C_20min_2

status: Public on Nov 18 2005

city: Chicago

first: Yakov

middle: N.

last: Kogan

state: IL

address: 2201 W. Campbell Park Dr.

institute: Integrated Genomics, Inc.

description: Total RNA harvested from bacteriophage T4-infected E. coli B, at various timepoints post-infection, compared to a total RNA 'universal' control pool representing all T4 genes.

data_processing: Microarray images were processed with GenePix Pro 3.0 software (Axon Instruments, Foster City, CA). The 635/532 nm ratio was calculated using GenePix Pro 3.0 and normalized results were imported into GeneSpring 4.0 (Silicon Genetics, Redwood City, CA) for further analysis.  Each feature is represented in quadruplicate on the Integrated Genomics T4 array.

organism: Tequatrovirus T4

source_name: T4 total RNA, experimental

tag: Total RNA harvested from bacteriophage T4-infected E. coli B at 0, 1, 3, 5, 9, 15, 20, or 25 min. after infection, containing distinct early, middle, and/or late classes of T4 transcripts.

source_name: T4 total RNA control pool

tag: A mixture of total RNA harvested from bacteriophage T4-infected E. coli B, at 5 and 20 min after infection, representing every gene in the T4 chromosome.


title: T4-infected E. coli cult.C_25min_1


title: T4-infected E. coli cult.C_20min_1


title: Pat5-ALC-CIR-1

tag: 79 years old man with alcoholic liver disease


title: Control5-2


title: T4-infected E. coli cult.B_15min_3


title: Pat3-HCV-CIR-3


title: Pat14-HCV-CIR-2


title: T4-infected E. coli cult.C_20min_3


title: T4-infected E. coli cult.B_15min_1


title: T4-infected E. coli cult.B_20min_1


title: Pat5-ALC-CIR-2


title: T4-infected E. coli cult.C_9min_1


title: T4-infected E. coli cult.C_9min_2


title: T4-infected E. coli cult.B_9min_1


title: T4-infected E. coli cult.B_9min_4


title: T4-infected E. coli cult.B_9min_3


title: T4-infected E. coli cult.A_9min_1


title: T4-infected E. coli cult.A_9min_2


title: T4-infected E. coli cult.B_9min_2


title: Pat5-ALC-CIR-3


title: T4-infected E. coli cult.C_25min_2


title: Control1-3

description: histologically normal liver taken away from a benign adenoma

tag: 45 years old woman


title: T4-infected E. coli cult.C_5min_1


title: T4-infected E. coli cult.B_15min_2


title: T4-infected E. coli cult.C_5min_2


title: Pat2-ALC-CIR-1

tag: 68 years old man with alcoholic liver disease


title: T4-infected E. coli cult.B_5min_5


title: T4-infected E. coli cult.B_5min_4


title: T4-infected E. coli cult.B_3min_5


title: T4-infected E. coli cult.B_5min_3


title: T4-infected E. coli cult.B_5min_2


title: Pat1-HCV-CIR-1

tag: 71 years old woman


title: Pat3-HCV-CIR-2


title: Control2-3


title: T4-infected E. coli cult.B_3min_4


title: T4-infected E. coli cult.B_3min_3


title: Pat4-HCV-CIR-2


title: Control1-2


title: Pat1-HCV-CIR-3

tag: 71 years old woman with hepatitis C


title: Control2-2


title: T4-infected E. coli cult.B_3min_2


title: Control1-1

tag: 74 years old man


title: T4-infected E. coli cult.B_5min_1


title: T4-infected E. coli cult.B_3min_1


title: T4-infected E. coli cult.A_3min_1


title: T4-infected E. coli cult.B_1min_5


title: Control2-1


title: T4-infected E. coli cult.A_3min_2


title: Control3-1

tag: 68 years old woman


title: T4-infected E. coli cult.B_1min_3


title: Pat4-HCV-CIR-3


title: T4-infected E. coli cult.B_1min_2


title: T4-infected E. coli cult.B_1min_4


title: T4-infected E. coli cult.B_0min_2


title: Pat1-HCV-CIR-2


title: T4-infected E. coli cult.B_0min_1


title: T4-infected E. coli cult.A_0min_2


title: T4-infected E. coli cult.A_1min_2


title: T4-infected E. coli cult.B_1min_1


title: T4-infected E. coli cult.A_1min_1


title: Control3-2


title: T4-infected E. coli cult.A_0min_1


title: Pat2-ALC-CIR-2


title: Control3-3


title: Pat2-ALC-CIR-3


title: LS vs HS-2 weeks HS-3_L14_10-31-10_2-18-01(4)Cy5_13HS3_Cy3_SSHS3

status: Public on Nov 17 2005

city: Milwaukee

first: Mingyu

last: Liang

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

data_processing: global normalization

organism: Rattus norvegicus

source_name: Rat kidney

tag: SSHS


title: SSLS vs SSHS-overnight 9-21-01-21_ss2 cy5_ss5 cy3

tag: SSLS


title: 13LS vs 13HS-overnight 9-21-01-43_13-5 Cy3_13-2 cy5


title: LS vs HS-2 weeks HS-2r_L15_10-31-6_2-15-01(3)_Cy5_SSHS2_Cy3_13HS2


title: LS vs HS-2 weeks HS-2_L13_10-31-7_2-15-01(4)_Cy5_13HS2_Cy3_SSHS2


title: 13LS vs 13HS-overnight 9-21-01-26_13-5 Cy5_13-2 cy3


title: SSLS vs SSHS-overnight 9-21-01-22_SS-6 Cy5_ss-3 cy3


title: SSLS vs SSHS-overnight 9-21-01-19_SS-4 Cy3_SS-1 Cy5


title: SSLS vs SSHS-overnight 9-21-01-18_SS-1 Cy3_SS-4 Cy5


title: LS vs HS-2 weeks HS-3r_L24_11-1-72_2-18-01(3)_Cy5_SSHS3_Cy3_13HS3


title: SSLS vs SSHS-overnight 9-21-01-20_SS-2 Cy3_SS-5 Cy5


title: SSLS vs SSHS-3 days 9-21-01-41_SS-3 Cy5_ss-9 cy3


title: LS vs HS-2 weeks HS-1_L23_10-31-5_2-15-01(2)_Cy5_13HS1_Cy3_SSHS1


title: LS vs HS-2 weeks LS-3r_L19_10-31-8_2-18-01(1)_Cy5_SSLS3_Cy3_13LS3


title: 13LS vs 13HS-overnight 9-21-01-33_13-3 Cy5_13-6 cy3


title: LS vs HS-2 weeks HS-1r_L22_10-31-4_2-15-01(1)_Cy5_SSHS1_Cy3_13HS1


title: SSLS vs SSHS-overnight 9-21-01-23_SS-6 Cy3_ss-3 cy5


title: SSLS vs SSHS-3 days 9-21-01-40_SS-3 Cy3_ss-9 cy5


title: 13LS vs 13HS-overnight 9-21-01-25_13-4 Cy3_13-1 cy5


title: 13LS vs 13HS-overnight 9-21-01-32_13-3 Cy3_13-6 cy5


title: LS vs HS-2 weeks LS-3_L20_10-31-9_2-18-01(2)_Cy5_13LS3_Cy3_SSLS3


title: SSLS vs SSHS-3 days 9-21-01-39_SS-2 Cy5_ss-8 cy3


title: LS vs HS-2 weeks LS-2_L18_11-1-77_2-12-01(4)_Cy5_13LS2_Cy3_SSLS2


title: LS vs HS-2 weeks LS-1_L21_10-31-15_2-27-01(5)_Cy5_13LS1_Cy3_SSLS1


title: LS vs HS-2 weeks LS-2r_L17_11-1-76_2-12-01(3)_Cy5_SSLS2_Cy3_13LS2


title: LS vs HS-2 weeks LS-1r_L16_11-1-74_2-12-01(1)_Cy5_SSLS1_Cy3_13LS1


title: 13 LS vs 13 HS-2 weeks SS-3r_L9_11-1-68_2-8-01(2)_Cy5_SSLS3_Cy3_SSHS3


title: LS vs HS-2 weeks ch3


title: 13LS vs 13HS-overnight 9-21-01-24_13-1 Cy3_13-4 cy5


title: SSLS vs SSHS-3 days 9-21-01-37_SS-7 Cy3_ss-1 cy5


title: LS vs HS-2 weeks ch2


title: SSLS vs SSHS-3 days 9-21-01-38_SS-8 Cy5_ss-2 cy3


title: 13 LS vs 13 HS-2 weeks ch3r

source_name: 13 LS vs 13 HS-2 weeks


title: LS vs HS-2 weeks ch2r


title: SSLS vs SSHS-3 days 9-21-01-36_SS-1 Cy3_ss-7 cy5


title: LS vs HS-2 weeks ch1r


title: LS vs HS-2 weeks ch1


title: LECs from cirrhotic rats 2

city: Barcelona

first: Manuel

last: Morales-Ruiz

address: Villarroel 170

department: Biochemistry and Molecular Genetics

country: Spain

institute: Hospital Clinic

description: The study was performed in liver-endothelial cells (LECs) isolated from adult male Wistar rats, undergoing a cirrhosis induction protocol as described previously by our group, and LECs isolated from control Wistar rats, according to the criteria of the Investigation and Ethics Committee of the Hospital Clínic Universitari (Spain).The aim of this study was to evaluate differences in the gene expression pattern between LECs from control and cirrhotic rats. Methods: LECs were isolated from livers by collagenase perfusion, isopycnic centrifugation and incubation of cells with magnetic beads coated with specific antibodies.Total RNA was extracted from LECs with Trizol reagent (Life Technologies, Rockville, MD) after the cell-isolation step described above. RNA quality and concentration were confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). cRNA samples were hybridized to the Rat Expression 230A oligonucleotide microarray (Affymetrix). Microarray samples preparation and processing procedures where performed at the IDIBAPS Genomic Unit (Hospital Clinic Universitari, Barcelona) following the protocol as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Inc, Santa Clara, CA).

source_name: Liver endothelial cells


title: LECs from cirrhotic rats 3


title: 13 LS vs 13 HS-2 weeks ch3


title: 13 LS vs 13 HS-2 weeks ch2r


title: 13LS vs 13HS-3 days 9-21-01-34_13-9 Cy5_13-3 cy3


title: 13LS vs 13HS-3 days 9-21-01-35_13-9 Cy3_13-3 cy5


title: 13LS vs 13HS-3 days 9-21-01-29_13-7 cy3_13-1 cy5


title: 13LS vs 13HS-3 days 9-21-01-28_13-7 cy5_13-1 cy3


title: LECs from cirrhotic rats 1


title: 13LS vs 13HS-3 days 9-21-01-31_13-2 Cy5_13-8 cy3


title: R5S1

status: Public on Nov 16 2005

description: RA patients, fulfilling the American College of Rheumatology (ACR) criteria were eligible if methotrexate treatment; disease activity score 28 (DAS28) ≥ 5.1 under the maximally tolerated dose of methotrexate ; resistance to at least one DMARD (methotrexate included). Exclusion criteria were : evolving infectious disease; age <18 years ; lack of birth control ; pregnancy ; cancer less than 5 years old ; cardiac failure (stage III–IV of the New York Heart Association); infliximab allergy. Before the start of infliximab, the doses of methotrexate and prednisone were 5-20 mg/week and 0-20 mg/day, respectively, and in any given patient the dose of methotrexate remained unchanged when associated with infliximab. All patients were treated with infliximab according to a usual outline (i.v. 3 mg/kg infliximab at weeks 0, 2, 6, and every 8th week). Before each infiximab infusion, DAS28, ESR, plasma level of CRP, tender and swollen joint counts, and patient’s assessment of pain (0-100 mm visual analogue scale, VAS), disease activity (0-100 mm VAS), duration of morning stiffness, and physical function using the Health Assessment Questionnaire (HAQ) [Guillemin et al 1991] for RA, were recorded. The patients were categorized as responders or non-responders with the DAS28 score as defined by the European League Against Rheumatism (EULAR) [Van Gestel et al 1996] and calculated just before the 4th infusion. The patients were categorized as responders when a change of DAS28 ≥1.2 was obtained.

data_processing: The scanned 16-bit image was imported in a Linux workstation and the spots were automatically identified and analyzed with the XDotsReader software, version 1.8 (COSE,  Le Bourget, France) [3]. Spot identification was done with the "algorithm 2" option (i.e. spot morphology is the critical parameter) and quantitation of every spot within an array was done with the "weighted mean intensity" option (i.e. the average of the pixel intensities of a spot is weighted by the distance to the center of this spot). A global background was calculated over the entire image as the mean of a local background measured around each spot ("global background" option) and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots (see above) was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substracted from the signal for every significant spot. Normalization was based on the mean of the signals provided by the complete set of spots per image.

source_name: PBMC

tag: PBMC OF RESPONDER 5


title: LECs from control rats 2

source_name: liver endothelial cells


title: LECs from control rats 3


title: R5S2


title: 13 LS vs 13 HS-2 weeks ch1r


title: R4S2

tag: PBMC OF RESPONDER 4


title: 13 LS vs 13 HS-2 weeks


title: 13LS vs 13HS-3 days 9-21-01-30_13-8 Cy5_13-2 cy3


title: 13 LS vs 13 HS-2 weeks ch2


title: R6S2

tag: PBMC OF RESPONDER 6


title: R5S3


title: R6S1


title: LECs from control rats


title: R4S1


title: SigB-PhoR null Series Transition T+4 hours

city: Newcastle upon Tyne

first: Nicholas

last: Allenby

state: Tyne and Wear

address: Leech Building, Medical School

department: Institute for Cell and Molecular Biosciences

institute: The University of Newcastle upon Tyne

description:
Total RNA was extracted from the wild-type strain (Bacillus subtilis, 168) and phoR and sigB-null mutants before, during (T0) and after transition to phosphate-limited growth.  Cell harvesting, preparation of RNA, synthesis of radioactively labeled  cDNA and hybridization  of B. subtilis macroarrays (Sigma-Genosys, The Woodlands, Tex., USA) were performed as described by Eymann and co-workers (Eymann, C., H. Mach, C. R. Harwood, and M. Hecker. 1996. Phosphate-starvation-inducible proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study. Microbiology 142:3163-70.). Each analysis was carried out twice, using two independently isolated RNA preparations and two different array batches. The arrays were exposed to a phosphorescent screen which was subsequently scanned with a Storm 860 PhosphorImager (Molecular Dynamics, Sunnyvale, CA, USA) at a resolution of 50 µm and a 16-bit color depth. For quantification of the hybridization signals and background subtraction, the ArrayVision software (Version 5.1, Imaging Research, Onteria, Canada) was used. Calculation of normalized intensity values of the individual spots was performed using the over-all-spot-normalization function of ArrayVision. To avoid extreme expression ratios for genes close to or below the detection limit, genes with signal intensity values corresponding to less that twice the background were not counted in the analysis. Subsequently, the average of the normalized intensity values of the duplicate spots of each gene was used to calculate the expression level ratios. Data analysis (statistical analysis, visualization and the generation of lists) was performed using the GeneSpring software (Version 4.2.12, Silicon Genetics, Redwood City, CA).
Keywords = phosphate starvation
Keywords = PhoP regulon
Keywords = signal transduction
Keywords = DNA-array
Keywords = gene expression

organism: Bacillus subtilis

source_name: Total RNA SeriesB


title: R3S2

tag: PBMC OF RESPONDER 2


title: R3S3

tag: PBMC OF RESPONDER 3


title: SigB-PhoR null Series Transition T-1.5 hours


title: PhoR-null SeriesB Transition T+3 hours


title: SigB-PhoR null Series Transition T-0.5 hours


title: SigB-PhoR null Series Transition T+0.5 hours


title: SigB-PhoR null Series Transition T+1.5 hours


title: R2S1

tag: PBMC OF RESPONDER 1


title: R2S2


title: R1S2


title: R3S1


title: R1S3


title: PhoR-null SeriesB Transition T-2 hours


title: PhoR-null SeriesB Transition T-1 hours


title: R1S1


title: PhoR-null SeriesB Transition T+2 hours


title: NR6S2

tag: PBMC OF NON RESPONDER 6


title: PhoR-null SeriesB Transition T0 hours


title: PhoR-null SeriesA Transition T+6.5 hours


title: NR7S1

tag: PBMC OF NON RESPONDER 7


title: PhoR-null SeriesA Transition T+0.5 hours


title: NR7S2


title: PhoR-null SeriesA Transition T+1.5 hours


title: PhoR-null SeriesB Transition T+1 hours


title: NR6S1


title: PhoR-null SeriesA Transition T-0.5 hours


title: NR5S2

tag: PBMC OF NON RESPONDER 5


title: NR4S3

tag: PBMC OF NON RESPONDER 4


title: NR5S1


title: SigB-null SeriesB Transition T+2.75 hours


title: SigB-null SeriesB Transition T+5.25 hours


title: NR4S2


title: SigB-null SeriesB Transition T+1.75 hour


title: PhoR-null SeriesA Transition T-2.5 hours


title: SigB-null SeriesB Transition T+0.25 hours


title: NR3S3

tag: PBMC OF NON RESPONDER 3


title: SigB-null SeriesB Transition T-0.5 hours


title: SigB-null SeriesA Transition T+4.25 hours


title: NR4S1


title: NR3S1


title: NR2S2

tag: PBMC OF NON RESPONDER 2


title: NR3S2


title: C13

description: internal control

tag: Pool of PBMCs from 3 normal patients


title: SigB-null SeriesA Transition T+2.75 hours


title: NR2S1

tag: pbmc OF NON RESPONDER 2


title: C12

description: internal control


title: SigB-null SeriesA Transition T+0.25 hours


title: C10

description: internal control


title: C14

description: internal control


title: C9

description: internal control


title: SigB-null SeriesA Transition T+0.75 hours


title: C11

description: internal control


title: C8

description: internal control


title: SigB-null SeriesA Transition T-0.5 hours


title: C7

description: internal control


title: C6

description: internal control


title: Wild-type SeriesB Transition T0 hours


title: Wild-type SeriesB Transition T+1.75 hours


title: C5

description: internal control

source_name: Peripheral blood mononuclear cells


title: Wild-type SeriesB Transition T0.75 hours


title: Wild-type SeriesB Transition -1 hours

source_name: Wild-type SeriesB


title: C4

description: internal control


title: C3

description: internal control


title: Wild-type Transition +8.5 hours

source_name: Total RNA


title: Wild-type Transition +3.5 hours


title: C1

description: internal control


title: C2

description: internal control


title: Wild-type Transition +1.5 hours


title: SigB-null SeriesA Transition T+1.75 hours


title: Wild-type Transition +2.5 hours


title: NR1S1

tag: PBMC of non responder (NR) to infliximab


title: Wild-type Transition -3 hours


title: Gastrin Knockout parietal cell replicate 2

status: Public on Nov 15 2005

city: ANN ARBOR

first: Linda

last: Samuelson

state: MI

address: MED SCI II, # 7761, 1150 W. MEDICAL CENTER DRIVE

department: Molecular and Integrative Physiology

institute: University of Michigan

description: Gastrin Knockout purified (>90% pure) parietal cells

data_processing: Affymetrix Microarray Suite version 4.0

label: biotin

source_name: Gastrin Knockout fundus

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately10-14Gastrin Knockout mice were dissected and the fundus was used to isolate parietal cells and purified by flow cytometry. Total RNA was extracted from the purified parietal cells by Trizol followed by an RNeasy kit (Qiagen).

tag: Gastrin Knockout, 2 month old male mice parietal cell


title: Gastrin Knockout parietal cell replicate 3


title: wild type parietal cell replicate 2

description: Wild type purified (>90% pure) parietal cells

source_name: WT fundus

extract_protocol: Approximately10-14 wild-type mice were dissected and the fundus was used to isolate parietal cells and purified by flow cytometry. Total RNA was extracted from the purified parietal cells by Trizol followed by an RNeasy kit (Qiagen).

tag: Wild type, 2 month old male mice parietal cell


title: wild type parietal cell replicate 3


title: Wild-type Transition -0.5 hours


title: wild type parietal cell replicate 1


title: Vehicle-16 hour 2

status: Public on Nov 14 2005

city: Newark

first: Vanita

last: Gupta

state: NJ

address: 185 South Orange Ave

department: Biochemistry & Molecular Biology

institute: UMDNJ

description: Vehicle-16 hour

data_processing: Affymetrix MAS 5.0

source_name: Human

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Vehicle-16 hour 2


title: DEX-16 hour 2

description: DEX-16 hour

tag: DEX-16 hour 2


title: Vehicle-16 hour 3

description: Vehicle-16 hour

tag: Vehicle-16 hour 3


title: DBA 1-1-3 Testes

status: Public on Nov 11 2005

city: La Jolla

first: Matthew

middle: A

last: Zapala

state: CA

address: 10010 N. Torrey Pines Road

department: Genetics

institute: Salk Intitute for Biological Sciences

description: Wild type inbred mice

data_processing: Affymetrix TeraGenomics

source_name: Testes

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated as described in Sandberg et al. PNAS 2000. via TRIzol and Qiagen RNeasy Mini Kit Protocols


title: Vehicle-16 hour 1

description: Vehicle-16 hour

tag: Vehicle-16 hour 1


title: DEX-16 hour 3

description: DEX-16 hour

tag: DEX-16 hour 3


title: Vehicle-4 hour 2

description: Vehicle-4 hour

tag: Vehicle-4 hour 2


title: DEX-4 hour 2

description: DEX-4 hour

tag: DEX-4 hour 2


title: DEX-16 hour 1

description: DEX-16 hour

tag: DEX-16 hour 1


title: DEX-4 hour 3

description: DEX-4 hour

tag: DEX-4 hour 3


title: Vehicle-4 hour 3

description: Vehicle-4 hour

tag: Vehicle-4 hour 3


title: DEX-4 hour 1

description: DEX-4 hour

tag: DEX-4 hour 1


title: Gastrin Knockout parietal cell replicate 1


title: Vehicle-4 hour 1

description: Vehicle-4 hour

tag: Vehicle-4 hour 1


title: DBA 1-1 Thymus

description: Wild type inbred mice

source_name: Thymus


title: sham-operated mouse at zeitgeber time (ZT) 2

city: Tsukuba

first: Norio

last: Ishida

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: The sham-operated mice served as controls and were fed standard chow and water ad libitum.

source_name: Male C57BL/6 mice liver


title: ADX mice at zeitgeber time (ZT) 14

description: Male C57BL/6 mice were used in the ADX experiments. Bilateral ADX was performed in mice using the dorsal approach under ketamine/xylazine anesthesia (ketamine 91 mg/kg BW and xylazine 3.6 mg/kg BW, i.m.). The ADX mice were also fed standard chow (CE-2, Clea Japan Inc.) and 0.9% NaCl in their drinking water ad libitum.


title: ADX mice at zeitgeber time (ZT) 2


title: sham-operated mouse at zeitgeber time (ZT) 14


title: Wild-type SeriesB Transition T+4.75 hours


title: 129 4-1 Adrenal

description: Wild type inbred mice

source_name: Adrenal


title: C3H 2-2 Muscle

description: Wild type inbred mice

source_name: Muscle


title: DBA 1-1 Muscle

description: Wild type inbred mice


title: B6 4-2 Adrenal

description: Wild type inbred mice


title: C3H 2-2 Thymus

description: Wild type inbred mice


title: DBA 1-1-1 Heart

description: Wild type inbred mice

source_name: Heart


title: B6 2000-1 Thymus

description: Wild type inbred mice


title: 129 2000-2 Heart

description: Wild type inbred mice


title: B6 2000-2 Liver

description: Wild type inbred mice

source_name: Liver


title: 129 2000-2 Testes

description: Wild type inbred mice


title: B6 2000-2 Heart

description: Wild type inbred mice


title: B6 2000-2 Kidney

description: Wild type inbred mice

source_name: Kidney


title: B6 2000-1 BAT

description: Wild type inbred mice

source_name: Brown Adipose Tissue


title: AJ 1-2 BAT

description: Wild type inbred mice

tag: A/J


title: 129 2000-2 Thymus

description: Wild type inbred mice


title: C3H 4-2 Adrenal

description: Wild type inbred mice


title: C3H 2-1 Kidney

description: Wild type inbred mice


title: AJ 1-2-1 Testes

description: Wild type inbred mice


title: DBA 1-1-1 BAT

description: Wild type inbred mice


title: DBA 1-1-1 Liver

description: Wild type inbred mice


title: DBA 1-1-4 Kidney

description: Wild type inbred mice


title: 129 2000-2 Kidney

description: Wild type inbred mice


title: AJ 3-1 Adrenal

description: Wild type inbred mice


title: C3H 2-1-2 Testes

description: Wild type inbred mice


title: B6 2000-1 Testes

description: Wild type inbred mice


title: DBA 3-2 Adrenal

description: Wild type inbred mice


title: AJ 12-2-1 Muscle

description: Wild type inbred mice


title: AJ 8-2-1 Kidney

description: Wild type inbred mice


title: AJ 1-2 Heart

description: Wild type inbred mice


title: DBA 11-2 WAT

description: Wild type inbred mice

source_name: White Adipose Tissue


title: 129 21-2 WAT

description: Wild type inbred mice


title: B6 2000-1 Muscle

description: Wild type inbred mice


title: 129 2000-1 BAT

description: Wild type inbred mice


title: C3H 2-1 Heart

description: Wild type inbred mice


title: C3H 11-1 WAT

description: Wild type inbred mice


title: AJ 12-1 Thymus

description: Wild type inbred mice


title: 129 21-3-2 Muscle

description: Wild type inbred mice


title: 129 18-3-1 Liver

description: Wild type inbred mice


title: 129 14-4-1 Spleen

description: Wild type inbred mice

source_name: Spleen


title: C3H 8-1 BAT

description: Wild type inbred mice


title: AJ 14-4-1 Spleen

description: Wild type inbred mice


title: AJ 8-1-2 Liver

description: Wild type inbred mice


title: B6 16-2-2 Spleen

description: Wild type inbred mice


title: B6:25-16-30 choroid plexus

description: Wild type inbred mice

source_name: Choroid Plexus


title: B6:21-1 spinal cord

description: Wild type inbred mice

source_name: Spinal Cord


title: DBA 7-3-2 Spleen

description: Wild type inbred mice


title: B6:23-11-20 choroid plexus

description: Wild type inbred mice


title: B6:19-7 cortex

description: Wild type inbred mice

source_name: Cortex


title: C3H 8-3.1 Spleen

description: Wild type inbred mice


title: B6 16-2 WAT

description: Wild type inbred mice


title: B6:16-2 olfactory bulbs

description: Wild type inbred mice

source_name: Olfactory Bulbs


title: C3H 8-3-1 Liver

description: Wild type inbred mice


title: B6:19-8 cortex

description: Wild type inbred mice


title: B6:17-10,11,12 amygdala

description: Wild type inbred mice

source_name: Amygdala


title: AJ 14-1 WAT

description: Wild type inbred mice


title: B6:17-7,8,9 superior colliculi

description: Wild type inbred mice

source_name: Superior Colliculi


title: B6:17-1,2,3 superior colliculi

description: Wild type inbred mice


title: B6:17-4,5,6 inferior colliculi

description: Wild type inbred mice

source_name: Inferior Colliculi


title: B6:16-1 olfactory bulbs

description: Wild type inbred mice


title: B6:17-7,8,9 inferior colliculi

description: Wild type inbred mice


title: B6:21-3 spinal cord

description: Wild type inbred mice


title: B6:4-5 striatum

description: Wild type inbred mice

source_name: Striatum


title: B6:4-4 striatum

description: Wild type inbred mice


title: B6:17-7,8,9 amygdala

description: Wild type inbred mice


title: B6:16-5 midbrain-thalamus

description: Wild type inbred mice

source_name: Midbrain-Thalamus


title: B6:16-4 midbrain-thalamus

description: Wild type inbred mice


title: B6:2-7 cerebellum

description: Wild type inbred mice

source_name: Cerebellum


title: B6:19-6 medulla

description: Wild type inbred mice

source_name: Medulla


title: B6 9:4-5 Dentate Gyrus

description: Wild type inbred mice

source_name: Dentate Gyrus


title: B6:2-9 cerebellum

description: Wild type inbred mice


title: B6:19-8 medulla

description: Wild type inbred mice


title: BL6: 2-3 motor cortex

description: Wild type inbred mice

source_name: Motor Cortex


title: B6 9:1-3 CA3

description: Wild type inbred mice

source_name: Hippocampus CA3


title: B6 JD2:1-4 CA3

description: Wild type inbred mice


title: BL6: 2-4 motor cortex

description: Wild type inbred mice


title: BL6:4-1 -4-5 pituitary

description: Wild type inbred mice

source_name: Pituitary


title: BL6:3-1 -3-5 pituitary

description: Wild type inbred mice


title: B6 9:1-3 CA1

description: Wild type inbred mice

source_name: Hippocampus CA1


title: B6:19-9 pons

description: Wild type inbred mice

source_name: Pons


title: B6 JD2:1-4 CA1

description: Wild type inbred mice


title: B6:2-5 retina

description: Wild type inbred mice

source_name: Retina


title: BL6:4-3 -4-5 BNST

description: Wild type inbred mice

source_name: BNST


title: B6:19-7 pons

description: Wild type inbred mice


title: BL6:3-3 hippocampus

description: Wild type inbred mice

source_name: Hippocampus


title: B6 4:1and2 CA1

description: Wild type inbred mice


title: 129:30-16-30 choroid plexus

description: Wild type inbred mice

source_name: Choroid Plexus


title: BL6:4-3 + 4-4 PAG

description: Wild type inbred mice

source_name: PAG


title: BL6:4-1 + 4-2 hypothalamus

description: Wild type inbred mice

source_name: Hypothalamus


title: B6:2M-3 retina

description: Wild type inbred mice


title: BL6:4-1 + 4-2 BNST

description: Wild type inbred mice


title: B6 JD2:1-4 Dentate Gyrus

description: Wild type inbred mice


title: BL6:3-1 hippocampus

description: Wild type inbred mice


title: 129:28-11-20 choroid plexus

description: Wild type inbred mice


title: BL6:3-1 + 3-2 hypothalamus

description: Wild type inbred mice


title: BL6:4-1 + 4-2 PAG

description: Wild type inbred mice


title: B6:2-4 retina

description: Wild type inbred mice


title: B6:2M-2 retina

description: Wild type inbred mice


title: 129:24-4 cortex

description: Wild type inbred mice

source_name: Cortex


title: 129:26-3 spinal cord

description: Wild type inbred mice

source_name: Spinal Cord


title: 129:23-4,5,6 inferior colliculi

description: Wild type inbred mice

source_name: Inferior Colliculi


title: 129:23-1,2,3 superior colliculi

description: Wild type inbred mice

source_name: Superior Colliculi


title: 129:26-2 spinal cord

description: Wild type inbred mice


title: 129:24-6 cortex

description: Wild type inbred mice


title: 129:23-4,5,6 amygdala

description: Wild type inbred mice

source_name: Amygdala


title: 129:22-3 midbrain-thalamus

description: Wild type inbred mice

source_name: Midbrain-thalamus


title: 129:23-7,8,9 superior colliculi

description: Wild type inbred mice


title: 129:23-7,8,9 inferior colliculi

description: Wild type inbred mice


title: 129:23-1,2,3 amygdala

description: Wild type inbred mice


title: 129:24-3 cerebellum

description: Wild type inbred mice

source_name: Cerebellum


title: 129:24-6 medulla

description: Wild type inbred mice

source_name: Medulla


title: 129:22-4 olfactory bulbs

description: Wild type inbred mice

source_name: Olfactory Bulbs


title: 129:4-4 striatum

description: Wild type inbred mice

source_name: Striatum


title: 129:3-1-2 entorhinal cortex

description: Wild type inbred mice

source_name: Entorhinal Cortex


title: 129:4-3 striatum

description: Wild type inbred mice


title: 129:3-3-5 entorhinal cortex

description: Wild type inbred mice


title: 129:24-4 cerebellum

description: Wild type inbred mice


title: 129:22-3 olfactory bulbs

description: Wild type inbred mice


title: 129:3-1-2 perirhinal cortex

description: Wild type inbred mice

source_name: Perirhinal Cortex


title: 129:24-6 pons

description: Wild type inbred mice

source_name: Pons


title: 129:3-3-5 perirhinal cortex

description: Wild type inbred mice


title: 129:24-5 medulla

description: Wild type inbred mice


title: 129:22-2 midbrain-thalamus

description: Wild type inbred mice


title: 129 16:4-6 Dentate Gyrus

description: Wild type inbred mice

source_name: Dentate Gyrus


title: 129 16:4-7 CA1

description: Wild type inbred mice

source_name: Hippocampus CA1


title: 129:24-4 pons

description: Wild type inbred mice


title: 129 JD2:1-4 CA3

description: Wild type inbred mice

source_name: Hippocampus CA3


title: 129 16:4-6 CA3

description: Wild type inbred mice


title: 129 JD2:1-4 CA1

description: Wild type inbred mice


title: 129 JD2:1-4 Dentate Gyrus

description: Wild type inbred mice


title: 129:4-3 + 4-4 PAG

description: Wild type inbred mice

source_name: PAG


title: 129:4-1 + 4-2 PAG

description: Wild type inbred mice


title: 129:3-2 hippocampus

description: Wild type inbred mice

source_name: Hippocampus


title: 129:4-1 -4-5 pituitary

description: Wild type inbred mice

source_name: Pituitary


title: 129:3-1 + 3-2 hypothalamus

description: Wild type inbred mice

source_name: Hypothalamus


title: 129:4-3 -4-5 BNST

description: Wild type inbred mice

source_name: BNST


title: con 5

city: Charlestown

first: Shumin

last: Dong

state: MA

department: Pathology and Neurosurgical services

institute: Massachusetts General Hospital

description: control cells (common tumor cells) in human glioblastoma, case 2

source_name: human glioblastoma


title: 129:3-1 hippocampus

description: Wild type inbred mice


title: 129:4-1 + 4-2 BNST

description: Wild type inbred mice


title: 129:2-1 + 2-2 hypothalamus

description: Wild type inbred mice


title: 129:3-1 -3-5 pituitary

description: Wild type inbred mice


title: con 6


title: con 9

description: control cells (common tumor cells) in human glioblastoma, case 3


title: con 8


title: con 7


title: Con 2

description: control cells (common tumor cells) in human glioblastoma, case 1

source_name: Human glioblastoma


title: con 4


title: DBA:2-1-2 entorhinal cortex

description: Wild type inbred mice


title: DBA:2-3-5 entorhinal cortex

description: Wild type inbred mice


title: DBA:2-3-5 perirhinal cortex

description: Wild type inbred mice


title: palisading 7

description: specific tumor cell type-pseudopalisading cells in human glioblastoma, case 3


title: DBA: 1-1 motor cortex

description: Wild type inbred mice

source_name: Motor Cortex


title: Con 3


title: DBA:2-1-2 perirhinal cortex

description: Wild type inbred mice


title: palisading 8

source_name: huamn glioblastoma


title: Con 1


title: palisading 9


title: palisading 6

description: specific tumor cell type-pseudopalisading cells in human glioblastoma, case 2


title: DBA: 1-5 motor cortex

description: Wild type inbred mice


title: palisading 4


title: palisading 5


title: DBA 2:1-2 CA3

description: Wild type inbred mice


title: palisading 3

description: specific tumor cell type-pseudopalisading cells in human glioblastoma, case 1


title: rVSMC_nEGFP

status: Public on Nov 10 2005

city: Ube

first: Hiroki

last: Aoki

state: Yamaguchi

address: 1-1-1 Minami Kogushi

department: Molecular Cardiovascular Biology

institute: Yamaguchi University School of Medicine

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Infection of adenoviral vector encoding nuclear localizing EGFP (100 moi) was performed at the time of serum starvation when VSMCs reached confluent. Fourty eight hours after the infection, total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus

source_name: Rat vascular smooth muscle cells


title: DBA 2:1-2 CA1

description: Wild type inbred mice


title: rVSMC_H2O2+nEGFP

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Infection of adenoviral vector encoding nuclear localizing EGFP (100 moi) was performed at the time of serum starvation when VSMCs reached confluent. Twenty four hours after the serum starvation, VSMCs were stimulated with 100 µM H2O2 for another 24 hours. Total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus


title: rVSMC_H2O2+APF

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Infection of adenoviral vector encoding dominant negative JNK1 (JNK1-APF,100 moi) was performed at the time of serum starvation when VSMCs reached confluent. Twenty four hours after the serum starvation, VSMCs were stimulated with 100 µM H2O2 for another 24 hours. Total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus


title: rVSMC_MKK7ED+JNK1WT

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Infection of adenoviral vectors encoding constitutively active MKK7 (MKK7ED,33 moi) and JNK1 (JNK1-WT, 66 moi) was performed at the time of serum starvation when VSMCs reached confluent. Fourty eight hours after the infection, total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus


title: DBA 3:3-4 CA1

description: Wild type inbred mice


title: rVSMC_H2O2

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Confluent VSMCs were serum starved for 24 hours and stimulated with 100 µM H2O2 for another 24 hours. Total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 43

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

organism: Rhodopseudomonas palustris

source_name: Calibration experiment (#2-1) of Fe strain (Fe nitrogenase only strain)

tag: Mixed RNA from Fe strain grown under N2-fixing and non-N2-fixing conditions


title: rVSMC_control

description:
Rat vascular smooth muscle cells (VSMCs) were obtained from the aorta of 8-week-old male Wistar rats by enzyme dispersion. Dispersed cells were plated and maintained in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum on culture plates coated with 20 µg/ml laminin. All experiments were performed using cells at the second passage. Confluent VSMCs were serum starved for 48 hours. Total RNA was isolated using RNeasy (Qiagen), pooled from 3 independent experiments and subjected to DNA microarray analyses.
First-strand cDNA was synthesized using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. cDNA corresponding to 6-8 micrograms of total RNA was then used for in vitro transcription using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was then fragmented to a size of approximately 50bp. GeneChips were hybridized over night with 20 micrograms of biotinylated cRNA probe. GeneChips were washed in Affymetrix Fluidics station using the standard protocol. Bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 48

source_name: Comparative experiment (#2-2) of Fe strain (Fe nitrogenase only strain)

tag: RNA from Fe strain grown under N2-fixing conditions

tag: RNA from Fe strain grown under non-N2-fixing conditions


title: palisading 2


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 40

source_name: Comparative experiment (#3-2) of V strain (V nitrogenase only strain)

tag: RNA from V strain grown under non-N2-fixing conditions (+V)

tag: RNA from V strain grown under N2-fixing conditions (+V)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 50

source_name: Comparative experiment (#3-2) of Fe strain (Fe nitrogenase only strain)


title: Transcriptome profiles of Rhodopseudomonas palustris nitrogenases by whole genome microarray 45

source_name: Comparative experiment (#1-1) of Fe strain (Fe nitrogenase only strain)