title: 14 olanzapine

status: Public on Apr 10 2007

type: RNA

city: Minneapolis

first: S.

middle: Hossein

last: Fatemi

state: MN

address: 420 Delaware St SE, MMC 392

department: Department of Psychiatry, Division of Neuroscience Research

country: USA

institute: University of Minnesota

description:
Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following:  1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days.
Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003).
RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003).

Keywords = olanzapine
Keywords = frontal cortex

molecule: total RNA

organism: Rattus norvegicus

source_name: male sprague-dawley rat, 21 days olanzapine


title: SKIN_K14-Agouti Transgenic_Hyb1_T27

status: Public on Apr 09 2007

city: Oak Ridge

first: Yesim

last: Aydin Son

state: TN

address: ORNL, Bethel Valley Road, Building 1061,MS-6445

department: Functional Genomics Group

institute: UT-ORNL Graduate School of Genome Science and Technology

description: Data processing: After local background correction with Imagene 5.2 output, average log (base 2) intensities were used for normalization. Each dye-swap experiment in this series were individually normalized with LOWESS analysis using BRB-ArrayTools software.

hyb_protocol: TIGR Protocol for hybridization. An optimized version of this protocol is available at http://web.utk.edu/~saydin/protocols.

scan_protocol: Fluorescence intensities were measured using ScanArray (GSI Lumonics), and Imagene 5.2 (BioDiscovery) was used for image acquisition and quantification. Composite images were generated by Imagene software.

data_processing: LOWESS normalization with BRBArrayTools

organism: Mus musculus

source_name: K14-Agouti Transgenic mice

label_protocol: TIGR Protocol for indirect amino-ally labeling of cDNAs

extract_protocol: isolated using TRIzol (Invitrogen), followed by on-column DNAse treatment and a purification step with  RNeasy Mini Kit (Qiagen)

treatment_protocol: no additional treatments

tag: Transgenic

value: Overexpresses agouti protein under regulatory control of keratin 14

tag: Background strain

tag: Gender

value: male

tag: Age

value: 8 weeks

tag: Tissue

value: dorsal skin

tag: Tumor stage

value: promotion ( increase susceptibility to carcinogenesis)

source_name: B6 littermate control mice

tag: Strain

tag: control sample


title: SKIN_K14-Agouti Transgenic_Hyb1_T54


title: 18 olanzapine


title: Mjannaschii_ts_1.5h_500atm_rep4

status: Public on Apr 05 2007

city: Berkeley

first: Boonchai

last: Boonyaratanakornkit

state: CA

address: 201 Gilman Hall #1462

department: Chemical Engineering

institute: UC Berkeley

description: Effect of lethal heat shock at 500 atm.

hyb_protocol: Slides were pre-hybridized in filter-sterilized buffer (5X SSC, 0.1% SDS, 1% BSA) at 42C for at least 1 h. Slides were then washed in Milli-Q (Millipore) ultrapure H2O for 10 min, then in isopropanol for 6 min, and spun dry. Dried, labeled cDNA targets were resuspended in at least 10 ul of hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 ug/ul salmon sperm DNA) for 15 min at RT so that the dye concentrations in samples hybridized on the same slide were approximately the same. Cy5 and Cy3 labeled targets were combined, and targets were heated for 10 min at 95C and cooled on ice for 30 sec. A clean 25 mm X 60 mm glass lifterslip (Erie Scientific) was placed onto the pre-hybridized slide and target was applied using capillary action. Slides were placed in hybridization chambers (Corning) and hybridized at 42C in the dark for 16 to 20 hours. All post-hybridization washes were performed in aluminum-foil wrapped glass dishes (VWR) on an orbital shaker. The first wash was performed in 1X SSC, 0.1% SDS at 42C for 5 min. The second wash was performed in 0.1X SSC, 0.1% SDS for 5 min and the final three washes were performed in 0.1X SSC for 5 min, all at room temperature. Slides were blow-dried with filtered house air.

scan_protocol: Slides were scanned on a GenePix 4000 dual-color confocal laser scanner (Axon). Images were collected in the Cy3 and Cy5 channels (532 nm and 635 nm, respectively) and stored as paired TIFF images.

data_processing: VALUES were quantified using Spot (http://experimental.act.cmis.csiro.au/Spot/index.php).

organism: Methanocaldococcus jannaschii

source_name: Methanocaldococcus jannaschii, 500 atm, heat shocked, 1.5 h

label_protocol: Two ug of total RNA and 6 ug of random hexamers (Invitrogen) were combined, incubated at 70C for 10 min, and snap frozen in a dry-ice/ethanol bath for 30 s. First-strand cDNA synthesis was carried out at 42C overnight with 400 U of SuperScript II (Invitrogen), 1X first-strand buffer (Invitrogen SuperScript II), 0.01 M DTT (Invitrogen SuperScript II), 12.5 mM dATP (Invitrogen), 12.5 mM dCTP (Invitrogen), 12.5 mM dGTP (Invitrogen), 4.16 mM dTTP (Invitrogen), and 8.33 mM aa-dUTP (Ambion). The reaction was quenched by adding 10 ul 0.5 M EDTA, and the RNA template was hydrolyzed with the addition of 10 ul 1 M NaOH followed by incubation at 65C for 15 min. The reaction was neutralized by adding 25 ul 1M Tris-HCl, pH 7.0 (Ambion). cDNA was separated from reaction reagents using a Microcon 30 spin column (Millipore) and lyophilized to dryness with a Speed Vac (Savant). For NHS-Cy dye coupling, sample was re-suspended in 4.5 ul 0.1 M sodium carbonate, pH 9.0, and 4.5 ul of either NHS-Cy3 or NHS-Cy5 (Amersham Pharmacia) and allowed to couple to the cDNA for 1 h at room temperature in the dark. The coupling reaction was quenched with 4.5 ul 4 M hydroxylamine and incubated in the dark for 15 min at room temperature. 35 ul 100 mM sodium acetate pH 5.2 was added and unincorporated dye was removed using QIAquick columns (Qiagen). The whole undiluted sample was analyzed using a spectrophotometer (Beckman) to determine dye incorporation and nucleotides per dye; targets with dye incorporation of over 10 pmol and nucleotides-per-dye ratios below 60 were used in hybridizations. The Cy3 and Cy5 labeled cDNA targets were lyophilized to dryness in a Speed Vac (Savant).

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 1.5 h.

extract_protocol: Samples were withdrawn from the high T-P bioreactor through a micrometer control valve (High Pressure Equipment, Co.), passed through a 0.45 um nitrocellulose filter (Millipore) to collect cells. This filter was placed in cold phenol with 1% SDS and 0.1 M sodium acetate and homogenized using a beadbeater (BioSpec Products, Inc.) for 5 min at the highest setting. The aqueous layer was removed and re-extracted with cold phenol. Total RNA was precipitated overnight at -20C with 3M sodium acetate and isopropanol, treated with DNase (Invitrogen), and cleaned with RNeasy columns (Qiagen).

tag: Methanocaldococcus jannaschii (DSM 2661) pressure

value: 500 atm temperature:shifted from 88C to 98C in mid-exponential growth; held at 98C for 1.5 h volume:200 ml medium

source_name: Methanocaldococcus jannaschii, 500 atm

value: 500 atm temperature:88C volume:200 ml medium


title: 19 saline

source_name: male sprague-dawley rat, 21 days saline


title: Mjannaschii_ps_1.5h_rep1

description: Effect of pressure shock to 500 atm.

source_name: Methanocaldococcus jannaschii, pressure shocked, 1.5 h

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. In mid-exponential phase, the bioreactor was raised from 7.8 atm to 500 atm with He in 15 min and held at 500 atm for 1.5 h.

value: shifted from 7.8 atm to 500 atm with He in mid-exponential growth; held at 500 atm for 1.5 h  temperature:88C volume:200 ml medium

source_name: Methanocaldococcus jannaschii, 7.8 atm

value: 7.8 atm temperature:88C volume:200 ml medium


title: Mjannaschii_ts_0.5h_rep1

description: Effect of lethal heat shock at 500 atm.

source_name: Methanocaldococcus jannaschii, 7.8 atm, heat shocked, 0.5 h

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 0.5 h.

value: 7.8 atm temperature:shifted from 88C to 98C in mid-exponential growth; held at 98C for 0.5 h volume:200 ml medium

source_name: Methanocaldococcus jannaschii, 500 atm, heat shocked, 0.5 h

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 0.5 h.

value: 500 atm temperature:shifted from 88C to 98C in mid-exponential growth; held at 98C for 0.5 h volume:200 ml medium


title: 14 saline


title: Mjannaschii_ts_0.5h_7.8atm_rep4

description: Effect of lethal heat shock at 500 atm.

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm.


title: SKIN_K14-Agouti Transgenic_Hyb1_T25


title: Mjannaschii_ps_1.5h_rep2

description: Effect of pressure shock to 500 atm.


title: Mjannaschii_ps_0.5h_rep3

description: Effect of pressure shock to 500 atm.

source_name: Methanocaldococcus jannaschii, pressure shocked, 0.5 h

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. In mid-exponential phase, the bioreactor was raised from 7.8 atm to 500 atm with He in 15 min and held at 500 atm for 0.5 h.

value: shifted from 7.8 atm to 500 atm with He in mid-exponential growth; held at 500 atm for 0.5 h  temperature:88C volume:200 ml medium


title: Mjannaschii_ps_0.5h_rep2

description: Effect of pressure shock to 500 atm.


title: Mjannaschii_ts_0.5h_rep4

description: Effect of lethal heat shock at 500 atm.


title: 9 olanzapine


title: 17 saline


title: Mjannaschii_ts_1.5h_500atm_rep3

description: Effect of lethal heat shock at 500 atm.

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He.


title: Mjannaschii_ts_1.5h_500atm_rep1

description: Effect of lethal heat shock at 500 atm.


title: Mjannaschii_ps_0.5h_rep1

description: Effect of pressure shock to 500 atm.


title: Mjannaschii_ts_1.5h_500atm_rep2

description: Effect of lethal heat shock at 500 atm.


title: Mjannaschii_ps_1.5h_rep3

description: Effect of pressure shock to 500 atm.


title: 19 olanzapine

description:
Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following:  1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days.
Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003).
RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003).
Keywords = olanzapine
Keywords = frontal cortex


title: SKIN_K14-Agouti Transgenic_Hyb2_T27


title: Mjannaschii_ts_1.5h_7.8atm_rep4

description: Effect of lethal heat shock at 500 atm.

source_name: Methanocaldococcus jannaschii, 7.8 atm, heat shocked, 1.5 h

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C. A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 1.5 h.

value: 7.8 atm temperature:shifted from 88C to 98C in mid-exponential growth; held at 98C for 1.5 h volume:200 ml medium


title: Mjannaschii_ts_0.5h_rep2

description: Effect of lethal heat shock at 500 atm.


title: SKIN_K14-Agouti Transgenic_Hyb2_T25


title: 15 saline


title: chpT depletion - rep2

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

description: chpT depletion vs. wild type in PYE + xylose

data_processing: raw genepix data

organism: Caulobacter vibrioides

source_name: chpT depletion strain ML808

tag: chpT depletion strain

source_name: wild type CB15N

tag: wild type CB15N


title: Mjannaschii_ts_1.5h_7.8atm_rep3

description: Effect of lethal heat shock at 500 atm.


title: chpT depletion - rep1


title: Umbilical cord blood cells cultivated 7 days then 1h-treatment with Estradiol - T00239853

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Human Umbilical Cord Blood cells was collected from full-term deliveries with written informed consent approved by the Internal Review Board of the Albert Einstein Hospital (n=5). Mononuclear cells were isolated by density gradient using Ficoll-PaqueTM PLUS (Amersham Pharmacia Biotech). CD133+ and CD34+ cells were purified by immunomagnetic separation with MiniMACS kit (Miltenyi Biotech), following the manufacturer’s protocol. The purity of isolated CD133+/CD34+ cells was generally greater than 90%, as evaluated by flow cytometry using a FACS Aria (Becton Dickinson). Total RNA was treated with RNAse free-DNAse and further purified with RNeasy spin columns (Qiagen). Hybridizations were carried out with oligonucleotide CodeLink™ Bioarrays (GE Healthcare) following the manufacturer’s protocol. One microgram of total RNA was reverse transcribed in the presence of T7- oligo dT primer. The resulting cDNA was used for in vitro transcription reaction using T7 RNA polymerase and biotinylated dUTP. Ten micrograms of target cDNA was fragmented at 94 °C for 20 min and hybridized to the bioarrays at 37°C for 18 h, under 300 rpm agitation. After staining with streptavidin-conjugated Cyanine-5 dye, the slides were washed and the fluorescence was measured. The fluorescence was measured using an Axon GenePix 4000B Scanner (Axon Instruments Inc).

data_processing: All the data processing was done by CodeLink™ Bioarrays software using default parameters set by the manufacturer.

organism: Homo sapiens

source_name: Umbilical cord blood cells

tag: CD133+/CD34+ umbilical cord blood cells after seven days in culture. After this period we added 10 nM Estradiol in the culture media.


title: Mjannaschii_ts_0.5h_500atm_rep4

description: Effect of lethal heat shock at 500 atm.


title: chpT depletion - rep3


title: Mjannaschii_ts_0.5h_7.8atm_rep2

description: Effect of lethal heat shock at 500 atm.

value: 7.8 atm

tag: temperature

tag: volume

value: 200 ml medium

value: shifted from 88C to 98C in mid-exponential growth; held at 98C for 0.5 h


title: Mjannaschii_ts_0.5h_500atm_rep1

description: Effect of lethal heat shock at 500 atm.

hyb_protocol: Slides were pre-hybridized in filter-sterilized buffer (5X SSC, 0.1% SDS, 1% BSA) at 42C for at least 1 h. Slides were then washed in Milli-Q (Millipore) ultrapure H2O for 10 min, then in isopropanol for 6 min, and spun dry. Dried, labeled cDNA targets were resuspended in at least 10 ul of hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 ug/ul salmon sperm DNA) for 15 min at RT so that the dye concentrations in samples hybridized on the same slide were approximately the same. Cy5 and Cy3 labeled targets were combined, and targets were heated for 10 min at 95C and cooled on ice for 30 sec.

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C . A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. Further increases in pressure to 500 atm were obtained by addition of He. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 0.5 h.

value: 500 atm


title: Mjannaschii_ts_0.5h_500atm_rep2

description: Effect of lethal heat shock at 500 atm.


title: Mjannaschii_ts_0.5h_7.8atm_rep1

description: Effect of lethal heat shock at 500 atm.


title: Mjannaschii_ts_1.5h_7.8atm_rep1

description: Effect of lethal heat shock at 500 atm.

growth_protocol: M. jannaschii was cultivated in a 1.15 L high pressure vessel (model GC-17; High Pressure Equipment Co.) containing 200 ml of medium prepared as previously described (Park, CB and Clark, DS, Appl Environ Microbiol 68:3, 1458-1463) at a temperature of 88C . A baffled glass liner was used to minimize cell contact with SS316. H2:CO2 (4:1 v/v) substrate was supplied into the head space of the reactor to bring the pressure to 7.8 atm. In mid-exponential phase, the bioreactor was raised from 88C to 98C in 1 h and held at 98C for 1.5 h.

value: shifted from 88C to 98C in mid-exponential growth; held at 98C for 1.5 h


title: 1258-2

status: Public on Mar 28 2007

city: Inage-ku

first: Hiroshi

last: Watanabe

state: Chiba-shi

address: Anagawa 4-9-1

country: Japan

institute: National institute of radiological sceiences

description: Biopsy sample

data_processing: CodeLink Expression Analysis version 4.1

label: biotin

source_name: biopsy

tag: squamous cell cartinoma of oral tongue, male


title: Mjannaschii_ts_1.5h_7.8atm_rep2

description: Effect of lethal heat shock at 500 atm.


title: Umbilical cord blood cells transcriptome - T00234774

tag: Freshly isolated CD133+/CD34+ umbilical cord blood cells prior to cultivation.


title: 1669-1

description: Biopsy sample


title: 1261-2

description: Biopsy sample


title: Umbilical cord blood cells cultivated 7 days and 1h - T00239851

tag: CD133+/CD34+ umbilical cord blood cells after seven days and 1 hour in culture.


title: 1257-1

description: Biopsy sample


title: SKIN_K14-Agouti Transgenic_Hyb2_T54

value: male

tag: Transgenic

value: Overexpresses agouti protein under regulatory control of keratin 14


title: Mjannaschii_ts_0.5h_7.8atm_rep3

description: Effect of lethal heat shock at 500 atm.


title: 1258-1

description: Biopsy sample


title: 1253-2

description: Biopsy sample


title: 1253-1

description: Biopsy sample


title: 1669-2

description: Biopsy sample


title: 1575-2

description: Biopsy sample


title: Col-0_PsmES4326_24hpi_C

status: Public on Mar 09 2007

city: Saint Paul

first: Raka

middle: Mustaphi

last: Mitra

address: 1500 Gortner Avenue

department: Plant Biology

description: Pseudomonas syringae ES4326 inoculated, 24hpi, set C

hyb_protocol: Standard Affymetrix Hybridization protocol, performed at University of Minnesota Microarray Facility

scan_protocol: Standard Affymetrix protocol performed at University of Minnesota Microarray Facility

data_processing: RMAexpress

label: Phycoerythrin

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana leaves, PsmES4326 treated, 24hpi

label_protocol: Affymetrix One-Cycle Target Labeling Kit (Affymetrix, USA)

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

extract_protocol: Trizol (Invitrogen, USA)

treatment_protocol: Individual leaves were injected in the morning using a needle-less syringe with 10E5 cfu cm-2 PsmES4326 (suspended in 5mM MgSO4) and harvested 24 hours later.

tag: Genotype

value: Col-0, Tissue:leaves, Age:33 days post planting


title: Mjannaschii_ts_0.5h_rep3

description: Effect of lethal heat shock at 500 atm.


title: 0990-1

description: Biopsy sample


title: 1575-1

description: Biopsy sample


title: 1480-2

description: Biopsy sample


title: 1480-1

description: Biopsy sample


title: Col-0_MgSO4_24hpi_C

description: Mock inoculated control, 24hpi, set C

source_name: Arabidopsis thaliana leaves, mock treated, 24hpi

treatment_protocol: Individual leaves were injected in the morning using a needle-less syringe with 5mM MgSO4 and harvested 24 hours later.


title: B SLE 10

status: Public on Dec 31 2006

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description: Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd, High Wycombe, United Kingdom); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, Rnase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The double-stranded cDNA was purified and served as a template for the overnight in vitro transcription reaction, carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35 minute incubation at 95°c. Because a minimal amount of 1 ug total RNA is required for the synthesis of cRNA, not all the CD20 cell samples could be processed, accounting for the lower number of CD20 cell hybridizations.

data_processing: Data were retrieved on GCOS software for the initial normalization and analysis steps. The number of positive genes was between 40 and 51% on each slide. After scaling on all probe set (to a value of 100), the amplification scale was reported between 1.5 and 2.5 for the CD4 slides, and between 5 and 10 for the CD20 slides. The signals given by the poly-A RNA controls, hybridization controls and housekeeping/control genes were indicative of the good quality of the amplification and hybridization procedures.

label: SA-PE

source_name: SLE patient

extract_protocol: Total RNA was extracted from both cell subsets using the Nucleospin® RNA II extraction kit (Macherey-Nagel GmbH & Co, Düren, Germany), including DNase treatment of the samples. RNA quality was assessed by capillary electrophoresis using RNA 6000 Pico LabChips on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc, Palo Alto, CA, USA).

treatment_protocol: PBMC were thawed in the presence of 10 mg/ml DNase I (Roche Diagnostics GmbH, Mannheim, Germany), then resuspended in Hanks’ medium without CaCl2 (supplemented with 1% fetal calf serum and 1mM EDTA) and stained with FITC-labeled CD4, APC-labeled CD20 and PE-labeled CD11c monoclonal antibodies (all purchased from BD-Pharmingen, Erembodegem, Belgium). The CD4 and CD20 positive cell populations were sorted out by flow cytometry using a FacsVantageTM cell sorter (BD-Pharmingen). Typically, 25 to 35% of the total PBMC population was positive for the CD4 staining versus 5 to 15% for the CD20 marker.

tag: B cells sorted from total PBMC of systemic lupus erythematosus patient


title: 1261-1

description: Biopsy sample


title: 0936-2

description: Biopsy sample


title: B SLE 2


title: B SLE 7


title: 0990-2

description: Biopsy sample


title: 0989-2

description: Biopsy sample


title: B SLE 8


title: B RA 3

source_name: Rheumatoid arthritis patient

tag: B cells sorted from total PBMC of RA patient


title: 0936-1

description: Biopsy sample


title: B SLE 9


title: 0989-1

description: Biopsy sample


title: B RA 2


title: B SLE 5


title: B CONT 13

source_name: Healthy individual

tag: B cells sorted from total PBMC of healthy subject


title: B SLE 3


title: B RA 6


title: B CONT 10


title: B RA 8


title: B CONT 7


title: B RA 7


title: B RA 4


title: CD4 SLE 7

tag: CD4 T cells sorted from total PBMC of patient with systemic lupus erythematosus


title: B CONT 2


title: B CONT 1

description:
Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd, High Wycombe, United Kingdom); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, Rnase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The double-stranded cDNA was purified and served as a template for the overnight in vitro transcription reaction, carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35 minute incubation at 95°c. Because a minimal amount of 1 ug total RNA is required for the synthesis of cRNA, not all the CD20 cell samples could be processed, accounting for the lower number of CD20 cell hybridizations.
GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 ug cRNA for the CD4 samples and 10 ug or less (down to 7 ug) for the CD20 samples. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.


title: CD4 SLE 5


title: CD4 SLE 4


title: B CONT 11


title: CD4 RA 8

source_name: RA patient

tag: CD4 T cells sorted from total PBMC of patient with rheumatoid arthritis


title: CD4 SLE 2


title: CD4 SLE 1


title: Mjannaschii_ts_0.5h_500atm_rep3

description: Effect of lethal heat shock at 500 atm.

source_name: Methanocaldococcus jannaschii, 500 atm


title: CD4 RA 7


title: CD4 RA 3


title: B RA 5


title: CD4 RA 4


title: CD4 RA 2


title: B CONT 8


title: CD4 RA 6


title: CD4 SLE 8


title: 1257-2

description: Biopsy sample


title: B CONT 3


title: CD4 RA 1


title: CD4 SLE 6


title: CD4 CONT 7

tag: CD4 T cells sorted from total PBMC of healthy subject


title: CD4 CONT 9


title: CD4 CONT 5


title: CD4 CONT 4


title: CD4 CONT 2


title: HCaRG-8_HG-U133 Plus 2

status: Public on Oct 27 2006

city: Montreal

first: Johanne

last: Tremblay

state: QUE

country: Canada

institute: CHUM Research Center, Hotel-Dieu

description: HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) plasmid containing HCaRG. Stable transfectants, overexpressing HCaRG, were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

data_processing: Chip was normalized using all probe sets scaling option and target signal at 500 (GCOS1.2)

label: Streptavidin Phycoerythrin

source_name: HEK293 cells

tag: Kidney HEK293 cells


title: CD4 SLE 3


title: NEO-6_HG-U133 Plus 2

description: HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) as control plasmid. Stable transfectants were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).


title: CD4 RA 5


title: EdTx study_macrophages_PA-treated_6h_rep3

status: Public on Oct 24 2006

city: Galveston

first: Ashok

middle: K

last: Chopra

state: TX

address: 301 University Blvd.

department: Microbiology & Immunology

institute: University of Texas Medical Branch

description: RAW 264.7 macrophages were treated with protective antigen (2.5 µg/ml) for 6 hr - used as a negative control to detect transcriptional responses to the binding moiety alone.

data_processing: GCOS

label: Affymetrix

source_name: Protective antigen-treated macrophages

tag: RAW 264.7 macrophages


title: EdTx study_macrophages_untreated_rep3

description: RAW 264.7 macrophages were untreated - used as a negative control and to filter out random variations between cell cultures.

source_name: Untreated macrophages


title: EdTx study_macrophages_PA-treated_6h_rep1


title: EdTx study_macrophages_PA-treated_6h_rep2


title: CD4 CONT 1


title: CD4 CONT 10


title: CD4 CONT 8


title: HCaRG-9_HG-U133_Plus_2_Rep2

data_processing: Chip was normalized using all probe sets scaling option and target signal at 500.


title: EdTx study_macrophages_untreated_rep1


title: CD4 CONT 6


title: CD4 CONT 3


title: EdTx study_macrophages_LPS-treated_6h_rep3

description: RAW 264.7 macrophages were treated with LPS (1 ng/ml) for 6 hr - used as a control for low levels of LPS contamination of purified Edema toxin.

source_name: LPS-treated macrophages


title: EdTx study_macrophages_untreated_rep2


title: NEO-1_HG-U133_Plus_2_Rep2


title: EdTx study_macrophages_LPS-treated_6h_rep1


title: EdTx study_macrophages_PA-treated_3h_rep3

description: RAW 264.7 macrophages were treated with protective antigen (2.5 µg/ml) for 3 hr - used as a negative control to detect transcriptional responses to the binding moiety alone.


title: EdTx study_macrophages_LPS-treated_3h_rep1

description: RAW 264.7 macrophages were treated with LPS (1 ng/ml) for 3 hr - used as a control for low levels of LPS contamination of purified Edema toxin.


title: EdTx study_macrophages_PA-treated_3h_rep1


title: EdTx study_macrophages_PA-treated_3h_rep2


title: EdTx study_macrophages_ET-treated_6h_rep3

description: RAW 264.7 macrophages were treated with Edema toxin (2.5 µg/ml of protective antigen and 0.625 µg/ml of Edema factor) for 6 hr.

source_name: Edema toxin-treated macrophages


title: EdTx study_macrophages_ET-treated_3h_rep2

description: RAW 264.7 macrophages were treated with Edema toxin (2.5 µg/ml of protective antigen and 0.625 µg/ml of Edema factor) for 3 hr.


title: Synechocystis cells grown under UV-irradiation for 3 hrs. Replicate 1

status: Public on Sep 04 2006

city: Blacksburg

first: Malcolm

last: Potts

state: VA

address: W. Campus Drive

department: Biochemistry

institute: Virginia Tech

description: Image intensity data were extracted with GenePix Pro analysis software.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a  GenePix 4000B Scanner at photomultiplier tube settings that afforded the best overall balance between Cy3 and Cy5 channels.

data_processing: After background correction and removal of flagged values, expression ratios were normalized using LOWESS method (from the Genespring software) to obtain values given in the data table.

organism: Synechocystis sp. PCC 6803

label_protocol: cDNA from the RNAs of control and irradiated cells was ligated to Cy5 and Cy3 monoreactive fluors, respectively, with T4 DNA ligase at 22°C, for 2h.  The Cy5 and Cy3 labeled  cDNAs were combined, concentrated with a Millipore Microcon  microconcentrator, and resuspended in a final 50-μl volume of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, and 10 μg human Cot1 DNA (to limit non-specific hybridization) for hybridization to the microarray.

growth_protocol: At the midpoint of the exponential phase of growth (~ 10^6 to 10^7 cells ml-1), 25-ml aliquots of the cell suspension were subjected to UV-irradiation (in 50-ml flasks), with a continuous photon flux density in the visible range of 330 μmol photons m-2 s-1. UV-A and UV-B maxima were 3.8 x 10^6 and 0.8 x 10^6 mW m-2, respectively.  Following growth at set time points, cells were disrupted for rapid recovery of RNA

extract_protocol: Cells were disrupted with glass beads and RNA was extracted with a buffer of acidified phenol (65°C), sodium acetate pH 5.1, EDTA and sodium dodecyl sulfate), followed by ethanol precipitation.  The RNA (10 μg) was annealed with 20 μg Random RT primer and reverse transcription into cDNA was achieved with Superscript II reverse transcriptase enzyme for 2h, at 42°C. The assay contained dGTP, dCTP, dATP and dTTP, each a final concentration of 0.5 mM.   After hydrolysis of RNA with 0.1M NaOH and 10 mM EDTA, then neutralization, cDNAs were purified using a Quiagen QIAquick PCR purification kit as modified in the Genisphere 3DNA Array 350RP protocol.

treatment_protocol: An axenic culture was grown at 25°C in BG-11 medium, on a rotary shaker at 70 rpm, at a photon flux density of 200 μmol photons m-2 s-1.

tag: As a control, RNA was obtained from Synechocystis cells grown without UV-irradiation

source_name: Synechocystis cells grown for 3 hrs under UV-irradiation

growth_protocol: At the midpoint of the exponential phase of growth (~ 10^6 to 10^7 cells ml-1), 25-ml aliquots of the cell suspension were subjected to UV-irradiation (in 50-ml flasks) with a continuous photon flux density in the visible range of 330 μmol photons m-2 s-1. UV-A and UV-B maxima were 3.8 x 10^6 and 0.8 x 10^6 mW m-2, respectively.  Following growth at set time points, cells were disrupted for rapid recovery of RNA.

treatment_protocol: An axenic culture was grown at 25°C in BG-11 medium, on a rotary shaker at 70 rpm, at a photon flux density of 200 μmol m-2 s-1.


title: EdTx study_macrophages_ET-treated_3h_rep1

tag: RAW 264.7 cells


title: Synechocystis cells grown during evaporation of 98% of H2O from culture. Replicate 1

label_protocol: cDNA from the RNAs of control and irradiated cells was ligated to Cy5 and Cy3 monoreactive fluors, respectively, with T4 DNA ligase at 22°C, for 2h.  The Cy5 and Cy3 labeled  cDNAs were combined, concentrated with a Millipore Microcon  microconcentrator, and resuspended in a final 50-ul volume of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, and 10 μg human Cot1 DNA (to limit non-specific hybridization) for hybridization to the microarray.

growth_protocol: At the midpoint of the exponential phase of growth (~10^6 to 10^7 cells ml-1), 25-ml aliquots of cell suspension were transferred to glass Petri dishes covered with lids.  After pre-adaptation, for 15h, the lids were removed and the culture medium was evaporated at a linear rate of 1.7 ml hr-1 until  complete dryness. At set time points during the dehydration, cells were disrupted for rapid recovery of RNA.

treatment_protocol: An axenic culture was grown in an Erlenmeyer flask at 25°C in BG-11 medium, on a rotary shaker at 70 rpm, at a photon flux density of 200 μmol photons m-2 s-1.

tag: As a control, RNA was obtained from Synechocystis cells grown without evaporation of H2O from medium


title: EdTx study_macrophages_ET-treated_6h_rep2


title: EdTx study_macrophages_LPS-treated_3h_rep2


title: B CONT 12


title: Synechocystis cells grown under UV-irradiation for 36 hrs. Replicate 3

hyb_protocol: The Cy5 and Cy3 labeled  cDNAs were combined, concentrated with a Millipore Microcon  microconcentrator, and resuspended in a final 50-μl volume of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, and 10 μg human Cot1 DNA (to limit non-specific hybridization) for hybridization to the microarray.

source_name: Synechocystis cells grown without UV-irradiation

source_name: Synechocystis cells grown for 36 hrs under UV-irradiation

label_protocol: cDNA from the RNAs of control and irradiated cells was ligated to Cy5 and Cy3 monoreactive fluors, respectively, with T4 DNA ligase at 22°C, for 2h.


title: EdTx study_macrophages_ET-treated_6h_rep1


title: Synechocystis cells grown during evaporation of 48% of H2O from culture. Replicate 2

source_name: Synechocystis cells grown without evaporation of H2O

growth_protocol: At the midpoint of the exponential phase of growth (~10^6 to 10^7 cells ml-1), 25-ml aliquots of cell suspension were transferred to glass Petri dishes covered with lids.  After pre-adaptation, for 15h, the lids were removed and the culture medium was evaporated at a linear rate of 1.7 ml hr-1 until  complete dryness. At set time points during the dehydration, cells were disrupted for rapid recovery of RNA


title: EdTx study_macrophages_LPS-treated_6h_rep2


title: Synechocystis cells grown under UV-irradiation for 36 hrs. Replicate 2

tag: Synechocystis cells grown for 36 hrs under UV-irradiation


title: Synechocystis cells grown under UV-irradiation for 36 hrs. Replicate 1


title: EdTx study_macrophages_ET-treated_3h_rep3


title: Synechocystis cells grown during evaporation of 98% of H2O from culture. Replicate 2


title: HUVEC/NmenMC58_frpC/frpA_4h_rep3_1117

status: Public on Sep 01 2006

city: Prague 4

first: Marek

last: Basler

address: Videnska 1083

department: Cell and Molecular Microbiology Division

country: Czech Republic

institute: Institute of Microbiology, Czech Academy of Sciences

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta frpC/frpA, 4 hours infection

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Agilent GeneArray scanner.

data_processing: The data were analyzed with RMA and MAS 5.0 algorithms using Biocondutor 1.7 and default analysis settings.

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)

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

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta frpC/frpA (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified on RNeasy minicolumns (Qiagen) and by NaOAc/ethanol precipitation.

treatment_protocol: Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta frpC/frpA were washed and collected into Trizol by cell-scraper

tag: Tissue

value: endothelial cells


title: HUVEC/NmenMC58_pilD_6h_rep1_1103

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 6 hours infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

treatment_protocol: Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta pilD were washed and collected into Trizol by cell-scraper


title: Synechocystis cells grown under UV-irradiation for 3 hrs. Replicate 3

tag: Synechocystis cells grown for 3 hrs under UV-irradiation


title: Synechocystis cells grown under UV-irradiation for 3 hrs. Replicate 2


title: HUVEC/NmenMC58_frpC/frpA_4h_rep1_1108


title: HUVEC/NmenMC58_frpC/frpA_4h_rep2_1112


title: HUVEC/NmenMC58_pilD_6h_rep2_1107


title: HUVEC/NmenMC58_pilD_4h_rep2_1107

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 4 hours infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours


title: HUVEC/NmenMC58_pilD_1h_rep1_1103

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 1 hour infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour


title: HUVEC/NmenMC58_WT_6h_rep2_1108

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 6 hours infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

treatment_protocol: Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 WT were washed and collected into Trizol by cell-scraper


title: EdTx study_macrophages_LPS-treated_3h_rep3


title: HUVEC/NmenMC58_WT_6h_rep1_1102


title: HUVEC/NmenMC58_WT_4h_rep3_1117

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 4 hours infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours


title: HUVEC/NmenMC58_WT_1h_rep1_1102

description: Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 1 hour infection

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour


title: HUVEC_6h_rep2_1107

description: Gene expression data from HUVEC, 6 hours incubation

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

treatment_protocol: Monolayers of HUVECs in 9 cm Petri dishes were washed and collected into Trizol by cell-scraper


title: HUVEC/NmenMC58_pilD_4h_rep1_1103


title: Cardian muscle Trained diabetic 1 week DT1

city: Jyväskylä

first: Mika

last: Silvennoinen

address: Rautpohjankatu 8, Viveca

country: Finland

institute: LIKES - Research Center

description: Effects of diabetes, physical training, and their combination on the gene expression of cardiac muscle

data_processing: The array images were analyzed with Microarray Suite 5.0 (Affymetrix) software. All chips were scaled (global scaling) to target intensity of 50 to minimize differences between chips caused by physical differences in chips, hybridization efficiencies and manual laboratory work. The data was subjected to robust normalization that reduces the errors, which are caused by binding capacity and linearity differences between probe sets.

source_name: Cardiac muscle

extract_protocol: Total RNA was extracted from the cardiac muscle with Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified with RNeasy columns (Qiagen, Valencia, CA) according to the manufacturers' protocols. Concentration and purity of RNA was determined by measuring absorbances at wavelengths 260 and 280 nm. Integrity of the RNA was checked with agarose gel electrophoresis. RNA samples were pooled within each group for microarray analyses. Concentration, purity and integrity of pooled RNA samples were checked as described above.

tag: Trained diabetic mice, time point 1 week


title: Cardian muscle Trained diabetic 5 week DT5

tag: Trained diabetic mice, time point 5 week


title: HUVEC/NmenMC58_WT_4h_rep2_1108


title: Cardian muscle Trained 1 week T1

tag: Trained mice, time point 1 week


title: HUVEC/NmenMC58_pilD_1h_rep2_1107


title: HUVEC_4h_rep2_1107

description: Gene expression data from HUVEC, 4 hours incubation

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours


title: HUVEC_6h_rep1_1103


title: Cardian muscle Diabetic 3 week D3

tag: Diabetic mice, time point 3 week


title: Cardian muscle Trained 5 week T5

tag: Trained mice, time point 5 week


title: Cardian muscle Diabetic 5 week D5

tag: Diabetic mice, time point 5 week


title: Cardian muscle Trained diabetic 3 week DT3

tag: Trained diabetic mice, time point 3 week


title: HUVEC/NmenMC58_WT_4h_rep1_1102


title: Cardian muscle Trained 3 week T3

tag: Trained mice, time point 3 week


title: Synechocystis cells grown during evaporation of 48% of H2O from culture. Replicate 1


title: HUVEC/NmenMC58_pilD_4h_rep3_1114


title: M6 #3 Cy5/Cy3

status: Public on Aug 31 2006

city: College Park

first: Kevin

middle: S

last: McIver

state: MD

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

description: details located in Ribardo et al 2006

hyb_protocol: 50C overnight

scan_protocol: genepix 6.1

data_processing: ratio-based Pearson centered normalization  using Acuity 4.0

organism: Streptococcus pyogenes

source_name: M6 (JRS4)

label_protocol: Amersham CyScribe Post labeling kit

growth_protocol: 37C in closed cap tubes to late exponential phase

extract_protocol: CsCl isolation with ultracentrifugation

tag: M6 (JRS4-Mga+) biological replicate #3

label_protocol: Amersham CyScribe post labeling kit

tag: M6 (JRS519-Mga-) biological replicate #3


title: HUVEC_1h_rep1_1103b

description: Gene expression data from HUVEC, 1 hour incubation

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

growth_protocol: Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour


title: HUVEC/NmenMC58_WT_1h_rep2_1108


title: Cardian muscle Healthy 3 week C3

tag: Healthy control mice, time point 3 week


title: HUVEC_1h_rep2_1107


title: M6 #2 Cy5/Cy3

description: details located in Ribardo et al 2006

tag: M6 (JRS4-Mga+) biological replicate #2

tag: M6 (JRS519-Mga-) biological replicate #2


title: M6 #2 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M6 (JRS4-Mga+) biological replicate #2 (dye swap)

tag: M6 (JRS519-Mga-) biological replicate #2 (dye swap)


title: Cardian muscle Diabetic 1 week D1

tag: Diabetic mice, time point 1 week


title: Cardian muscle Healthy 5 week C5

tag: Healthy control mice, time point 5 week


title: Cardian muscle Healthy 1 week C1

tag: Healthy control mice, time point 1 week


title: M6 #3 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M6 (JRS4-Mga+) biological replicate #3 (dye swap)

tag: M6 (JRS519-Mga-) biological replicate #3 (dye swap)


title: M6 #1 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M6 (JRS4-Mga+) Biological replicate #1 (dye swap)

tag: M6 (JRS519-Mga-) biological replicate #1 (dye swap)


title: M4 #2 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M4 (Mga+) Biolgoical replicate #2 (dye swap)

tag: M4.586 (Mga-) biological replicate #2 (dye swap)


title: M4 #3 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M4 (Mga+) biological replicate #3 (dye swap)

tag: M4.586 (Mga-) biological replicate #3 (dye swap)


title: M4 #1 Cy5/Cy3

description: details located in Ribardo et al 2006

tag: M4 (Mga+) biological replicate #1

tag: M4.586 (Mga-) biological replicate #1


title: M4 #3 Cy5/Cy3

description: details located in Ribardo et al 2006

tag: M4 (Mga+) biological replicate #3

tag: M4.586 (Mga-) biological replicate #3


title: M6 #1 Cy5/Cy3

description: details located in Ribardo et al 2006

tag: M6 (JRS4-Mga+) biological replicate #1

tag: M6 (JRS519-Mga-) biological replicate #1


title: M4 #1 Cy3/Cy5

description: details located in Ribardo et al 2006

tag: M4 (Mga+) Biological replicate #1 (dye swap)

tag: M4.586 (Mga-) Biological replicate #1 (dye swap)


title: M4 #2 Cy5/Cy3

description: details located in Ribardo et al 2006

tag: M4 (Mga+) biological replicate #2

tag: M4.586 (Mga-) biological replicate #2


title: M1 #2 Cy5/Cy3

description: Details located in Ribardo et al, 2006

data_processing: ratio-based Pearson Centered normalization using Acuity 4.0

tag: M1T1 SF370 (Mga+) Biological Replicate #2

source_name: M1 KSM165L

tag: M1T1 KSM165L (Mga-) Biological Replicate #2


title: M1 #2 Cy3/Cy5

description: Details located in Ribardo et al, 2006

tag: M1T1 SF370 (Mga+) Biological replicate #2 (Dye Swap)

tag: M1T1 KSM165L (Mga-) Biological Replicate #2 (Dye swap)


title: M1 #1 Cy5/Cy3

description: Details located in Ribardo et al, 2006

tag: M1T1 SF370 (Mga+) Biological Replicate #1

tag: M1T1 KSM165L (Mga-) Biological Replicate #1


title: M1 #3 Cy5/Cy3

description: Details located in Ribardo et al, 2006

tag: M1T1 SF370 (Mga+) Biological replicate #3

tag: M1T1 KSM165L (Mga-) Biological Replicate #3


title: MCF-7 Oncostatin M 60 mins array 1

status: Public on Aug 01 2006

city: Birmingham

first: Nick

last: Underhill-Day

address: Edgbaston

department: Biosciences

country: United Kingdom

institute: University of Birmingham

description: MCF-7 Oncostatin M 60 minutes array1: control cy5, Oncostatin M cy3

hyb_protocol: Equal amounts of Cy3 and Cy5 labelled probe from control and stimulated samples were mixed together in the presence of human Cot-1 DNA (GibcoBRL) and concentrated using YM30 filter (Millipore). Pre-warmed (37degreesC) hybridisation buffer (Invitrogen), formamide (BDH) and pd-dA40-60 (Amersham Pharmacia Biotech) were mixed with the probe. This was heated at 92degreesC for 3 minutes and cooled to room temperature for 10 minutes before application to the array (covered by a Lifterslip (Erie Scientific Company)). Hybridisation was performed overnight at 42degreesC in a hybridisation chamber (Corning). The array was washed five times in pre-warmed (42degreesC) 2X SCC buffer (Sigma) containing 0.2% SDS and once each in 1X SCC and 0.5X SCC buffer respectively. The array was dried quickly with nitrogen gas.

scan_protocol: Fluorescent array images were obtained with an Axon slide scanner 4000B and GenePix Pro 3 software (Axon Instruments Inc.) at a resolution of 10μm at 100% laser power and photo-multiplier tube voltage of between 550 - 650.

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was transformed into log base 2 expression ratios and normalised using “Lowess” per spot & per chip intensity-dependent normalisation.

source_name: MCF-7 breast tumour cells

label_protocol: Equal amounts of RNA used as starting material for cDNA synthesis. This was performed overnight at 42°C using Superscript II Rnase H-reverse transcriptase (Invitrogen). Random nonamers (3mg/ml), Oligo dTs (1.0μg/μl) and Cy3-dCTP or Cy5-dCTP were obtained from Amersham Biosciences. The RNA template was removed by alkaline hydrolysis and unincorporated nucleotides removed with Qiaquick PCR purification spin columns as per manufacturer’s instructions (Qiagen).

growth_protocol: Cells cultured in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% foetal calf serum, 1mM glutamine and 1mM streptomycin/1mM penicillin prior to RNA extraction.

extract_protocol: Total RNA isolated with Trizol extraction according to manufacturer’s instructions (GibcoBRL).

treatment_protocol: Unstimulated

tag: Cells originally isolated from a pleural effusion obtained from a patient with an infiltrating ductal carcinoma of the breast

treatment_protocol: stimulated with oncostatin M (100ng/ml) 60 mins.


title: M1 #1 Cy3/Cy5

description: Details located in Ribardo et al, 2006

tag: M1T1 KSM165L (Mga-)


title: MDA-MB-231 Oncostatin M 60 mins array 1

description: MDA-MB-231 Oncostatin M 60 minutes array1: control cy5, Oncostatin M cy3

source_name: MDA-MB-231 breast tumour cells

treatment_protocol: unstimulated.


title: T47D Leukaemia Inhibitory Factor 60 mins array 1

description: T47D LIF 60 minutes array 1: control cy5, LIF cy3

source_name: T47D breast tumour cells

treatment_protocol: unstimulated

treatment_protocol: stimulated with LIF (100ng/ml) 60 minutes.


title: MCF-7 Oncostatin M 60 mins array 2

description: MCF-7 Oncostatin M 60 minutes array2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M + LIF-05 60 mins array 1

description: T47D Oncostatin M + LIF-05 60 minutes array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 60 minutes in the presence of LIF-05 (500ng/ml).


title: MDA-MB-231 Oncostatin M 60 mins array 2

description: MDA-MB-231 Oncostatin M 60 minutes array2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M 180 mins array 1

description: T47D Oncostatin M 180 minutes array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 180 mins.


title: T47D Oncostatin M + LIF-05 30 mins array 1

description: T47D Oncostatin M + LIF-05 30 minutes array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 30 minutes in the presence of LIF-05 (500ng/ml).


title: T47D Interleukin-6 60 mins array 2

description: T47D interleukin-6 60 minutes array 2: control cy3, interleukin-6 cy5

treatment_protocol: stimulated with interleukin-6 (100ng/ml) 60 minutes.


title: T47D Oncostatin M + LIF-05 60 mins array 2

description: T47D Oncostatin M + LIF-05 60 minutes array 2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M 3 days array 1

description: T47D Oncostatin M 3 days array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 3 days.


title: T47D LIF-05 60 mins array 1

description: T47D LIF-05 60 minutes array1: control cy5, LIF-05 cy3

treatment_protocol: stimulated with LIF-05 (500ng/ml) 60 minutes


title: T47D Oncostatin M 6 days array 1

description: T47D Oncostatin M 6 days array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 6 days.


title: T47D Oncostatin M + LIF-05 30 mins array 2

description: T47D Oncostatin M + LIF-05 30 minutes array 2: control cy3, Oncostatin M cy5


title: T47D Interleukin-6 30 mins array 2

description: T47D interleukin-6 30 minutes array 2: control cy3, interleukin-6 cy5

treatment_protocol: stimulated with interleukin-6 (100ng/ml) 30 minutes.


title: T47D Oncostatin M 180 mins array 2

description: T47D Oncostatin M 180 minutes array 2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M 6 days array 2

description: T47D Oncostatin M 6 days array 2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M 3 days array 2

description: T47D Oncostatin M 3 days array 2: control cy3, Oncostatin M cy5


title: T47D LIF-05 60 mins array 2

description: T47D LIF-05 60 minutes array2: control cy3, LIF-05 cy5


title: T47D Oncostatin M 1 day array 1

description: T47D Oncostatin M 1 day array 1: control cy5, Oncostatin M cy3

treatment_protocol: stimulated with oncostatin M (100ng/ml) 1 day.


title: T47D Oncostatin M 1 day array 2

description: T47D Oncostatin M 1 day array 2: control cy3, Oncostatin M cy5


title: T47D Oncostatin M 60 mins array 2

description: T47D Oncostatin M 60 minutes array 2: control cy3, Oncostatin M cy5


title: T47D Leukaemia Inhibitory Factor 60 mins array 2

description: T47D LIF 60 minutes array 2: control cy3, LIF cy5


title: T47D Interleukin-6 30 mins array 1

description: T47D interleukin-6 30 minutes array 1: control cy5, interleukin-6 cy3


title: T47D Oncostatin M 60 mins array 1

description: T47D Oncostatin M 60 minutes array 1: control cy5, Oncostatin M cy3


title: T47D Oncostatin M 30 minutes array 1

description:
T47D Oncostatin M 30 minutes array 1:
Control cy5
Oncostatin M cy3

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was transformed into log base 2 expression ratios and normalised using “Lowess” intensity-dependent normalisation.

treatment_protocol: Stimulated with oncostatin M (100ng/ml) 30 mins


title: Ad GFP p53 k.o.

status: Public on Jul 01 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Ad GFP p53 k.o.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Ad GFP p53 k.o.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNAzol B, WAK-Chemie Medical GmbH

tag: genetic modification:

tag: tissue

value: hepatocytes


title: T47D Oncostatin M 30 minutes array 2

description:
T47D Oncostatin M 30 minutes array 2:
Control cy3
Oncostatin M cy5


title: Ad TRF2DBDM p53 k.o.

description: Ad TRF2DBDM p53 k.o.

source_name: Ad TRF2DBDM p53 k.o.


title: Md02h035

status: Public on Jun 01 2006

city: Indianapolis

first: Matthew

last: Grow

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

description: Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD and cultured for 12 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human hepatoma cell line (HepG2)

tag: Human hepatoma cell line (HepG2), grown for 6 or 12 hours, and then total RNA harvested with Trizol and Qiagen Rneasy kit.


title: Md02h031

description: Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ and cultured for 12 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

treatment_protocol: Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ (Beta-galactosidase control)


title: HAL703T1 HCC (mTERC-)

description: HAL703T1 HCC (mTERC-)

source_name: HAL703T1 HCC (mTERC-)


title: HAL691T1 HCC (mTERC-)

description: HAL691T1 HCC (mTERC-)

source_name: HAL691T1 HCC (mTERC-)


title: Md02h032


title: Md02h030


title: HAL1181T3 HCC (mTERC-)

description: HAL1181T3 HCC (mTERC-)

source_name: HAL1181T3 HCC (mTERC-)


title: HAL975T1 HCC (mTERC+)

description: HAL975T1 HCC (mTERC+)

source_name: HAL975T1 HCC (mTERC+)


title: Md02h021

description: Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ and cultured for 6 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.


title: Md02h029


title: Md02h028

description: Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD and cultured for 6 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.


title: Md02h026

treatment_protocol: Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD


title: Md02h033


title: Md02h036


title: Md02h034


title: Md02h023


title: HAL1093T7 HCC (mTERC+)

description: HAL1093T7 HCC (mTERC+)

source_name: HAL1093T7 HCC (mTERC+)


title: HAL1061T1 HCC (mTERC+)

description: HAL1061T1 HCC (mTERC+)

source_name: HAL1061T1 HCC (mTERC+)


title: HUVEC_4h_rep1_1103

description: Gene expression data from HUVEC, 4 hours incubation

treatment_protocol: Monolayers of HUVECs in 9 cm Petri dishes were washed and collected into Trizol by cell-scraper

tag: Tissue


title: TLR7 gene duplication accelerates autoimmunity and promotes nucleolar-specific B cells (sample3)

city: Rockville

first: Prapaporn

last: Pisitkun

address: 12441 Parklawn Drive, TW2, Room 217

department: NIAID

institute: NIH

description:
Criteria for data extraction.
Signal calculation: Median Intensity minus Median Background
Any Features designated Control was excluded.
Normalization method: 50th Percentile (Median) using all spot filtered Genes
Spot Filter Options:
Include Spots not flagged BAD or Not Found
 AND Target diameter >= 50 um AND Target diameter <= 300 um
 AND Both Chan A and Chan B Signal/Background Ratios >= 2.000
 AND Both Chan A and Chan B Percentage Target Pixels 1 SD above Background >= 25%
Override other Chan A & B criteria and Include if Chan A Signal >= 5000 OR Chan B Signal >= 5000.

data_processing: Flagged bad or not found spot by GenePix and analyzed by mAdb using the criteria as in description.

source_name: Follicular B cells from spleen, fresh Isolation

tag: C57BL/6, male, 2 months, follicular B cells, fresh Isolation

tag: C57BL/6.Yaa, male, 2 months, follicular B cells, fresh Isolation


title: Md02h027


title: Md02h022


title: Md02h025


title: Md02h024


title: ESC Tcl1_shRNAi d6 post transduction MOE430B

status: Public on May 31 2006

city: Princeton

first: Ihor

last: Lemischka

state: NJ

address: Washington Rd

institute: Princeton University

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d6 post transduction.

hyb_protocol: 15 micrograms of biotin-labeled cRNA was fragmented for 35min. at 94C in fragmentation buffer (Affymetrix; Santa Clara, CA), and hybridized to Affymetrix MOE 430 A and B oligonucleotide microarrays.

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

source_name: ES cells (CCE cell line) d6 post Tcl1_shRNAi transduction.

label_protocol: Biotinylated cRNA probes were synthesized using the BioArray High-Yield Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: Cells were maintained in the presence of LIF 1000 unit/ml.

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

treatment_protocol: 48 hours after transduction cells were re-plated at the density 0.3x10^6 cells per 10 cm dish. Simultaneously, GFP+ cells were FACS purified and used as day 0 time point. Re-plated cells were maintained in the presence of LIF. GFP+ cells from each culture were FACS purified every day for 7 consecutive days to obtain 8 day time course (d0-d7).

tag: Mouse embrionic stem cells

tag: Gender

tag: Strain


title: TLR7 gene duplication accelerates autoimmunity and promotes nucleolar-specific B cells (sample4)


title: TLR7 gene duplication accelerates autoimmunity and promotes nucleolar-specific B cells


title: d3 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d3 days.

source_name: ES cells (CCE cell line) d3 after the addition of retinoic acid (RA).

growth_protocol: Cells were maintained without LIF in the presence of retinoic acid (RA) 5 micro molars.

tag: Mouse embrionic stem cells passage 25-30.


title: d6 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d6 days.

source_name: ES cells (CCE cell line) d6 after the addition of retinoic acid (RA).

treatment_protocol: Cells were maintained without LIF in the presence of retinoic acid (RA) 5 micro molars.


title: ESC Tcl1_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Tcl1_shRNAi transduction.


title: d5 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d5 days.

source_name: ES cells (CCE cell line) d5 after the addition of retinoic acid (RA).


title: d4 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d4 days.

source_name: ES cells (CCE cell line) d4 after the addition of retinoic acid (RA).


title: ESC Tcl1_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Tcl1_shRNAi transduction.


title: TLR7 gene duplication accelerates autoimmunity and promotes nucleolar-specific B cells (sample2)

tag: C57BL/6.Yaa, male, 2, months, follicular B cells, fresh Isolation


title: ESC Tbx3_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Tbx3_shRNAi transduction.


title: ESC Tcl1_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Tcl1_shRNAi transduction.


title: ESC Tcl1_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Tcl1_shRNAi transduction.


title: d0 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d0 days.

source_name: ES cells (CCE cell line) d0 after the addition of retinoic acid (RA).


title: ESC Tbx3_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Tbx3_shRNAi transduction.


title: ESC Tcl1_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Tcl1_shRNAi transduction.


title: ESC Tbx3_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Tbx3_shRNAi transduction.


title: d1 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d1 days.

source_name: ES cells (CCE cell line) d1 after the addition of retinoic acid (RA).


title: ESC Tcl1_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Tcl1_shRNAi transduction.


title: ESC Tbx3_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Tbx3_shRNAi transduction.


title: ESC Sox2_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Sox2_shRNAi transduction.


title: d2 RA treatment MOE430B

description: Gene expression data from ES cells treated with RA for d2 days.

source_name: ES cells (CCE cell line) d2 after the addition of retinoic acid (RA).


title: ESC Sox2_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Sox2_shRNAi transduction.


title: ESC Tbx3_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Tbx3_shRNAi transduction.


title: ESC Oct4_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Oct4_shRNAi transduction.


title: ESC Sox2_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Sox2_shRNAi transduction.


title: T47D Interleukin-6 60 mins array 1

description: T47D interleukin-6 60 minutes array 1: control cy5, interleukin-6 cy3

source_name: T47D breast tumour cells

treatment_protocol: unstimulated


title: ESC Oct4_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Oct4_shRNAi transduction.


title: M1 #3 Cy3/Cy5

description: Details located in Ribardo et al, 2006

tag: M1T1 SF370 (Mga+) Biological replicate #3 (dye swap)

source_name: M1 KSm165L

tag: M1T1 KSM165L (Mga-) Biological replicate #3 (dye swap)


title: ESC Oct4_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Oct4_shRNAi transduction.


title: ESC Nanog_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Nanog_shRNAi transduction.


title: ESC Mm343880_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Mm343880_shRNAi transduction.


title: ESC Nanog_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Nanog_shRNAi transduction.


title: ESC Mm343880_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Mm343880_shRNAi transduction.


title: ESC Oct4_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Oct4 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Oct4_shRNAi transduction.


title: ESC Mm343880_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Mm343880_shRNAi transduction.


title: ESC Mm343880_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Mm343880_shRNAi transduction.


title: ESC Mm343880_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Mm343880_shRNAi transduction.


title: ESC Mm343880_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Mm343880_shRNAi transduction.


title: ESC Esrrb_shRNAi d7 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Esrrb_shRNAi transduction.


title: ESC Nanog_shRNAi d4 post transduction MOE430B

description: Gene expression data from ES cells transduced with Nanog shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Nanog_shRNAi transduction.


title: ESC Esrrb_shRNAi d6 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d2 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Esrrb_shRNAi transduction.


title: ESC Mm343880_shRNAi d1 post transduction MOE430B

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Mm343880_shRNAi transduction.


title: ESC Esrrb_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d3 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Esrrb_shRNAi transduction.


title: d4 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d4.

source_name: ES cells (CCE cell line) d4 empty vector


title: ESC Esrrb_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Esrrb shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Esrrb_shRNAi transduction.


title: ESC Tcl1_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Tcl1_shRNAi transduction.


title: d7 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d7.

source_name: ES cells (CCE cell line) d7 empty vector


title: d6 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d6.

source_name: ES cells (CCE cell line) d6 empty vector


title: d5 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d5 days.

source_name: ES cells (CCE cell line) d5 after the addition of retinoic acid (RA).


title: d4 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d4 days.

source_name: ES cells (CCE cell line) d4 after the addition of retinoic acid (RA).


title: d6 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d6 days.

source_name: ES cells (CCE cell line) d6 after the addition of retinoic acid (RA).


title: d0 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d0.

source_name: ES cells (CCE cell line) d0 empty vector


title: d0 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d0 days.

source_name: ES cells (CCE cell line) d0 after the addition of retinoic acid (RA).


title: d3 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d3 days.

source_name: ES cells (CCE cell line) d3 after the addition of retinoic acid (RA).


title: d3 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d3.

source_name: ES cells (CCE cell line) d3 empty vector


title: d1 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d1.

source_name: ES cells (CCE cell line) d1 empty vector


title: ESC Tcl1_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Tcl1_shRNAi transduction.


title: ESC Tcl1_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Tcl1_shRNAi transduction.


title: ESC Tcl1_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Tcl1_shRNAi transduction.


title: ESC Tcl1_shRNAi d5 post transduction MOE430A


title: ESC Tcl1_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Tcl1_shRNAi transduction.


title: ESC Tcl1_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Tcl1_shRNAi transduction.


title: d2 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d2 days.

source_name: ES cells (CCE cell line) d2 after the addition of retinoic acid (RA).


title: d2 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d2.

source_name: ES cells (CCE cell line) d2 empty vector


title: d5 empty vector MOE430B

description: Gene expression data from ES cells transduced with empty vector at d5.

source_name: ES cells (CCE cell line) d5 empty vector


title: ESC Tcl1_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Tcl1_shRNAi transduction.


title: ESC Tbx3_shRNAi d5 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Tbx3_shRNAi transduction.


title: d1 RA treatment MOE430A

description: Gene expression data from ES cells treated with RA for d1 days.

source_name: ES cells (CCE cell line) d1 after the addition of retinoic acid (RA).


title: ESC Tcl1_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tcl1 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Tcl1_shRNAi transduction.


title: ESC Tbx3_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Tbx3_shRNAi transduction.


title: ESC Tbx3_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Tbx3_shRNAi transduction.


title: ESC Oct4_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Oct4_shRNAi transduction.


title: ESC Sox2_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d5 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Sox2_shRNAi transduction.


title: ESC Oct4_shRNAi d5 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Oct4_shRNAi transduction.


title: ESC Sox2_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Sox2_shRNAi transduction.


title: ESC Sox2_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Sox2_shRNAi transduction.


title: ESC Oct4_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Oct4_shRNAi transduction.


title: ESC Tbx3_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Tbx3_shRNAi transduction.


title: ESC Oct4_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Oct4_shRNAi transduction.


title: ESC Sox2_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Sox2 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Sox2_shRNAi transduction.


title: ESC Oct4_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Oct4_shRNAi transduction.


title: ESC Oct4_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Oct4 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Oct4_shRNAi transduction.


title: ESC Nanog_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Nanog_shRNAi transduction.


title: ESC Mm343880_shRNAi d5 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Mm343880_shRNAi transduction.


title: ESC Sox2_shRNAi d5 post transduction MOE430B

description: Gene expression data from ES cells transduced with Sox2 shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Sox2_shRNAi transduction.


title: ESC Mm343880_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Mm343880_shRNAi transduction.


title: ESC Nanog_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Nanog_shRNAi transduction.


title: ESC Nanog_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Nanog_shRNAi transduction.


title: ESC Mm343880_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Mm343880_shRNAi transduction.


title: ESC Tbx3_shRNAi d0 post transduction MOE430B

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Tbx3_shRNAi transduction.


title: ESC Nanog_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Nanog_shRNAi transduction.


title: ESC Mm343880_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Mm343880_shRNAi transduction.


title: ESC Mm343880_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Mm343880_shRNAi transduction.


title: ESC Mm343880_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Mm343880_shRNAi transduction.


title: ESC Esrrb_shRNAi d7 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d7 post transduction.

source_name: ES cells (CCE cell line) d7 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d3 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d3 post transduction.

source_name: ES cells (CCE cell line) d3 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d0 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d0 post transduction.

source_name: ES cells (CCE cell line) d0 post Esrrb_shRNAi transduction.


title: d7 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d7.

source_name: ES cells (CCE cell line) d7 empty vector


title: ESC Esrrb_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Esrrb_shRNAi transduction.


title: d6 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d6.

source_name: ES cells (CCE cell line) d6 empty vector


title: ESC Esrrb_shRNAi d5 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d5 post transduction.

source_name: ES cells (CCE cell line) d5 post Esrrb_shRNAi transduction.


title: ESC Esrrb_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Esrrb_shRNAi transduction.


title: d5 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d5.

source_name: ES cells (CCE cell line) d5 empty vector


title: d3 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d3.

source_name: ES cells (CCE cell line) d3 empty vector


title: ESC Esrrb_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Esrrb_shRNAi transduction.


title: d4 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d4.

source_name: ES cells (CCE cell line) d4 empty vector


title: d1 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d1.

source_name: ES cells (CCE cell line) d1 empty vector


title: ESC Esrrb_shRNAi d6 post transduction MOE430A

description: Gene expression data from ES cells transduced with Esrrb shRNAi d6 post transduction.

source_name: ES cells (CCE cell line) d6 post Esrrb_shRNAi transduction.


title: S. Typhimurium relAspoT aerated LB high salt rep 4

status: Public on May 30 2006

type: mixed

city: Norwich

first: Arthur

last: Thompson

state: Norfolk

address: Colney Lane

department: Food Safety Science

institute: Institute of Food Research

description: Intensity ratios of RNA (channel 1) divided by DNA (channel 2) signals minus respective local background signals. Total array is 16 blocks arranged in 4X4 configuration

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centring process.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: F635 Median-B635

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: S. Typhimurium SL1344 relAspoT mutant grown to OD600 = 1.324 in aerated Lennox Broth containing 0.3M NaCl

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

treatment_protocol: RNA labelled during reverse transcription into cDNA with Cy5-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

tag: RNA labelled with Cy5-dCTP and laser scanned at 635nm with local background subtracted from feature signal

molecule: genomic DNA

source_name: F532 Median-B532

growth_protocol: S. Typhimurium SL1344 grown to stationary phase

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

treatment_protocol: Genomic DNA labelled with Cy3-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

tag: Genomic DNA labelled with Cy3-dCTP and laser scanned at 532nm with local background subtracted from feature signal


title: S. Typhimurium wild-type LB high salt low oxygen rep 3

growth_protocol: S. Typhimurium SL133 wild-type grown to OD600 = 0.478 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions


title: S. Typhimurium wild-type LB high salt low oxygen rep 4


title: S. Typhimurium relAspoT aerated LB high salt rep 1


title: S. Typhimurium relAspoT LB high salt low oxygen rep 3

growth_protocol: S. Typhimurium SL133 relAspoT mutant strain grown to OD600 = 0.348 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions


title: d2 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d2.

source_name: ES cells (CCE cell line) d2 empty vector


title: S. Typhimurium relAspoT aerated LB high salt rep 2


title: S. Typhimurium wild-type aerated LB high salt rep 2

growth_protocol: S. Typhimurium SL1344 wild-type grown to OD600 = 1.412 in aerated Lennox Broth containing 0.3M NaCl


title: d0 empty vector MOE430A

description: Gene expression data from ES cells transduced with empty vector at d0.

source_name: ES cells (CCE cell line) d0 empty vector


title: S. Typhimurium relAspoT LB high salt low oxygen rep 4

growth_protocol: S. Typhimurium SL133 relAspoT mutant grown to OD600 = 0.348 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions


title: S. Typhimurium relAspoT aerated LB high salt rep 3


title: S. Typhimurium wild-type LB high salt low oxygen rep 1


title: S. Typhimurium wild-type LB high salt low oxygen rep 2

growth_protocol: S. Typhimurium SL133 wild-type grown to late-log phase OD600 = 0.478 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions