title: yeastcells_control6hrsafterO.D.1.0_control10.

status: Public on May 30 2006

city: College Station

first: Coran

middle: MH

last: Watanabe

address: Texas A&M Dept. Chemistry MS 3255

department: Chemistry

institute: Texas A*M University

description: We have examined azinomycin B against cultures of Saccharomyces cerevisiae and observed cytotoxic activity at moderate concentrations (ED50 = 10 ug/mL Azinomycin B). In this report, we have used yeast as a model organism to establish the cellular origin of cytotoxicity exhibited by this agent.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip YeastS98 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

source_name: Saccharomyces cerevisiae cells

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

growth_protocol: Cells were grown in YPD media at 30 degrees Celsius at 250 rpm shaker.

extract_protocol: SDS/double phenol RNA extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown to O.D. of 1.0 and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.

tag: Saccharomyces cerevisiae, wt, maintianed on YPD plates, started from 48 hrs growth on a new YPD agar plate


title: 1 hr transplanted kidney sample from brain dead donor B23

status: Public on Jun 21 2006

type: RNA

city: Toyoake

first: Mamoru

last: Kusaka

state: Aichi

address: 1-98 Kutsukake

department: Department of Urology

country: Japan

institute: Fujita-Health University

description:
Kidney sample was obtained 1 hr after transplantation from brain dead donor (6hrs after induction of brain death).
A mixture of 3 normal kidney samples was used for a template control.

data_processing: Data processed with FeatureExrtraction v7.1

molecule: total RNA

organism: Rattus norvegicus

source_name: B23 with Cy3

source_name: normal control with Cy5

tag: A mixture of kidney tissue from normal rats


title: yeastcells_treatment6hrsafterO.D.1.0_treatment10.

state: TX

country: USA

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 100.

label: biotin

organism: Saccharomyces cerevisiae

treatment_protocol: Cells were grown to O.D. of 1.0, given 10?g/ml Azinomycin B in minimal ethanol, and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.


title: 1 hr transplanted kidney sample from normal donor C25

source_name: C25 with Cy3

source_name: Normal control with Cy5


title: yeastcells_treatment6hrsafterO.D.1.0_treatmentB100.

treatment_protocol: Cells were grown to O.D. of 1.0, given 100?g/ml Azinomycin B in minimal ethanol, and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.


title: 1 hr transplanted kidney sample from normal donor C24

source_name: C24 with Cy3


title: Normal kidney sample NK3

source_name: NK3 with Cy3

tag: Normal kidney sample NK3


title: NF66-HL-control-2

status: Public on Jul 08 2006

city: Bethesda

first: Biswajit

last: Das

state: MD

address: 18 Library Drive, Building 18T, Room 106

department: Laboratory of Gene Regulation and Development

institute: National Institutes of Health/National Institute of Child Health and Human Development

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.   The manual can be found at  https://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=34961,  or through a WEB search on the manual title.

scan_protocol: Scanned using Agilent microarray scanner

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Xenopus laevis

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol

extract_protocol: standard method using TRIZOL reagent

treatment_protocol: Nontransgenic siblings of F1 progeny Xenopus laevis juvenile frogs (NF66) containing thyroid receptor dominant negative receptor (expressed with muscle specific promoter) were treated with 50µg doxycycline hyclate for 2weeks in 0.1xMMR solution. This treatment served as control group for transgenic siblings. Total RNA was isolated from dissected hindlimbs.

tag: Total RNA isolated from hindlimb of indicated treatment group of NF Stage 66 (juvenile) tadpoles

molecule: polyA RNA

source_name: Universal mRNA

extract_protocol: mRNAs were extracted with QuickPrep Micro mRNA Purification Kit from Amersham

tag: Universal mRNA extracted from whole body of unknown sex Xenopus laevis tadpoles from NF50-66


title: NF66-HL-control-3


title: Kidney sample from brain dead donor (6hrs after induction of brain death) BD1

source_name: BD1 with Cy3


title: 1 hr transplanted kidney sample from normal donor C22

source_name: C22 with Cy3


title: 1 hr transplanted kidney sample from brain dead donor B27

source_name: B27 with Cy3


title: Kidney sample from brain dead donor(6hrs after induction of brain death) BD3

source_name: BD3 with Cy3


title: 1 hr transplanted kidney sample from brain dead donor B21

source_name: B21 with Cy3


title: Kidney sample from brain dead donor(6hrs after induction of brain death) BD2

source_name: BD2 with Cy3


title: Normal kidney sample NK2

source_name: NK2 with Cy3

tag: Normal kidney sample NK2


title: yeastcells_control6hrsafterO.D.1.0_controlB100.


title: pCarTRDN-2w-HL-3

treatment_protocol: Transgenic F1 progeny Xenopus laevis tadpoles (NF55) containing thyroid receptor dominant negative receptor (expressed with muscle specific promoter) were treated with 50µg doxycycline hyclate for 2weeks in 0.1xMMR solution. This treatment induced and maintained expression of the dominant negative thyroid hormone receptor exclusively in the muscle of transgenic tadpoles for 2 weeks. Total RNA was isolated from dissected hindlimbs.

tag: Total RNA isolated from hindlimb of indicated treatment group of NF Stage 54 (premetamorphic) tadpoles


title: egy wt sibling embryos at d5, biological rep3

status: Public on Jan 31 2007

city: Boston

first: Gerhard

middle: J

last: Weber

state: MA

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Children's Hospital Boston, Harvard Medical School

description: Gene expression data from zebrafish wt embryos at day 5 post fertilization.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

organism: Danio rerio

source_name: earl grey embryos at day 5 post fertilization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryos were obtained by pairwise matings of adult egy heterozygote fish, raised at 28 ºC

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

treatment_protocol: egy mutant embryos and wild-type siblings were collected in triplicates at the 72 and 120hpf stage and separately processed. After homogenization (Tekmar Tissumizer, Cincinnati, OH), total RNA was extracted by using TRIzol reagent (Invitrogen) and purified on RNeasy resins (Qiagen) according to the manufacturer’s recommendations.

tag: strain background

value: AB/WIK, Genotype:egy, Allele:cz3,  isolated wt sibling embryos.

tag: Age

value: 5 days post fertilization


title: Normal kidney sample NK1

source_name: NK1 with Cy3

tag: Normal kidney sample NK1


title: pCarTRDN-6w-HL-3

treatment_protocol: Transgenic F1 progeny Xenopus laevis tadpoles (NF55) containing thyroid receptor dominant negative receptor (expressed with muscle specific promoter) were treated with 50µg doxycycline hyclate for 6 weeks in 0.1xMMR solution. This treatment induced and maintained expression of the dominant negative thyroid hormone receptor exclusively in the muscle of transgenic tadpoles for 6 weeks. Total RNA was isolated from dissected hindlimbs.


title: pCarTRDN-6w-HL-1


title: yeastcells_control6hrsafterO.D.1.0_controlA100.

source_name: Saccharomyces cerevisiae cells


title: Uey-ate-rep3

status: Public on Jan 12 2006

city: Houston

first: rui

last: chen

address: One Baylor Plaza

department: HGSC, Department of Molecular and Human Gentics

institute: Baylor College of Medicine

description: Genome-Wide Identification of Direct Targets of the Drosophila Retinal Determination Protein Eyeless

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented and sequentially hybridized to the Affymetrix Drosophila Genome Array 2 following the manufacturer’s instructions.

scan_protocol: Standard Affymetrix protocol.

data_processing: dChip

organism: Drosophila melanogaster

source_name: third instar antennal discs

label_protocol: cDNA synthesis was carried out as described in the Expression Analysis Technical Manual (Affymetrix, two-cycle protocol) using 100 ng of total RNA for each sample. The cRNA reactions were carried out using the BioArray High-Yield Transcript Labeling kit (Enzo).

extract_protocol: Trizol total RNA

tag: Third instar UAS-ey/dpp-GAL4 antennal discs


title: yeastcells_treatment6hrsafterO.D.1.0_treatmentA100.


title: Uey-ate-rep1


title: Uey-ate-rep2


title: wildtype-wingdisc-rep3

status: Public on Jan 11 2006

source_name: third instar wing discs

tag: Third instar wild type wing discs


title: liver_LDLr-KO, biological replicate 2

status: Public on Aug 10 2006

first: Eric

last: Billings

address: 10 Center Drive

institute: NHLBI

description: Gene expression data comparing ABCA1 over-expression in LDL receptor +/- genetic background

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix (HP) GeneArray Scanner G2500A.

data_processing: RMA-normalization

organism: Mus musculus

source_name: liver, LDLr-KO

label_protocol: Samples prepared with Arcturus RiboAmp protocol from 2 ug of total RNA

growth_protocol: Male mice were sacrificed at 5 to 6 months old

extract_protocol: Trizol extraction, Qiagen RNEasy clean-up with on-column DNAse treatment

treatment_protocol: Diet: NIH36, livers were snap-frozen and stored at -80C

tag: Strain


title: UASey_legdisc_rep1

source_name: third instar leg discs

tag: Third instar lavae leg discs from UAS-ey/dpp-GAL4


title: wildtype-wingdisc-rep1


title: pCarTRDN-2w-HL-2


title: UASey_legdisc_rep2


title: wildtype-legdisc-rep3

tag: Third instar wild type leg discs


title: pCarTRDN-6w-HL-2


title: wildtype-legdisc-rep2


title: NF55-control-HL-1

treatment_protocol: Nontransgenic siblings of F1 progeny Xenopus laevis tadpoles (NF55) containing thyroid receptor dominant negative receptor (expressed with muscle specific promoter) were treated with 50µg doxycycline hyclate for 2weeks in 0.1xMMR solution. This treatment served as control group for transgenic siblings. Total RNA was isolated from dissected hindlimbs.

tag: Total RNA isolated from hindlimb of indicated treatment group of NF Stage 55 (premetamorphic) tadpoles


title: wildtype-legdisc-rep1


title: wildtype-eyedisc-rep2

source_name: third instar eye discs

tag: Third instar lavae eye discs


title: wildtype-eyedisc-rep1


title: wildtype-eyedisc-rep4


title: wildtype-wingdisc-rep2


title: NF66-HL-control-1


title: wildtype-eyedisc-rep3


title: UASey_wingdisc_rep3

tag: Third instar lavae wing discs from UAS-ey/dpp-GAL4


title: wt-ate-rep3

tag: wild type third instar antennal discs


title: NF55-control-HL-2

tag: Total RNA isolated from hindlimb of indicated treatment group of NF Stage 55(premetamorphic) tadpoles


title: pCarTRDN-2w-HL-1


title: NF55-control-HL-3


title: wt-ate-rep1


title: UASey_wingdisc_rep2


title: ato_mutant_UASey_legdisc_rep3

tag: Third instar lavae leg discs from ato1; UAS-ey/dpp-GAL4


title: UASey_legdisc_rep3


title: ato_mutant_UASey_legdisc_rep1

tag: third instar lavae.  UAS-eyeless/dpp-Gal4 in ato1 mutant


title: egr1 48 hrs U133A

status: Public on Dec 01 2005

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: HUVEC cells infected with egr1-Adenovirus for 48 hrs

organism: Homo sapiens

source_name: HUVEC


title: UASey_wingdisc_rep1


title: egr1 24 hrs U133A

description: HUVEC cells infected with egr1-Adenovirus for 24 hrs


title: egr1 24 hrs cv U133A

description: HUVEC cells infected with control Adenovirus for 24 hrs


title: ato_mutant_UASey_legdisc_rep2

tag: third instar lavae leg discs from ato1; UAS-ey/dpp-GAL4


title: egr1 24 hrs ctrl U133A

description: HUVEC cells control/wildtype cultured for 24 hrs; not treated with Adenovirus


title: egr1 24 hrs cv U133B


title: egr1 16 hrs U133A

description: HUVEC cells infected with egr1-Adenovirus for 16 hrs


title: egr1 48 hrs U133B


title: egr1 48 hrs cv U133B

description: HUVEC cells infected with control Adenovirus for 48 hrs


title: egr1 48 hrs cv U133A


title: egr1 16 hrs cv U133A

description: HUVEC cells infected with control Adenovirus for 16 hrs


title: egr1 24 hrs ctrl U133B

description: HUVEC cells control/wildtype cultured for 24 hrs , not infected with Adenovirus


title: egr1 16 hrs U133B


title: egr1 24 hrs U133B

description: HUVEC cells infected with egr1- Adenovirus for 24 hrs


title: normal human skeletal muscle sample 12

status: Public on Jan 29 2004

first: Judith

last: Haslett

institute: Harvard Medical School

description:
biopsy sample obtained from 30-year-old male normal  individual
Keywords = gene expression profile of normal human skeletal muscle
Keywords = Affymetrix HG-U95A array [version 1]

source_name: skeletal muscle (intercostal muscle)


title: JEG3 B

status: Public on May 30 2005

city: Madison

first: David

middle: W

last: Burleigh

state: WI

address: 1220 Capital Court

institute: Wisconsin National Primate Research Center

description:
JEG3 choriocarcinoma cell line total RNA
Keywords = trophoblast
Keywords = JEG3
Keywords = placenta
Lot batch = 4001570

source_name: JEG3 cell line


title: naive vs. influenza A virus d1

status: Public on Jul 12 2006

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were done as two-color hybridizations. RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 4 µg of total RNA (derived from five lungs in each group and time point, respectively) with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with either cyanine 3-CTP (Cy3-CTP) or cyanine 5-CTP (Cy5-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was precipitated overnight with LiCl, ethanol washed and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP and A650nm for Cy5-CTP. Before hybridization, 1.25 µg labeled cRNA of each product were fragmented and mixed with control targets and hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were done overnight for approximately 17 h at 60°C. The slides were washed according to the manufacturer's manual and scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap was performed. The RNA samples were labeled vice verse with the two fluorescent dyes (fluorescence reversal).

data_processing: Agilent FE 6.1.1.1 / Rosetta Resolver Built 3.2.2

source_name: naive

tag: C57Bl/6 naive control mice received virus-free allantoic fluid intranasally

source_name: influenza A virus strain HKx31(x31; H3N2) infected d1

tag: C57BL/6 mice were intranasally infected with a sublethal dose (360 hemagglutinating units) in 30 µl allantoic fluid


title: egr1 16 hrs cv U133B


title: wt-ate-rep2