title: RES_Subject 2_48H vs PRE

status: Public on Apr 15 2006

city: Ottawa

first: Douglas

middle: Joseph

last: Mahoney

address: 401 Smyth Rd

department: Apoptosis Research Center

institute: CHEO Research Institute

description: Skeletal muscle biopsies were taken from the vastus lateralis before (baseline) or 48H after 300 single leg maximal eccentric contractions. Total RNA was extracted and amplified using a MessageAmp aRNA Linear Amplification Kit. Amplified RNA was converted to cDNA, labeled with either Cy3 or Cy5 and hybridized to our arrays (Genisphere, Kit 350RP). For each array, we used 976 buffer controls to differentiate signal from noise. Chips were scanned using a Packard Bioscience scanner (Hewlett Packard), ScanArray Express software (version 1.1), a PMT laser setting of 75, and power of 80.

data_processing: TIFF files were analyzed using Genepix 4, using median values for each spot. The data was LOWESS-normalized using GeneTraffic software (Iobion).

source_name: 48H Post-RES exercise

tag: 48H Sample

source_name: Baseline Sample


title: IM2(3)Cy5_II

status: Public on Apr 20 2006

type: RNA

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: OPMD experiment

data_processing: Rosetta Resolver Genepix error model

molecule: polyA RNA

organism: Mus musculus

source_name: Reference IM2

tag: Reference IM2


title: IM2(2)Cy3_II

description: OPMD experiment


title: IM2(1)Cy3_II

description: OPMD experiment


title: IM2(3)Cy5_I

description: OPMD, cell line, untransfected

molecule: total RNA


title: RES_Subject 3_48H vs PRE

state: ON

country: Canada

organism: Homo sapiens

tag: Baseline Sample


title: RES_Subject 4_3H vs PRE

description: Skeletal muscle biopsies were taken from the vastus lateralis before (baseline) or 3H after 300 single leg maximal eccentric contractions. Total RNA was extracted and amplified using a MessageAmp aRNA Linear Amplification Kit. Amplified RNA was converted to cDNA, labeled with either Cy3 or Cy5 and hybridized to our arrays (Genisphere, Kit 350RP). For each array, we used 976 buffer controls to differentiate signal from noise. Chips were scanned using a Packard Bioscience scanner (Hewlett Packard), ScanArray Express software (version 1.1), a PMT laser setting of 75, and power of 80.

source_name: 3H Post-RES exercise

tag: 3H Sample


title: RES_Subject 2_3H vs PRE

tag: Baseline sample


title: RES_Subject 1_48H vs PRE


title: RES_Subject 3_3H vs PRE


title: RES_Subject 1_3H vs PRE


title: IM2(2)Cy3_I

description: OPMD, cell line, untransfected


title: slbo_Non-Migratory cells_rep3

status: Public on Apr 04 2006

city: Baltimore

first: Xuejiao

last: Wang

state: MD

address: WBSB413, 725 N. Wolfe Str.

department: Biological Chemistry

country: USA

institute: Johns Hopkins Univ.

description: Non-mCD8-GFP expressing cells were purified using magnetic beads coated with an anti-mouse CD8 antibody.

data_processing: MAS5.0 scaled to 150.

label: Biotin

organism: Drosophila melanogaster

source_name: Non-migratory cells in the slbo mutant Drosophila ovary

tag: Gender

value: female

tag: Age

value: 2-7 days

tag: Tissue

value: ovary


title: slbo_Non-Migratory cells_rep2

tag: Genotype

tag: Age:2-7 days


title: IM2(1)Cy5_I

description:
OPMD
cell line
untransfected


title: IM2(3)Cy3_I

description: OPMD, cell line, untransfected


title: IM2(2)Cy5_II

description: OPMD experiment


title: IM2(1)Cy5_II

description: OPMD experiment

tag: Reference IM2, pooled IM2

tag: IM2, control, untransfected


title: IM2(1)Cy3_I

description:
mouse cell line
OPMD
untransfected

source_name: reference IM2


title: slbo_Migratory cells_rep3

description: mCD8-GFP expressing cells were purified using magnetic beads coated with an anti-mouse CD8 antibody.

source_name: Migratory cells in the slbo mutant Drosophila ovary


title: slbo_Non-Migratory cells_rep1


title: slbo_Migratory cells_rep1

value: slbo-Gal4, slboe7b/UAS-mCD8-GFP,slboLy6


title: WT_Migratory cells_rep1

description: mCD8-GFP expressing cells were purified using Magnetic beads coated with an anti-mouse CD8 antibody.

data_processing: MAS5.0, scaled to 150

label: biotin

source_name: Migratory cells in the Drosophila ovary

value: slbo-Gal4, UAS-mCD8-GFP/+


title: slbo_Migratory cells_rep2


title: WT_Non-Migratory cells_rep2

source_name: Non-migratory cells in the wild type Drosophila ovary


title: WT_Migratory cells_rep3

description: mCD8 expressing cells were purified using magnetic beads coated with an anti-mouse CD8 antibody.

source_name: Migratory cells in the wild type Drosophila ovary


title: WT_Non-Migratory cells_rep3


title: WT_Migratory cells_rep2


title: WT_Non-Migratory cells_rep1


title: ArsRS_Regulon_1

status: Public on Apr 01 2006

city: Wuerzburg

first: Dagmar

last: Beier

address: Am Hubland

country: Germany

institute: Universität Wuerzburg

description:
scanning software: ScanArray express
software version: 3.0

data_processing: value: log2 transformed ratio of normalized channel 2 median to channel 1 median; normalization method: LOWESS algorithm

organism: Helicobacter pylori

source_name: 20 µg total RNA, WT pH5.0, 60 min

tag: strain

source_name: 20 µg total RNA, ArsSdelta pH5.0, 60 min

value: ArsSdelta, pH5.0, 60 min


title: ArsRS_Regulon_3

description:
scanning software: ScanArray express
software version 3.0

source_name: 20 µg of total RNA, WT, pH5.0, 60 min

source_name: 20 µg of total RNA, ArsSdelta, pH5.0, 60 min


title: ArsRS_Regulon_4

description:
scanning software: ScanArray express
sofware version 3.0

value: G27ArsSdelta, pH5.0, 60 min


title: ArsRS_Regulon_2


title: 5T

city: Groningen

first: Marije

last: Booman

department: Pathology

institute: University Medical Center Groningen

description: A mix of 5 hyperplastic tonsils was used as a common reference. Each hybridization was repeated as a dye-reversal.

hyb_protocol: Each hybridization was repeated as a dye reversal. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm

scan_protocol: Fluorescent signals were extracted from the arrays by a DNA Microarray Scanner (Agilent, Palo Alto, California) and quantified using Imagene 5.5 software (Biodiscovery, El Segundo, California).

data_processing: Data were normalized and corrected for various biases according to Yang et al (PMID: 11842121). Ratios of expression in DLBCL (sample) compared to tonsil (reference) were calculated; weighted averages of dye-reversal experiments and confidence levels were calculated according to the Rosetta error model (Hughes et al, PMID: 10929718). Based on MA plots and the results from the error model, spots with an average intensity measurement A (0.5 log2 (Cy3Cy5)) lower than 7 over all experiments were excluded from further analysis.

label: Cy5 or Cy3 (dye-reversal)

source_name: Testicular DLBCL 5T

label_protocol: Cy3 or Cy5 molecules were directly incorporated during a cDNA synthesis reaction using amplified cRNA as starting material. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm

extract_protocol: Total RNA was isolated and submitted to one round of linear amplification. Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm

value: Testicular diffuse large B cell lymphoma

tag: Sample origin

value: whole frozen tissue sections

tag: Sample type

value: RNA

tag: Amplification

value: linear, one-round

source_name: Reference tonsil mix

value: 5 hyperplastic tonsils


title: 18T

source_name: Testicular DLBCL 18T


title: 8T

source_name: Testicular DLBCL 8T


title: 7T

source_name: Testicular DLBCL 7T


title: 2T

source_name: Testicular DLBCL 2T


title: 25T

source_name: Testicular DLBCL 25T


title: 16T

source_name: Testicular DLBCL 16T


title: 4T

source_name: Testicular DLBCL 4T


title: 10T

source_name: Testicular DLBCL 10T


title: 6T

source_name: Testicular DLBCL 6T


title: 24T

source_name: Testicular DLBCL 24T


title: 13T

source_name: Testicular DLBCL 13T


title: 17T

source_name: Testicular DLBCL 17T


title: 1T

source_name: Testicular DLBCL 1T


title: 14T

source_name: Testicular DLBCL 14T


title: 15T

source_name: Testicular DLBCL 15T


title: 11T

source_name: Testicular DLBCL 11T


title: 19T

source_name: Testicular DLBCL 19T

source_name: Reference tonsil mix


title: 20T

source_name: Testicular DLBCL 20T


title: 12T

source_name: Testicular DLBCL 12T


title: 3T

source_name: Testicular DLBCL 3T


title: 9T

source_name: Testicular DLBCL 9T


title: 26T

source_name: Testicular DLBCL 26T


title: 21T

source_name: Testicular DLBCL 21T


title: 23T

source_name: Testicular DLBCL 23T


title: Lung_Rep4_TaqMan

status: Public on Mar 15 2006

city: Foster City

first: Yulei

state: CA

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: Lung tissue, Taqman

data_processing: Data was processed using SDS 2.1 software (Applied Biosystems, Foster City, CA), and the Ct value (threshold cycle, the fractional cycle number at which the fluorescence passes the threshold for a given gene within a sample) was determined using auto-baseline and a threshold value of 0.15.

label: FAM dye

source_name: Lung tissue

extract_protocol: Commercial available (Stratagene)

tag: Human tissue


title: Lung_Rep1_TaqMan

description: Lung tissue, Taqman


title: UHR_Rep3_TaqMan

description: UHR tissue, Taqman

source_name: UHR tissue


title: Liver_Rep4_TaqMan

description: Liver tissue, Taqman

source_name: Liver tissue


title: Lung_Rep2_TaqMan

description: Lung tissue, Taqman


title: 9N

source_name: Nodal DLBCL 9N

value: Nodal diffuse large B cell lymphoma


title: UHR_Rep4_TaqMan

description: UHR tissue, Taqman


title: 2N

source_name: Nodal DLBCL 2N


title: 1N

source_name: Nodal DLBCL 1N


title: 3N

source_name: Nodal DLBCL 3N


title: 22T

source_name: Testicular DLBCL 22T


title: Liver_Rep3_TaqMan

description: Liver tissue, Taqman


title: Lung_Rep3_TaqMan

description: Lung tissue, Taqman


title: UHR_Rep1_TaqMan

description: UHR tissue, Taqman


title: UHR_Rep2_TaqMan

description: UHR tissue, Taqman


title: Liver_Rep2_TaqMan

description: Liver tissue, Taqman


title: 6N

source_name: Nodal DLBCL 6N


title: 8N

source_name: Nodal DLBCL 8N

source_name: Reference tonsil mix


title: 7N

source_name: Nodal DLBCL 7N


title: E. coli BW25113 K-12 mutant yceP in LB glu after 24 hr

city: College Station

first: Thomas

middle: K.

last: Wood

state: TX

address: 220 Jack E. Brown Building

department: Artie McFerrin Department of Chemical Engineering

institute: Texas A & M University

description: RNA extracted from biofilm cells of E. coli K12 mutant yceP after 24 hours of growth in LB glu with glass wool

data_processing: MAS 5.0 Expression Analysis Default Settings

organism: Escherichia coli

source_name: Channel 1


title: Liver_Rep1_TaqMan

description: Liver tissue, Taqman


title: BW25113 w/t LB glu 24hr biofilm cells (2nd set)

description: RNA extracted from biofilm cells of E. coli K12 wild type after 24 hours of growth in LB glu (2nd set)


title: 10N

source_name: Nodal DLBCL 10N


title: 5N

source_name: Nodal DLBCL 5N


title: BW25113 w/t LB glu 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 wild type after 24 hours of growth in LB glu with glass wool


title: 4N

scan_protocol: Fluorescent signals were extracted from the arrays by a DNA Microarray Scanner (Agilent, Palo Alto, California) and quantified using Imagene 5.5 software (Biodiscovery, El Segundo, California). Detailed protocols can be found at http://www.nki.nl/nkidep/pa/microarray/protocols.htm

source_name: Nodal DLBCL 4N

value: whole frozen tissue section


title: Brain_Rep3_TaqMan

description: Brain tissue, Taqman

source_name: Brain tissue


title: Brain_Rep1_TaqMan

description: Brain tissue, Taqman


title: E. coli BW25113 K-12 mutant yliH in LB glu after 24 hr

description: RNA extracted from biofilm cells of E. coli K12 mutant yliH after 24 hours of growth in LB glu with glass wool


title: Brain_Rep4_TaqMan

description: Brain tissue, Taqman


title: Brain_Rep2_TaqMan

description: Brain tissue, Taqman


title: wild-type (wt) replicate 3

city: Philadelphia

first: Natalie

last: Terry

state: PA

address: 421 Curie Blvd

department: Department of Cell and Developmental Biology

institute: University of Pennsylvania

description: dissected wild-type adult testes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: wild-type testes

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

extract_protocol: 150 bgcn- adult male testes were dissected and collected in RNAlater.  Total RNA was extracted using TRIzol (Invitrogen) and purified with an RNAeasy column (Qiagen).

tag: wild-type genotype, adult males, dissected whole testes


title: Os+bgcn replicate 1

description: dissected Os+bgcn- adult testes

source_name: Os+bgcn- testes

extract_protocol: 150 Os+bgcn- adult male testes were dissected and collected in RNAlater.  Total RNA was extracted using TRIzol (Invitrogen) and purified with an RNAeasy column (Qiagen).

tag: Os+bgcn- genotype, adult males, dissected whole testes


title: wild-type (wt) replicate 4

description: dissected wild-type adult testes


title: Os+bgcn replicate 5

description: dissected Os+bgcn- adult testes


title: wild-type (wt) replicate 2

description: dissected wild-type adult testes


title: Os+bgcn replicate 6

description: dissected Os+bgcn- adult testes


title: bgcn replicate 2

description: dissected bgcn- adult testes

source_name: bgcn- testes

extract_protocol: 750 bgcn- adult male testes were dissected and collected in RNAlater.  Total RNA was extracted using TRIzol (Invitrogen) and purified with an RNAeasy column (Qiagen).

tag: bgcn- genotype, adult males, dissected whole testes


title: bgcn replicate 5

description: dissected bgcn- adult testes


title: wild-type (wt) replicate 5

description: dissected wild-type adult testes


title: Os+bgcn replicate 2

description: dissected Os+bgcn- adult testes


title: Os+bgcn replicate 4

description: dissected Os+bgcn- adult testes


title: wild-type (wt) replicate 1

description: dissected wild-type adult testes


title: Os+bgcn replicate 3

description: dissected Os+bgcn- adult testes


title: bgcn replicate 4

description: dissected bgcn- adult testes


title: bgcn replicate 3

description: dissected bgcn- adult testes


title: bgcn replicate 1

description: dissected bgcn- adult testes


title: Bradyrhizobium japonicum irr mutant strain LODTM5, low iron, biological rep_3

city: Buffalo

first: Mark

middle: R.

last: O'Brian

state: NY

address: 140 Farber Hall

department: Biochemistry

institute: State University of New York at Buffalo

description: Cells grown in low iron media

hyb_protocol: Modification of Affymetrix protocol used for P.aeruginosa

data_processing: GeneChip Operating Software (GCOS) version 1.1 (Affymetrix)

organism: Bradyrhizobium japonicum

source_name: Cells

label_protocol: Approx. 10ug total RNA used to synthesize biotinylated cDNA

growth_protocol: Grown in 0.5 GSY media with no added iron

extract_protocol: Cells prepared as described in Yang et al. (2006) Mol. Microbiol., in press

tag: irr mutant strain LODTM5 grown in low iron media


title: UHR_Rep3_AB

description: human UHR tissue

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC.  Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

label: DIG-UTP

source_name: UHR tissue

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 ?g of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).


title: UHR_Rep2_AB

description: human UHR tissue

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).


title: Lung_Rep4_AB

description: human lung

source_name: Lung tissue


title: Bradyrhizobium japonicum irr mutant strain LODTM5, low iron, biological rep_2

description: Cells grown in low iron media


title: UHR_Rep4_AB

description: human UHR tissue


title: Lung_Rep1_AB

description: human lung


title: Bradyrhizobium japonicum irr mutant strain LODTM5, low iron, biological rep_1

description: Cells grown in low iron media


title: Bradyrhizobium japonicum strain LO, high iron, biological rep_2

description: Cells grown in high iron media

growth_protocol: Grown in 0.5 GSY media supplemented with 12 uM ferric chloride

tag: Parent strain LO grown in high iron media


title: Lung_Rep3_AB

description: human lung


title: UHR_Rep1_AB

description: human UHR tissue


title: Lung_Rep2_AB

description: human lung


title: Brain_Rep4_AB

description: human brain


title: Liver_Rep2_AB

description: human liver

source_name: Liver tissue


title: Bradyrhizobium japonicum strain LO, low iron, biological rep_3

description: Cells grown in low iron media

tag: Parent strain LO grown in low iron media


title: Liver_Rep3_AB

description: human liver


title: Liver_Rep4_AB

description: human liver


title: Bradyrhizobium japonicum strain LO, high iron, biological rep_3

description: Cells grown in high iron media


title: Lung_Rep4_Agilent

description:
Lung tissue
Universal Human Reference RNA sample (Stratagene)

hyb_protocol: cRNA hybridized according to standard Agilent protocols

scan_protocol: arrays were scanned according to standard Agilent protocols

data_processing: Data processed with FeatureExtraction v7.5.1

source_name: Lung_Rep4_Agilent with Cy5

label_protocol: Amplified and labeled according to standard Agilent protocols

source_name: Universal Human Reference (Stratagene) with Cy3

tag: Common Reference RNA sample


title: Bradyrhizobium japonicum strain LO, low iron, biological rep_1

description: Cells grown in low iron media


title: Lung_Rep3_Agilent

source_name: Lung_Rep3_Agilent with Cy5


title: Brain_Rep1_AB

description: human brain


title: Bradyrhizobium japonicum strain LO, low iron, biological rep_2

description: Cells grown in low iron media


title: Liver_Rep1_AB

description: human liver


title: Liver_Rep2_Agilent

description:
Liver tissue
Universal Human Reference RNA sample (Stratagene)

source_name: Liver_Rep2_Agilent with Cy5


title: Bradyrhizobium japonicum strain LO, high iron, biological rep_1

description: Cells grown in high iron media


title: Lung_Rep2_Agilent

source_name: Lung_Rep2_Agilent with Cy5


title: Brain_Rep3_AB

description: human brain


title: Lung_Rep1_Agilent

source_name: Lung_Rep1_Agilent with Cy5


title: Liver_Rep4_Agilent

source_name: Liver_Rep4_Agilent with Cy5


title: HCT116p53+ hypoxia 24hrs rep1

status: Public on Mar 07 2006

city: Stanford

first: Nicholas

last: Denko

address: Rm 1245 269 campus dr

department: Radiation Oncology

institute: Stanford University

description: Affymetrix Genechip Protocol

hyb_protocol: Affymetrix Genechip Protocol

scan_protocol: Affymetrix Genechip Protocol

data_processing: Affymetrix Microarray Suite version 4

label: biotin - streptavidin phycoerythrin (Affymetrix)

source_name: HCT116 p53 wildtype cells exposed to hypoxia 24hrs

label_protocol: Affymetrix Genechip Protocol

growth_protocol: Standard monolayer tissue culture

extract_protocol: Affymetrix Genechip Protocol

treatment_protocol: Cells in monolayer culture were exposed to <0.01% oxygen in an anoxic incubator for the indicated times.

tag: Cell Line

value: HCT116 (p53 wildtype)

tag: Cell Type

value: colon carcinoma


title: HCT116p53+ hypoxia 12hrs rep1

description: Affymetrix Genechip Protocol

source_name: HCT116 p53 wildtype cells exposed to hypoxia 12hrs


title: HCT116p53+ hypoxia 0hrs rep1

description: Affymetrix Genechip Protocol

source_name: HCT116 p53 wildtype cells exposed to hypoxia 0hrs


title: Brain_Rep3_Agilent

description:
Brain tissue
Universal Human Reference RNA sample (Stratagene)

source_name: Brain_Rep3_Agilent with Cy5


title: Brain_Rep4_Agilent

source_name: Brain_Rep4_Agilent with Cy5


title: HCT116p53- hypoxia 12hrs rep1

description: Affymetrix Genechip Protocol

source_name: HCT116 p53 null cells exposed to hypoxia 12hrs

value: HCT116 (p53 null)


title: H1299p53+ hypoxia 24hrs rep1

description: Affymetrix Genechip protocol

hyb_protocol: Affymetrix Genechip protocol

scan_protocol: Affymetrix Genechip protocol

source_name: H1299 p53 wildtype cells exposed to hypoxia 24 hrs

label_protocol: Affymetrix Genechip protocol

growth_protocol: Standard monolayer culture

extract_protocol: Affymetrix Genechip protocol

value: H1299, p53 reintroduced

tag: Cell type

value: non-small cell lung cancer


title: Liver_Rep3_Agilent

source_name: Liver_Rep3_Agilent with Cy5


title: HCT116p53- hypoxia 24hrs rep1

description: Affymetrix Genechip Protocol

source_name: HCT116 p53 null cells exposed to hypoxia 24hrs


title: H1299p53+ hypoxia 0hrs rep1

description: Affymetrix Genechip protocol

source_name: H1299 p53 wildtype cells exposed to hypoxia 0hrs


title: HCT116p53- hypoxia 0hrs rep1

description: Affymetrix Genechip Protocol

source_name: HCT116 p53 null cells exposed to hypoxia 0hrs


title: Brain_Rep2_Agilent

source_name: Brain_Rep2_Agilent with Cy5

source_name: Universal Human Reference (Stratagene) with Cy3


title: Brain_Rep2_AB

description: human brain

source_name: Brain tissue


title: Liver_Rep1_Agilent

source_name: Liver_Rep1_Agilent with Cy5


title: Brain_Rep1_Agilent

description:
Brain tissue
Universal Human Reference

source_name: Brain_Rep1_Agilent with Cy5

tag: Common reference


title: RCC4vhl+ hypoxia 18hrs reoxygenation 4hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 18hrs and reoxygenation 4hrs

tag: Cell line

value: RCC4, wildtype vhl reintroduced

tag: Tissue type

value: renal carcinoma


title: H1299p53- hypoxia 0hrs rep1

description: Affymetrix Genechip protocol

source_name: H1299 p53 null cells exposed to hypoxia 0hrs


title: H1299p53- hypoxia 24hrs rep1

description: Affymetrix Genechip protocol

source_name: H1299 p53 null cells exposed to hypoxia 24hrs


title: RCC4vhl- hypoxia 18hrs reoxygenation 1hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 18hrs and reoxygenation 1 hrs

value: RCC4 (vhl null)


title: RCC4vhl- hypoxia 18hrs reoxygenation 4hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 18hrs and reoxygenation 4hrs


title: RCC4vhl+ hypoxia 18hrs reoxygenation 1hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 18hrs and reoxygenation 1hrs


title: RCC4vhl+ hypoxia 4hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 4hrs


title: RCC4vhl+ hypoxia 2hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 2hrs


title: RCC4vhl- hypoxia 4hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 4hrs


title: RCC4vhl- hypoxia 2hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cell exposed to hypoxia 2hrs


title: RCC4vhl+ hypoxia 0hrs rep2

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 0hrs


title: RCC4vhl+ hypoxia 1hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 1hrs


title: RCC4vhl- hypoxia 1hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 1hrs


title: RCC4vhl+ hypoxia 6hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 6hrs


title: RCC4vhl+ hypoxia 18hrs rep2

description: Affymetrix Genechip protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 18hrs


title: RCC4vhl- hypoxia 0hrs rep2

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 0hrs


title: RCC4vhl- hypoxia 18hrs rep2

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 18hrs


title: RCC4vhl- hypoxia 6hrs rep1

description: Affymetrix Genechip protocol

source_name: RCC4 vhl null cells exposed to hypoxia 6hrs

value: RCC4  (vhl null)


title: RCC4vhl- hypoxia 18hrs rep1

description: Affymetrix GeneChip Protocol

hyb_protocol: Affymetrix GeneChip Protocol

scan_protocol: Affymetrix GeneChip Protocol

label_protocol: Affymetrix GeneChip Protocol

extract_protocol: Affymetrix GeneChip Protocol


title: Liver_POR-null_2

status: Public on Mar 01 2006

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description: Total RNA from the tissues of 3 male mice were pooled into a single sample and hybridized to the Affymetrix 430A GeneChip. The colon was defined as the tissue below the caecum and above the rectum. The small intestine was defined as the tissue below the stomach and above the caecum, and was divided into three equal parts corresponding to the duodenum, jejunum, and ileum. The epithelial layer of intestinal tissues was scraped off for RNA processing. Whole liver was extracted. All tissues were rinsed with PBS.

data_processing: as defined in header descriptions: MAS 5.0, RMA

source_name: Liver

tag: Strain

tag: Sex

value: Male,

tag: Age

value: between 6-8 weeks,

tag: Diet

value: RM3 (E) 801710 Soya-free powdered diet from B.S & S.,

tag: Tissue

value: Liver


title: RCC4vhl+ hypoxia 18hrs rep1

description: Affymetrix GeneChip Protocol

source_name: RCC4 vhl wildtype cells exposed to hypoxia 18 hrs


title: RCC4vhl+ hypoxia 0hrs rep1

description: Affymetrix GeneChip Protocol


title: Liver_POR-null+quercetin_1

value: RM3 (E) 801710 Soya-free powdered diet + 7mg quercetin from B.S & S.,


title: Liver_POR-null+quercetin_2


title: RCC4vhl- hypoxia 0hrs rep1

description: Affymetrix GeneChip Protocol


title: Liver_Wild Type+Quercetin_3


title: Liver_Wild Type+Quercetin_2


title: Liver_POR-null_1


title: Liver_POR-null+quercetin_3


title: Liver_POR-null_3


title: Liver_Wild Type_3


title: Liver_Wild Type_2


title: Jejunum_Wild Type+Quercetin_2

source_name: Jejunum

value: Jejunum


title: Jejunum_POR-null_3


title: Jejunum_POR-null_1


title: Jejunum_POR-null+quercetin_1


title: Jejunum_POR-null+quercetin_3


title: Liver_Wild Type+Quercetin_1


title: Liver_Wild Type_1


title: Jejunum_POR-null_2


title: Jejunum_POR-null+quercetin_2


title: Jejunum_Wild Type+Quercetin_1


title: Jejunum_Wild Type+Quercetin_3


title: Jejunum_Wild Type_3


title: Ileum_POR-null+quercetin_2

source_name: Ileum

value: Ileum


title: Jejunum_Wild Type_2


title: Ileum_POR-null+quercetin_1


title: Jejunum_Wild Type_1


title: Ileum_POR-null_3


title: Ileum_POR-null_1


title: Ileum_POR-null+quercetin_3


title: Ileum_Wild Type+Quercetin_2


title: Ileum_Wild Type+Quercetin_3


title: Ileum_POR-null_2


title: Low shear modeled microgravity sample 25th generation_rep1

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: This sample is grown in low-shear modeled microgravity (LSMMG).

data_processing: CEL file RMA normalized

organism: Saccharomyces cerevisiae

source_name: Whole cells from LSMMG HARV culture

label_protocol: Approximately 6 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

growth_protocol: T=30C; grown for 5 generations; harvested in log phase in YPD

extract_protocol: Cells were collected from the HARVs, the OD600 was measured, and the cells were pelleted by centrifugation at 5000 X g for 5 min at room temperature. The cell pellets were flash frozen in dry ice/ethanol and stored at -80 oC. Total RNA was extracted using the QIAGEN® RNeasy® Midi Kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer’s instructions with the following modification to the cell lysis step. We added 0.1mm diameter sterile zirconia/silica beads (BioSpec Products, Inc., Bartlettsville, OK) to the yeast cells in buffer RLT, then bead beat in the Savant Fast Prep bead beater (Savant Instruments, Inc., Farmingdale, NY) at speed 6.5 for 45 seconds, and immediately cooled the samples on ice.  Samples for microarray analysis were further cleaned-up and concentrated using the QIAGEN® RNeasy® MinElute Cleanup Kit (QIAGEN, Inc., Valencia, CA). RNA quality was evaluated by 1.2% formaldehyde/agarose gel electrophoresis according to the QIAGEN protocol in Appendix H of the RNeasy® Mini Handbook.

tag: S. cerevisiae BY4743 grown in YPD in HARV bioreactor modeling low-shear microgravity


title: Low shear modeled microgravity sample 25th generation_rep2

tag: S. cerevisiae BY4743 grown in YPD in HARV bioreactor modeling low-shear microgravity.


title: Ileum_Wild Type+Quercetin_1


title: Colon_POR-null+quercetin_2

source_name: Colon

value: Colon


title: Low shear modeled microgravity sample 5th generation_rep3


title: Low shear modeled microgravity sample 25th generation_rep3


title: Ileum_Wild Type_3


title: Low shear modeled microgravity sample 5th generation_rep2

source_name: Whole  cells from LSMMG HARV culture


title: Colon_POR-null_2


title: Colon_Wild Type_3


title: Ileum_Wild Type_2


title: Control sample 25th generation_rep1

description: This sample is a control for comparison against samples grown in low-shear modeled microgravity (LSMMG).

source_name: Whole cells from horizontal HARV culture

tag: S. cerevisiae BY4743 grown in YPD in horizontal HARV bioreactor.


title: Colon_POR-null_3


title: Control sample 25th generation_rep3


title: Low shear modeled microgravity sample 5th generation_rep1

source_name: Whole cells from LSMM HARV culture


title: Colon_POR-null+quercetin_1


title: Colon_POR-null+quercetin_3


title: Colon_Wild Type+Quercetin_1


title: Colon_Wild Type_2


title: Colon_POR-null_1


title: Colon_Wild Type+Quercetin_2


title: Control sample 25th generation_rep2


title: Control sample 5th generation_rep2


title: Colon_Wild Type+Quercetin_3


title: Colon_Wild Type_1


title: Control sample 5th generation_rep3

tag: S. cerevisiae BY4743 grown in YPD in horizonal HARV bioreactor.


title: Ileum_Wild Type_1


title: Adp300wt T24

city: Portland

last: Kuninger

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Biochemistry and Molecular Biology

institute: Oregon Health & Science University

description: Adp300wt infected C2AS12 cells following 24h in DM

data_processing: Chip data (.cel files) were normalized using global scaling values (200), and analyzed with Affymetrix Microarray Suite 5.0 software using default parameters except for a Tau setting of 0.015. Filtered pair-wise comparisons were performed with the following criteria:  only expression signal values greater or equal to 100 for Ad-p300 wild type samples were considered and mean fold-change greater or equal to 4 vs both Ad-p300 +Dox and Ad-p300deltaTAZ2 samples was required for selection.

source_name: C2-derived myoblast

label_protocol: ~8 ug total RNA was labeled using standard Affymetrix protocols

growth_protocol: Cells were infected with recombinant adenoviruses encoding either wild type or mutant p300 in the presence or absence doxycline and were incubated in low serum differentiation medium for 24 h.

extract_protocol: Trizol reagent with additional Na_acetate/EtOH precipitation

tag: C3H strain

tag: C2 myoblasts stably expressing antisense IGF-II cDNA (C2AS12 cells)


title: Control sample 5th generation_rep1


title: Adp300wt T0

description: Adp300wt infected C2AS12 cells prior to addition of DM


title: Adp300wt T24 +Dox

description: Adp300wt infected C2AS12 cells 24h following addition of DM + Doxycyclin


title: Adp300mut T0

description: Adp300mut infected C2AS12 cells prior to addition of DM


title: Adp300wt T0 + Dox

description: Adp300wt infected C2AS12 cells + doxyclin prior to addition of DM


title: Adp300mut T24

description: Adp300mut infected C2AS12 cells 24h following addition of DM


title: rpn11D122E_prof_rep2

status: Public on Feb 28 2006

city: Boston

first: Pamela

middle: A

last: Silver

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description:
Grown at 25C

See Casolari et al Cell 2004 for transcriptional profiling protocols.

data_processing: Log2 ratio representing experimental channel over reference channel

source_name: Wild type

tag: PSY3337 (sDL205) MATalpha his3∆1 leu2∆0 ura3∆0 MET15/met15∆0 LYS2/lys2∆0 mpl1∆::KanR [pDL96 (LEU-CEN-RPN11)]

tag: PSY3336 (sDL204) MATalpha his3∆1 leu2∆0 ura3∆0 MET15/met15∆0 LYS2/lys2∆0 mpl1∆::KanR [pDL94 (LEU-CEN-rpn11D122E)]


title: rpt1S_prof_rep3

description:
Grown at 30C.
See Casolari et al Cell 2004 for transcriptional profiling protocols.


title: spt23tsA_prof_rep2

description:
Grown at 25C with 6hr shift to 37C.
See Casolari et al Cell 2004 for transcriptional profiling protocols.

tag: PSY3160 MATa ura3∆0 leu2∆0 trp1∆63 his3∆200 met? lys2∆0 mga2∆::HIS3 spt23∆::HIS3 <SPT23 TRP1>

source_name: spt23ts MATA

tag: PSY3161 MATa ura3∆0 leu2∆0 trp1∆63 his3∆200 met? lys2∆0 mga2∆::HIS3 spt23∆::HIS3 <spt23ts TRP1>


title: spt23tsA_prof_rep3


title: spt23tsA_prof_rep1

description: Grown at 25C with 6hr shift to 37C. See Casolari et al Cell 2004 for transcriptional profiling protocols.


title: rpn11D122E_prof_rep1

description:
Grown at 25C
See Casolari et al Cell 2004 for transcriptional profiling protocols.


title: pre1-1_prof_rep3

description: See Casolari et al Cell 2004 for transcriptional profiling protocols.

tag: PSY3332 MATalpha ura3 leu2-3,112 his3-11,15 CanS Gal+

tag: Grown at 30C with 2hr shift to 38C

tag: PSY3331 MATalpha ura3 leu2-3,112 his3-11,15 CanS Gal+ pre1-1


title: rpt1S_prof_rep2


title: rpn11D122E_prof_rep3

source_name: Wild-type


title: rpt1S_prof_rep1


title: 32868_532

city: Moffett Field

first: Waraporn

last: Tongprasit

institute: NASA Ames Research Center

description:
"Global Identification of Noncoding RNAs in S. cerevisiae by Modulating an
Essential RNA Processing Pathway", Manoj Pratim Samanta, Waraporn
Tongprasit, Himanshu Sethi, Chen-shan Chin and Viktor Stolc, Proc. Nat.
Acad. Sci. USA

data_processing: In-house software package

source_name: cells of wild type

tag: time point = 4h


title: 32980_532

description:
"Global Identification of Noncoding RNAs in S. cerevisiae by Modulating an
Essential RNA Processing Pathway", Manoj Pratim Samanta, Waraporn
Tongprasit, Himanshu Sethi1, Chen-shan Chin and Viktor Stolc, Proc. Nat.
Acad. Sci. USA

tag: Control (time point = 30h)


title: pre1-1_prof_rep1

description:
See Casolari et al Cell 2004 for transcriptional profiling protocols.

Grown at 30C with 2hr shift to 38C


title: Spt23(710)_ChIP2_rep2

type: other

description: See Casolari et al Cell 2004 for genomic localization analysis (chip2) protocols.

molecule: other

source_name: ChIP of Spt23(710)-9myc

tag: MATalpha ura3-52 leu2∆1 trp1∆63 Spt23(710)-9myc [TRP]

source_name: Whole cell extract from Spt23(710)-9myc


title: npl4-1_prof_rep1

tag: PSY3322 MATalpha ura3-52 leu2∆1 trp1∆63

tag: grown at 25C with 1hr shift to 37C

tag: PSY3323 MATalpha ura3-52 leu2∆1 trp1∆63 Npl4-1


title: Spt23(710)A_ChIP2_rep2

source_name: ChIP of Spt23(710)-9myc (matA)

tag: MATa ura3-52 leu2∆1 trp1∆63 Spt23(710)-9myc [TRP]

source_name: Whole cell extract from Spt23(710)-9myc (matA)


title: Spt23(710)_ChIP2_rep1


title: 32899_532

tag: Time point = 21h


title: Spt23(710)_ChIP2_rep3


title: Rpn11_ChIP2_rep2

source_name: ChiP of Rpn11-9myc

tag: MATalpha ura3-52 leu2∆1 trp1∆63 Rpn11-9myc [TRP1]

source_name: Whole cell extract from Rpn11-9myc


title: pre1-1_prof_rep2


title: Rpn11_ChIP2_rep3

source_name: ChIP of Rpn11-9myc


title: Pre1_ChIP2_rep2

source_name: ChIP of Pre1-9myc

tag: MATalpha ura3-52 leu2∆1 trp1∆63 Pre1-9myc [TRP1]

source_name: Whole cell extract from Pre1-9myc


title: 32927_532

tag: Time point = 30h


title: Spt23(710)A_ChIP2_rep1


title: 32981_532

tag: Time point = 0


title: 32876_532

tag: Time point = 7h


title: Rpt1_ChIP2_rep2

source_name: ChIP of Rpt1-9myc

tag: MATalpha ura3-52 leu2∆1 trp1∆63 Rpt1-9myc [TRP1]

source_name: Whole cell extract from Rpt1-9myc


title: Rpt1_ChIP2_rep3


title: Spt23(710)A_ChIP2_rep3


title: 32863_532

tag: Time point = 16h


title: 32889_532

tag: Time point = 12h


title: MGAS9887_OD=0.4_1b

city: Houston

first: Stephen

middle: B.

last: Beres

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

institute: Houston Methodist Research Institute

description: Hybridization data from custom Affymetrix chip was masked to include only probe sets designed relative to the GAS metagenome sequence data

hyb_protocol: Hybridization was performed as described by Graham et. al., American Journal of Pathology, 2005 166 #2 pg. 455-465

scan_protocol: Scanning was performed as described by Graham et. al., American Journal of Pathology, 2005 166 #2 pg. 455-465

data_processing: Data were normalized using dchip 2005 software using the PM-MM model-based expression index

label: biotin-ddUTP, fluorescent labeling was performed by the NIAID Affymetrix core facility

organism: Streptococcus sp. 'group A'

source_name: Group A Streptococcus

label_protocol: Labeling was performed as described by Graham et. al., American Journal of Pathology, 2005 166 #2 pg. 455-465

growth_protocol: Medium = Todd Hewit broth supplemented with 2% w/v yeast extract (THY broth)

extract_protocol: Extraction was performed as described by Graham et. al., American Journal of Pathology, 2005 166 #2 pg. 455-465

tag: Serotype M3 strain MGAS9887


title: MGAS9887_OD=0.4_1a

growth_protocol:
Medium = Todd Hewit broth supplemented with 2% w/v yeast extract (THY broth)
Conditions = 37°C, atmosphere supplemented with 5% CO2, without aeration (statically)
Cells were harvested at an OD 600nm = 0.4, exponential phase growth


title: MGAS9887_OD=0.4_2a


title: MGAS9887_OD=0.4_3a


title: MGAS9887_OD=0.4_2b


title: Rpt1_ChIP2_rep1


title: MGAS315_OD=0.4_3a

tag: Serotype M3 strain MGAS315


title: Rpn11_ChIP2_rep1


title: MGAS315_OD=0.4_3b


title: Pre1_ChIP2_rep3


title: Pre1_ChIP2_rep1


title: MGAS315_OD=0.4_2b


title: MGAS315_OD=0.4_1a

growth_protocol:
Medium = Todd Hewit broth supplemented with 2% w/v yeast extract (THY broth)
Conditions = 37°C, atmosphere supplemented with 5% CO2, without aeration (statically)

tag: Serotype = M3

tag: Strain = MGAS315


title: MGAS315_OD=0.4_1b


title: MGAS315_OD=0.4_2a


title: Mock control IP, adults (2a)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54277.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Extract tot. RNA, yw, adults (2a)

tag: Extract tot. RNA, yw, adults (2a)

source_name: Mock IP RNA, adults (2)

tag: Mock IP RNA, adults (2)


title: dPum-TAP IP, adults (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52987.gif; format: GIF

source_name: Extract tot. RNA, adults (1)

tag: Extract tot. RNA, adults (1)

source_name: RNA  TEV eluate, adults (1)

tag: RNA  TEV eluate, adults (1)


title: npl4-1_prof_rep2

description: Grown at 25C with 1hr shift to 37C. See Casolari et al Cell 2004 for transcriptional profiling protocols.

source_name: Wild type

tag: PSY3322 MATalpha ura3-52 leu2∆1 trp1∆63

tag: PSY3323 MATalpha ura3-52 leu2∆1 trp1∆63 Npl4-1


title: dPum-TAP IP, embryo (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55857.gif; format: GIF

source_name: Extract total RNA

tag: Extract total RNA

source_name: RNA from TEV-eluate

tag: RNA from TEV-eluate


title: spt23tsalpha_prof_rep3

source_name: spt23ts MATalpha

tag: PSY3365 MATalpha trp1∆63 ura3∆0 leu2∆0 his3∆200 met? mga2∆:HIS3 spt23∆:HIS3 <YCp Spt23ts TRP1>

tag: PSY3097 MATalpha trp1∆63 ura3∆0 leu2∆0 his3∆200 met? mga2∆::HIS3 spt23∆::HIS3  <YCp SPT23 URA3>


title: Mock control IP, embryo (1)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55235.gif; format: GIF

source_name: Embryo tot. RNA extract

tag: Embryo tot. RNA extract

source_name: RNA, TEV eluate

tag: RNA, TEV eluate


title: Embryo vs. mock IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55398.gif; format: GIF

source_name: Mock isolated RNA

tag: Mock isolated RNA

source_name: TAP-PumHD IP RNA (1)

tag: TAP-PumHD IP RNA (1)


title: Mock control IP, adults (2b)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54594.gif; format: GIF

source_name: Extract tot. RNA, mock (2)

tag: Extract tot. RNA, mock (2)

source_name: IP RNA, mock (2)

tag: IP RNA, mock (2)


title: Embryo vs. mock IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55858.gif; format: GIF

source_name: RNA IP mock from embryos (2)

tag: RNA IP mock from embryos (2)

source_name: RNA IP with TAP-PumHD, embryos (2)

tag: RNA IP with TAP-PumHD, embryos (2)


title: Mock control IP, embryo (2)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55399.gif; format: GIF

source_name: Extract tot. RNA (2)

tag: Extract tot. RNA (2)

source_name: RNA TEV eluate (2)

tag: RNA TEV eluate (2)


title: dPum-TAP IP, embryo (1)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54590.gif; format: GIF

source_name: Extract tot. RNA, embryo (1)

tag: Extract tot. RNA, embryo (1)

source_name: IP RNA, embryo (1)

tag: IP RNA, embryo (1)


title: spt23tsalpha_prof_rep1


title: Mga2(914)_ChIP2_rep3

source_name: ChIP of Mga2(914)-9myc

tag: MATalpha ura3-52, leu2∆1, trp1∆63, Mga2(914)-9myc [TRP]

source_name: Whole cell extract from Mga2(914)-9myc


title: Mock control IP, adults (1)

description:
Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53531.gif; format: GIF

source_name: Extract tot. RNA, yw adults (1)

tag: Extract tot. RNA, yw adults (1)

source_name: Mock IP RNA, yw adults (1)

tag: Mock IP RNA, yw adults (1)


title: Adult vs. Embryo (1R)

description:
Simple annotation: Development, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55234.gif; format: GIF

source_name: Embryo total RNA

tag: Embryo total RNA

source_name: Adult fly total RNA

tag: Adult fly total RNA


title: WT vs. Pum mutant flies (1)

description:
Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55659.gif; format: GIF

source_name: WT (yw) total RNA

tag: WT (yw) total RNA

source_name: Pum13 total RNA

tag: Pum13 total RNA


title: Adult vs. Embryo (2)

description:
Simple annotation: Development, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55661.gif; format: GIF


title: spt23tsalpha_prof_rep2

source_name: Wild type

tag: PSY3097 MATalpha trp1∆63 ura3∆0 leu2∆0 his3∆200 met? mga2∆::HIS3 spt23∆::HIS3  <YCp SPT23 URA3>

source_name: spt23ts MATalpha

tag: PSY3365 MATalpha trp1∆63 ura3∆0 leu2∆0 his3∆200 met? mga2∆:HIS3 spt23∆:HIS3 <YCp Spt23ts TRP1>


title: dPum-TAP IP, adults (3a)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54253.gif; format: GIF

source_name: Extract tot. RNA, adults (3)

tag: Extract tot. RNA, adults (3)

source_name: IP RNA, EDTA, adults (3)

tag: IP RNA, EDTA, adults (3)


title: Adult vs. Embryo (1)

description:
Simple annotation: Development, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55233.gif; format: GIF

source_name: Adult (male & female 1:1) total RNA.

tag: Adult (male & female 1:1) total RNA.

source_name: Embryo total RNA (0-16 hours)

tag: Embryo total RNA (0-16 hours)


title: dPum-TAP IP, adults (2)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53530.gif; format: GIF

source_name: Extract tot. RNA, adults (2)

tag: Extract tot. RNA, adults (2)

source_name: IP RNA, EDTA, adults (2)

tag: IP RNA, EDTA, adults (2)


title: dPum-TAP IP, adults (3b)

description:
Simple annotation: RNA coimmunoprecipitation, Identify Target Genes
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54596.gif; format: GIF

source_name: IP RNA, adults (3)

tag: IP RNA, adults (3)


title: Mga2(914)_ChIP2_rep2

description: See Casolari et al Cell 2004 for genomic localization analysis (chip2) protocols.

source_name: ChIP of Mga2(914)-9myc


title: Brain_Wake_4hr_3

status: Public on Feb 27 2006

first: John

middle: E

last: Zimmerman

address: 125 South 31st Street

department: Center for Sleep & Respiratory Neurobiology

institute: University of Pennsylvania School of Medicine

description: This is one of 3 time points (4 Hour Wake) in a study of the effects of stimulation during the active period on gene expression in the Drosophila brain.

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to 1 microarray. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

data_processing: Ten time groups were used in this study, each with three biological replicates. Seven time groups were used to determine differential gene expression between normal and sleep-deprived flies while three time groups were used as an experimental control to test for differential gene expression due to the effect of mechanical stimulation. Probe intensity data from all 30 arrays was read into the R software environment (http://www.R-project.org) directly from .CEL files using the R/AFFY package (Gautier et al., 2004). R/AFFY was also used to extract and manipulate probe level data to assess data quality and to create expression summary measures. Normalization was carried out using the robust multi-array average (RMA) method (Irizarry et al., 2003) on all probe intensity data sets together in order to form one expression measure for each gene on each array. Briefly, the RMA method adjusted the background of perfect match (PM) probes, applied a quantile normalization of the corrected PM values, and calculated final expression measures using the median polish algorithm.

source_name: Whole Brain_Wake_4hr

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 5.0 ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

growth_protocol: Females were collected as newly eclosed virgins and kept in populations of 50 flies at 25°C under 12 hour light: 12 hour dark conditions in vials containing standard cornmeal media until time of sacrifice.

extract_protocol: Total RNA was extracted from the pools of 139 (min) to 193 (max) brains using TRIZOL Reagent (U.S.Patent No.5,346,994) following the manufactrurers instructions (Invitrogen)

treatment_protocol: Animals were sacrificed by immersion in >95°C distilled water, removed from water and stored at -70 ° C until tissue dissection performed within 24 hours of sacrifice. Brains were removed from the head and cleared of surrounding tissues using forceps under a dissecting microscope under ice cold insect ringers (130 mM NaCl, 4.7 mM KCl, 1.9 mM CaCl2) and immediately placed in Trizol® Reagent (U.S.Patent No.5,346,994).

tag: Strain

value: Canton-S

tag: Gender

value: Female

tag: Age

value: 5 days

tag: Tissue

value: Whole Brain

tag: Time of Sacrifice

tag: Condition

value: Undisturbed Control


title: Brain_ZT10_0hr_3

description: This is one of 3 time points (0 Hour anchor point, ZT10) in a study of the effects of stimulation during the active period on gene expression in the Drosophila brain.

source_name: Whole Brain_No Treatment_ZT10

value: 0 Hour Control, No Treatment


title: Mga2(914)_ChIP2_rep1

tag: MATalpha ura3-52, leu2∆1, trp1∆63, Mga2(914)-9myc [TRP]

source_name: Whole cell extract from Mga2(914)-9myc


title: WT vs. Pum mutant flies (2R)

description:
Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59448.gif; format: GIF

tag: Pum13 total RNA

tag: WT (yw) total RNA


title: WT vs. Pum mutant flies (1R)

description:
Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55660.gif; format: GIF


title: Array 31045 HeLa E2F1 Sample C

type: genomic

city: Calgary

last: Bieda

state: AB

address: 3330 Hospital Dr NW

institute: University of Calgary

description: HeLa E2F1 ChIP to localize binding sites. See Bieda et al. (2006) Genome Research for information

hyb_protocol: Performed by NimbleGen using their standard procedures. Note that only ENCODE regions are included.

data_processing: by NimbleGen

label: Cy5 red

molecule: genomic DNA

source_name: Red HeLa E2F1 ChIP C

tag: Processed by NimbleGen

label: Cy3 Green

source_name: Total DNA (matched) (Green channel)


title: Brain_ZT10_0hr_1


title: WT vs. Pum mutant flies (2)

description:
Simple annotation: Mutant vs Wild-type, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59447.gif; format: GIF

source_name: WT (yw) total RNA


title: Brain_Wake_4hr_2


title: 18503

first: Andrei

middle: V

last: Tkatchenko

address: 220 Longwood Avenue, B2-201

department: Neurobiology

description: Juvenile primates develop myopia when their visual experience is degraded by lid fusion. In response to the abnormal visual input, retinal neural networks cause an excessive growth of the postequatorial segment of the eye, but the mechanism underlying this axial elongation is unknown. By combining analysis of gene expression, injection of the thymidine analog 5-bromo-2'-deoxyuridine and immunocytochemistry, we show that the retinal periphery in both juvenile rhesus macaques and green monkeys harbors a population of mitotically active neuroprogenitor cells that proliferate when the visual experience is altered by lid fusion. Furthermore, the number of dividing cells is highly correlated with the axial elongation of the eye and the resulting myopic refractive error. Thus, the retina undergoes active growth during the postnatal development of the primate eye. This growth is modulated by the visual input and accelerates considerably when the eye develops axial myopia.

data_processing: GenePix Pro 5.1, data were normalized by GAPDH

organism: Macaca mulatta

source_name: eye, retina, form deprivation

value: female

tag: Date of birth

tag: Form deprivation

tag: End of form deprivation

tag: Tissue harvest

value: retina

source_name: eye, retina, control


title: Array 31041 HeLa E2F1 Sample B

source_name: Red HeLa E2F1 ChIP B

tag: processed by NimbleGen

source_name: Cy3 Total green


title: Brain_ZT10_0hr_2


title: Brain_APStimulation_4hr_2

description: This is one of 3 time points (4 Hour Active Period Stimulation) in a study of the effects of stimulation during the active period on gene expression in the Drosophila brain.

source_name: Whole Brain_APStimulation_4hr

value: Stimulated during Active Period


title: Brain_ZT14_0hr_2

description: This is one of seven timepoints (0 Hour anchor point, ZT14) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_No Treatment_ZT14


title: Brain_Deprived_6hr_3

description: This is one of seven timepoints (6 Hour deprived) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Deprived_6hr

value: Sleep Deprived


title: Brain_ZT14_0hr_3


title: Brain_Sleeping_2hr_3

description: This is one of seven timepoints (2 Hour sleeping) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Sleeping_2hr


title: Brain_APStimulation_4hr_1

description: This is one of 3 experimental conditions(4 Hour Active Period Stimulation) in a study of the effects of stimulation during the active period on gene expression in the Drosophila brain.

value: Stmulated during active period


title: Brain_Wake_4hr_1

description: This is one of 3 timepoints (4 Hour wake) in a study of the effects of stimulation during the active period on gene expression in the Drosophila brain.


title: 18503 color swap


title: Brain_Deprived_4hr_3

description: This is one of seven timepoints (4 Hour deprived) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_deprived_4hr


title: 15103 color swap

source_name: eye, retina, left eye

source_name: eye, retina, right eye


title: Array 31017 HeLa E2F1 Sample A

source_name: E2F1 ChIP (Red channel)

tag: Arrays processed by NimbleGen

tag: processed by NimbleGen. Note that only ENCODE regions are included.


title: Brain_Sleeping_2hr_2

description: This is one of seven timepoints (2 Hour Seeping) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.

tag: Strain


title: PO47 color swap

tag: Gender


title: Brain_APStimulation_4hr_3

tag: Age


title: 15103

tag: Tissue


title: Brain_ZT14_0hr_1

source_name: Whole Brain_No treatment_ZT14

tag: Time of Sacrifice


title: PO47


title: PO49

value: male


title: Brain_Deprived_2hr_3

description: This is one of seven timepoints (2 Hour deprived) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Deprived_2hr

tag: Condition


title: PO49 color swap


title: Brain_Sleeping_6hr_3

description: This is one of seven timepoints (6 Hour Sleep) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Sleeping_6hr


title: Brain_Deprived_6hr_2

description: This is one of seven timepoints (6 Hour Deprivation) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.


title: Brain_Sleeping_2hr_1

description: This is one of seven timepoints (2 Hour Seep) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.


title: Brain_Sleeping_4hr_3

description: This is one of seven timepoints (4 Hour Sleep) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Sleeping_4hr


title: Brain_Deprived_6hr_1


title: Brain_Deprived_2hr_2

description: This is one of seven timepoints (2 Hour Deprivation) in a study of the effects of sleep deprivation on gene expression in the Drosophila brain.


title: Brain_Sleeping_4hr_2

description: This is one of seven timepoints (4 Hour Sleep) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.


title: Brain_Sleeping_4hr_1

source_name: whole brain_Sleeping_4hr


title: Brain_Sleeping_6hr_1


title: Affymetrix chip HG-U133A, siPTHrP 3

status: Public on Feb 25 2006

city: Halle (Saale)

first: Juergen

last: Dittmer

department: Clinic of Gynecology

institute: University of Halle

description: This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (3).

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.05, and alpha2=0.065

source_name: Breast cancer

extract_protocol: RNeasy

tag: Cell line


title: Brain_Deprived_2hr_1

description: This is one of seven timepoints (2 Hour Deprivation) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.


title: Brain_Deprived_4hr_1

description: This is one of seven timepoints (4 Hour Deprivation) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

source_name: Whole Brain_Deprived_4hr


title: Affymetrix chip HG-U133A, siPTHrP 2

description: This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (2).


title: Affymetrix chip HG-U133A, siLuc 3

description: This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siLuc (2).


title: 42NM CLL vs reference

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description: For all 29 specimens, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA) according to the manufacturer’s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Moreover, cRNA products were purified using RNeasy columns (Qiagen). 1 g of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and then mixed cRNAs were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized on Agilent Human 1A Oligo Microarray, ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).33 After hybridization for 17 h at 60°C, slides were washed according to Agilent SSC protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).

data_processing: linear and lowess normalization (Agilent settings)

source_name: RNA REFERENCE

tag: CLL case with unmutated IgVH gene


title: Brain_Sleeping_6hr_2


title: Affymetrix chip HG-U133A, siLuc 2


title: 49NM CLL vs reference

tag: Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment.


title: 43NM CLL vs reference


title: 70M CLL vs reference

tag: CLL case with mutated IgVH gene


title: Affymetrix chip HG-U133A, siPTHrP 1

description: This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (1).


title: 48NM CLL vs reference


title: 51NM CLL vs reference


title: 47NM CLL vs reference


title: Affymetrix chip HG-U133A

description: This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siLuc


title: 11NM CLL vs reference


title: 23NM CLL vs reference


title: 32NM CLL vs reference


title: 24NM CLL vs reference


title: 85M CLL vs reference


title: 16NM CLL vs reference


title: 26NM CLL vs reference


title: 63M CLL vs reference


title: 64M CLL vs reference


title: 51M CLL vs reference


title: 78M CLL vs reference

tag: CLL case with mutated IgVh gene


title: 7M CLL vs reference

description: fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA) according to the manufacturer’s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Moreover, cRNA products were purified using RNeasy columns (Qiagen). 1 mg of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and then mixed cRNAs were fragmented to an average size of ~50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized on Agilent Human 1A Oligo Microarray, ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).33 After hybridization for 17 h at 60°C, slides were washed according to Agilent SSC protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).

data_processing: linear and lowess normalization of raw data

source_name: RNA reference

source_name: 7M CLL

tag: B-CLL patient with mutated Ig genes


title: 59M CLL vs reference

tag: CLL with mutated IgVH gene


title: 45M CLL vs reference

tag: CLL case with IGVH mutated genes


title: 60M CLL vs reference


title: 65M CLL vs reference


title: 43M CLL vs reference

tag: CLL case with IgVH mutated gene


title: P46DR (dark reared) non-deprived visual cortex replicate 2

status: Public on Feb 24 2006

first: Marta

last: Majdan

address: 220 Longwood Ave.

description: Wild type P46 (dark reared to P42) mouse visual cortex ipsilateral to monocular enucleation

data_processing: Affymetrix Microarray Suite version 5.0

source_name: visual cortex

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

extract_protocol: 5 wild-type (C57Bl6) mice were dark reared from birth to P42, then underwent monocular enucleation at P42. They were then placed in a normal light-dark environment for 4 days, after which they were sacrificed (at P46). Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).

tag: Wild type, P46 (dark reared to P42) mouse visual cortex ipsilateral to 4 day monocular enucleation


title: 27NM CLL vs reference

description: For all 29 specimens, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA) according to the manufacturer’s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Moreover, cRNA products were purified using RNeasy columns (Qiagen). 1 mg of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and then mixed cRNAs were fragmented to an average size of ~50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized on Agilent Human 1A Oligo Microarray, ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).33 After hybridization for 17 h at 60°C, slides were washed according to Agilent SSC protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).

tag: B-CLL case with unmutated Ig


title: 5M CLL vs reference

source_name: reference

tag: Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments.


title: 44NM CLL vs reference


title: P46DR (dark reared) deprived visual cortex replicate 2

description: Wild type P46 (dark reared to P42) mouse visual cortex contralateral to monocular enucleation

tag: Wild type, P46 (dark reared to P42) mouse visual cortex contralateral to 4 day monocular enucleation


title: 5NM CLL vs reference

tag: B-CLL case with unmutated Ig genes


title: P46DR (dark reared) deprived visual cortex replicate 1


title: P104 deprived visual cortex replicate 2

description: Wild type P104 mouse visual cortex contralateral to monocular enucleation

extract_protocol: 4 wild-type (C57Bl6) mice underwent monocular enucleation at P100 and were sacrificed 4 days later at P104. Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).

tag: Wild type, P46 mouse visual cortex contralateral to 4 day monocular enucleation


title: 76M CLL vs reference


title: P104 non-deprived visual cortex replicate 3

description: Wild type P104 mouse visual cortex ipsilateral to monocular enucleation

tag: Wild type, P46 mouse visual cortex ipsilateral to 4 day monocular enucleation


title: P104 deprived visual cortex replicate 1


title: P46 non-deprived visual cortex replicate 4

description: Wild type P46 mouse visual cortex ipsilateral to monocular enucleation

extract_protocol: 5 wild-type (C57Bl6) mice underwent monocular enucleation at P42 and were sacrificed 4 days later at P46. Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).


title: P104 non-deprived visual cortex replicate 2


title: P46 non-deprived visual cortex replicate 2


title: P46DR (dark reared) non-deprived visual cortex replicate 1


title: P104 non-deprived visual cortex replicate 1


title: MGAS9887_OD=0.4_3b

description: Hybridization data from custom Affymetrix chip was masked to include only probe sets designed relative to the GAS metagenome sequence data

source_name: Group A Streptococcus

tag: Serotype M3 strain MGAS9887


title: P46 deprived visual cortex replicate 4

description: Wild type P46 mouse visual cortex contralateral to monocular enucleation


title: P46 deprived visual cortex replicate 3


title: P104 deprived visual cortex replicate 3


title: P46 deprived visual cortex replicate 2


title: P46 non-deprived visual cortex replicate 3


title: P24 non-deprived visual cortex replicate 2

description: Wild type P24 mouse visual cortex ipsilateral to monocular enucleation

extract_protocol: 4 wild-type (C57Bl6) mice underwent monocular enucleation at P20 and were sacrificed 4 days later at P24. Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).

tag: Wild type, P24 mouse visual cortex ipsilateral to 4 day monocular enucleation


title: P24 deprived visual cortex replicate 3

description: Wild type P24 mouse visual cortex contralateral to monocular enucleation

tag: Wild type, P24 mouse visual cortex contralateral to 4 day monocular enucleation


title: P24 non-deprived visual cortex replicate 4


title: P46 non-deprived visual cortex replicate 1


title: P46 deprived visual cortex replicate 1


title: P24 deprived visual cortex replicate 4


title: P24 deprived visual cortex replicate 2


title: P24 non-deprived visual cortex replicate 3


title: P24 deprived visual cortex replicate 1


title: fermentation 60 min

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 1-2-12 Kannondai

department: Applied Microbiology

country: Japan

institute: National Food Research Institute

description: fermentation 60min

hyb_protocol: DNA microarray hybridization was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual. In brief, hybridization was at 45C in a hybridization oven (model 640, Affymetrix) at 60 rpm for 16 h. The EukGE-WS2v4 fluidics protocol of the Affymetrix Microarray Suite Version 5.0 (MASv5.0) software was used to perform staining and washing procedures.

scan_protocol: The arrays were subsequently read using a GeneArray Scanner (Agilent technologies, Palo Alto, CA).

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: mRNA T128

label_protocol: Labeling was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual.

growth_protocol: Mini-scale fed-batch pre-cultivation was done using a jar fermentor (1-liter, B. E. Marubishi, Japan) and peristaltic pump (EYELA, Japan) with a sequential controller (B. E. Marubishi). After 18 h cultivation, cells in stationary phase were collected by centrifugation (2,700g for 5 min). Some of the cell pellets were suspended in 900 ml of sterilized water (4C). Cells for no-fermentation control were harvested after the fed-butch cultivation and stored at -80C until RNA extraction. (before_fermentation)

extract_protocol: Each time samples of total RNA were extracted using the hot phenol method. Poly (A)+ RNA was isolated from the total RNA by using an Oligotex® dt30 (super) mRNA purification kit (Takara, Japan) according to the manufacturer’s instructions. Yeast genome arrays (YGS98 GeneChip®, Affymetrix, Santa Clara, CA) were used as DNA microarrays in this study.

treatment_protocol: Cell pellets (11,700 OD units) were suspended in 390 ml of LF medium in a 500-ml flask and then fermented at 30C for 300 min.To investigate gene expression profiles during initial stages of dough-fermentation, cell samples for DNA microarray analysis were obtained from each culture medium at 15 min, 30 min, and 60 min.(after_15min, after_30min, after_60min)

tag: Typical commercial baker’s yeast used in Japan


title: P24 non-deprived visual cortex replicate 1


title: fermentation 15 min 2

description: fermentation 15min (replicate)


title: fermentation 30 min

description: fermentation 30min


title: P18 non-deprived visual cortex replicate 4

description: Wild type P18 mouse visual cortex ipsilateral to monocular enucleation

extract_protocol: 4 wild-type (C57Bl6) mice underwent monocular enucleation at P14 and were sacrificed 4 days later at P18. Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).

tag: Wild type, P18 mouse visual cortex ipsilateral to 4 day monocular enucleation


title: fermentation 15 min

description: fermentation 15min


title: P18 deprived visual cortex replicate 3

description: Wild type P18 mouse visual cortex contralateral to monocular enucleation

tag: Wild type, P18 mouse visual cortex contralateral to 4 day monocular enucleation


title: P18 non-deprived visual cortex replicate 5


title: P18 deprived visual cortex replicate 5


title: P18 deprived visual cortex replicate 4


title: before fermentation 2

description: before fermentation (replicate)


title: MRP29_INTEGRATED_REP2

city: Cambridge

middle: Robert

last: Pett

state: Cambridgeshire

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Medical Research Council

description: Clone MRP29 contained only integrated HPV16

data_processing: MAS5.0 transformation

source_name: Clone MRP29 generated from W12 cell line, integrated HPV16

label_protocol: Labelled cRNA was generated using the BioArray High Yield RNA Transcript Labelling Kit (Enzo)

growth_protocol: Keratinocyte cultures were supported with lethally irradiated Swiss 3T3 feeder cells and cultured in GMEM (Sigma) supplemented with 10% (v/v) FBS (Bioclear), 10-10M cholera toxin (Sigma) and 0.5ugml-1 hydrocortisone (Sigma). EGF (Sigma) at 10ng/ml was added 24-48 hours after plating.

extract_protocol: TRIzol (Invitrogen) extraction followed by cleanup with RNeasy Mini Kit (Qiagen)

tag: W12 cell line was generated via explant culture of an ectocervical biopsy diagnosed as CIN1


title: P18 non-deprived visual cortex replicate 1


title: P18 non-deprived visual cortex replicate 3


title: Smooth_muscle_carbachol_unstretched_muscle5_ArrayCH20_Cy5

status: Public on Feb 23 2006

first: Marc

middle: E.

last: Lenburg

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

description: sample is described in other fields.

hyb_protocol: The Cy3- and Cy5-labeled aRNAs were combined, dried, and  dissolved in 15 micro-liter of a hybridization cocktail composed of: 5X SSC, 0.1% SDS, 0.1 mg/mL salmon sperm DNA. The hybridization mixture was incubated at 95 degrees Celsius for 5 min., 45 degrees Celsius for 5 min, then cooled to room temperature. The mixture was pipetted onto the array and covered with a 22 mm x 22 mm coverslip. The arrays were then hybridized for 16-20 hours at 45 degrees Celsius in a humidified chamber.  The arrays were washed, with agitation on a shaker, in 2X SSC, 0.1 % SDS at 55 degrees Celsius 10 min. This was followed by washing at room temp. with agitation on a shaker with 0.1X SSC, 0.1 % SDS for 10 min, 2 x 1X SSC for 5 min each, and finally water for 10 min. The arrays were then spun dry at 900 rpm for 10 min.

data_processing: Spot intensities were determined using GenePix 1.3 as recommended by the manufacturer.  The value column corresponds to the mean signal for all pixels in the feature as determined by GenePix 1.3

organism: Bos taurus

source_name: smooth muscle from bovine trachea

label_protocol: Labeling of RNA was achieved using an Amino Allyl MessageAmp aRNA Amplification Kit (Ambion, Austin, TX) along with Cy3-and Cy5-NHS esters (Amersham Biosciences; Piscataway, NJ) following the manufacturer's protocol. RNA transcripts corresponding to the Alien sequences spotted on the array are spiked into the total RNA prior to processing.

extract_protocol: After completion of each experiment, the muscle strips were homogenized in 300 micro-liter of lysis solution with 1% 2-mercaptoethanol (GenElute Mammalian Total RNA Kit; Sigma).  Tissue homogenate was then digested with proteinase K solution (Sigma) for 10 minutes at 55 degrees Celsius followed by centrifugation at 10,000 rpm for 10 minutes at 23 degrees Celsius.  RNA extraction was carried out on the supernatant using mini columns according to the manufacturer's instructions.  The concentration of the eluted RNA was determined by ultraviolet spectrophotometry (DU-64 spectrophotometer; Beckman).   To remove any contaminating DNA, the RNA was treated with DNase I (RNase-free DNase I; Sigma) following the manufacturer's protocol.  The ImProm-II Reverse transcription system (Promega) was used for reverse transcription of the RNA.  RNA (0.25 micro-gram) was first combined with 0.5 micro-gram of random primers, and water was added to a final volume of 5 micro-liter.  The RNA/primer mixture was next incubated in a 70 degrees Celsius heat block for 5 minutes, followed by 10 minutes on ice.  The following reagents (Promega) were then added to the tube for reverse transcription, giving a final volume of 20 micro-liter:  4 micro-liter of ImProm-II 5x reaction buffer, 2.8 micro-liter of 25 mM MgCl2 (final concentration 3.5 mM), 1 micro-liter of 10mM dNTP mix (final concentration 0.5 mM), 20 units of recombinant RNasin, 1 micro-liter of ImProm-II reverse transcriptase, 1 micro-liter of 25 mM DTT (final concentration 1.25 mM), 2 micro-gram of acetylated-BSA and 2.7 micro-liter of nuclease-free water.  The reverse transcription reaction was run in a GeneAmp PCR system 2400 thermocycler (Applied Biosystems) using the following conditions as recommended by Promega:  5 minutes at 25 degrees Celsius, then 60 minutes at 42 degrees Celsius, and finally 15 minutes at 70 degrees Celsius to inactivate the reverse transcriptase enzyme.

treatment_protocol: Carbachol / No Oscillation: muscle strips were incubated in carbachol-containing PSS (1 micro-molar) without any mechanical stretch.

tag: Bovine tracheae were collected from a slaughterhouse and transported to the laboratory in ice-cold physiological salt solution.  The smooth muscle layer together with adventitia and mucosa was excised from a tracheal segment, and placed in a petri dish of cold PSS.  The mucosal and adventitial layers were dissected away from the smooth muscle layer under a microscope. Smooth muscle strips, approximately 4 mm in width, were prepared along the direction of muscle fibers.  The ends of each muscle strip were tied with surgical silk. The procedures for tissue equilibration and length manipulation have been described (Am J Physiol Cell Physiol 2004 287

value: C1697-C1708; Am J Physiol Cell Physiol 2000 279:C1375-C1384;  Am J Physiol Lung Cell Mol Physiol 1992 262:L53-L62).  Briefly, a computer program controls the sending of voltages to the length input port of the lever system at regular time intervals, thereby inducing sinusoidal oscillation of the lever arm and the muscle strip attached to the lever arm.  For length oscillation experiments, muscle strips were first stretched to 12 g and then allowed to equilibrate for 1 hr in PSS bubbled with air at 37 degrees Celsius.  The muscle strips were then activated for 3 min with K-PSS, a solution similar to PSS in composition except that 104.95 mM NaCl was substituted by an equimolar concentration of KCl.  Viable muscle strips were then allowed to relax in PSS for 15 min, and stretched to 12 g every 15 minutes during another hr of equilibration in PSS.  Muscle strips were adjusted to reference length for contraction by releasing the muscle strips quickly to 2.5 g, and then stimulated by K-PSS for 10 minutes.  Muscle strips were then allowed to relax in PSS for 15 min, and the muscle length was measured using a caliper (resolution = 0.1 mm).  Solutions were refreshed every hour, and the total duration of treatment was 4 hr.


title: P18 deprived visual cortex replicate 2


title: Smooth_muscle_saline_stretched_muscle5_ArrayCH20_Cy3

description: sample is described in other fields.

treatment_protocol: No drug / Oscillation:  muscle strips were incubated in PSS with sinusoidal length oscillation at amplitude of 10% muscle length and frequency of 1 hz.


title: Smooth_muscle_carbachol_stretched_muscle5_ArrayCH18_Cy5

description: sample is described in other fields.

treatment_protocol: Carbachol / Oscillation: muscle strips were incubated in carbachol-containing PSS (1 micro-molar) with sinusoidal length oscillation at amplitude of 10% muscle length and frequency of 1 hz.


title: Smooth_muscle_saline_unstretched_muscle5_ArrayCH19_Cy5

description: sample is described in other fields.

treatment_protocol: No drug / No Oscillation:  muscle strips were incubated in PSS without any mechanical stretch.


title: Smooth_muscle_carbachol_stretched_muscle5_ArrayCH19_Cy3

description: sample is described in other fields.


title: P18 deprived visual cortex replicate 1


title: MRP29_INTEGRATED_REP1

source_name: Clone MRP29 generated from the W12 cell line, integrated HPV16


title: P18 non-deprived visual cortex replicate 2


title: MRP20_MIXED_REP2

description: Clone MRP20 contained an intracellular mixture of episomal (approximately 5 copies per cell) and integrated HPV16

source_name: Clone MRP20 generated from the W12 cell line, mixed episomal and integrated HPV16


title: before fermentation

description: before fermentation

growth_protocol: Mini-scale fed-batch pre-cultivation was done using a jar fermentor (1-liter, B. E. Marubishi, Japan) and peristaltic pump (EYELA, Japan) with a sequential controller (B. E. Marubishi). After 18 h cultivation, cells in stationary phase were collected by centrifugation (2,700g for 5 min). Some of the cell pellets were suspended in 900 ml of sterilized water (4C). Cells for no-fermentation control were harvested after the fed-butch cultivation and stored at -80C until RNA extraction. (shima_0)

treatment_protocol: Cell pellets (11,700 OD units) were suspended in 390 ml of LF medium in a 500-ml flask and then fermented at 30C for 300 min.To investigate gene expression profiles during initial stages of dough-fermentation, cell samples for DNA microarray analysis were obtained from each culture medium at 15 min, 30 min, and 60 min.(shima_15, shima_30, shima_60)


title: MRP20_MIXED_REP1


title: W12p10_EPISOMAL_REP2

description: W12 passage 10 retained episomal HPV16 at approximately 100 copies per cell

source_name: W12 cell line at passage 10, episomal HPV16

label_protocol: Labelled cRNA was generated using the BioArray High Yield RNA Transcript Labeling Kit (Enzo)

tag: W12 cell line was generated via explant culture of an ectocervical biospy diagnosed as CIN1


title: Smooth_muscle_saline_unstretched_muscle5_ArrayCH18_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle4_ArrayCH16_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle4_ArrayCH16_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle5_ArrayCH17_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle5_ArrayCH17_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle4_ArrayCH14_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle4_ArrayCH15_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle4_ArrayCH15_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle4_ArrayCH14_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle1_ArrayCH11_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle2_ArrayCH11_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle2_ArrayCH9_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle4_ArrayCH13_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle1_ArrayCH10_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle2_ArrayCH8_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle1_ArrayCH12_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle4_ArrayCH13_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle3_ArrayCH12_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle2_ArrayCH8_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle3_ArrayCH7_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle3_ArrayCH10_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle2_ArrayCH7_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle2_ArrayCH9_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle3_ArrayCH5_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle3_ArrayCH5_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle1_ArrayCH6_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_stretched_muscle3_ArrayCH6_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle1_ArrayCH4_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle3_ArrayCH3_Cy5

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle1_ArrayCH1_Cy5

description: sample is described in other fields.


title: W12p10_EPISOMAL_REP1


title: Smooth_muscle_carbachol_stretched_muscle3_ArrayCH3_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle2_ArrayCH2_Cy5

description: sample is described in other fields.


title: Smooth_muscle_saline_unstretched_muscle2_ArrayCH2_Cy3

description: sample is described in other fields.


title: Smooth_muscle_saline_stretched_muscle1_ArrayCH1_Cy3

description: sample is described in other fields.


title: Smooth_muscle_carbachol_unstretched_muscle1_ArrayCH4_Cy3

description: sample is described in other fields.


title: 0 dyn/cm^2  2 Hz Rep 3

status: Public on Feb 22 2006

city: Durham

first: Heather

middle: Anne

last: Himburg

state: NC

address: PO Box 90281

department: Biomedical Engineering

institute: Duke Univeristy

description: Amplification with Message Amp II kit

data_processing: Lowess Normalization

organism: Sus scrofa

source_name: Sheared endothelial cells

growth_protocol: Cells were grown in M199 supplemented with antibiotic/mycotic and porcine serum.

extract_protocol: AMBION Paris kit

treatment_protocol: Cells were sheared for 24 hours at 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 2 Hz.

tag: Cultured Porcine Aortic Endothelial Cells

tag: Passages 1-6

source_name: Reference

growth_protocol: Cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum.

treatment_protocol: Static culture


title: 7.5 dyn/cm^2 2 Hz Rep 4

description: Amplified with Message Amp II kit

extract_protocol: AMBION Paris Kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 2 Hz.

tag: passages 1-6


title: 0 dyn/cm^2  3 Hz Rep 2

description: Amplification with Message Amp II kit

data_processing: Lowess normalization

treatment_protocol: Cells were sheared for 24 hours at 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal 3 Hz waveform.


title: 0 dyn/cm^2  3 Hz Rep 1

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2  2 Hz Rep 2

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2  1 Hz Rep 2

description: Amplification with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 1 Hz.


title: 0 dyn/cm^2  3 Hz Rep 3

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2 2 Hz Rep 4

description: Amplification with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 3 Hz.


title: 0 dyn/cm^2  3 Hz Rep 4

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2 1 Hz Rep 1

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2  1 Hz Rep 3

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2  0 Hz Rep 4

description: Amplification with Message AMP II kit

treatment_protocol: Cells were sheared for 24 hours at a mean of 0 dyn/cm^2 in a parallel plate flow chamber. There was minimal flow through the channel.


title: 0 dyn/cm^2  1 Hz Rep 4

description: Amplification with Message Amp II kit


title: 0 dyn/cm^2  Physiological Rep 3

description: Amplification with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a physiological waveform.


title: 0 dyn/cm^2 Physiological Rep 4

description: Amplification with Message AMP II kit

treatment_protocol: Cells were sheared for 24 hours at a mean of 0 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a physiological waveform.


title: 0 dyn/cm^2  0 Hz Rep 1

description: Amplification with Message AMP II kit


title: 0 dyn/cm^2  0 Hz Rep 2

description: Amplification with Message AMP II kit


title: 0 dyn/cm^2  0 Hz Rep 3

description: Amplification with Message AMP II kit


title: 0 dyn/cm^2 Physiological Rep 2

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2 Physiological Rep 4

description: Amplification with Message AMP II kit

source_name: sheared endothelial cells

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a physiological waveform.


title: 0 dyn/cm^2 Physiological Rep 1

description: Amplification with Message AMP II kit


title: 0 dyn/cm^2  2 Hz Rep 1

description: Amplification with Message Amp II kit


title: HCC2279

city: Bethesda

first: William

middle: Wallace

last: Lockwood

address: 50 South Drive

institute: National Human Genome Research Institute

description:
cyanine 3 = sample
cyanine 5 = reference

label: Cyanine 3

source_name: HCC2279 Adenocarcinoma Cell Line

tag: HCC2279 Adenocarcinoma Cell Line

label: cyanine 5

source_name: Male Genomic

tag: NOVAGEN POOLED MALE REFERENCE GENOMIC DNA


title: HCC827

source_name: HCC827 Adenocarcinoma Cell Line

tag: HCC827 Adenocarcinoma Cell Line

source_name: Male genomic


title: H3255

source_name: H3255 Adenocarcinoma Cell Line

tag: H3255 Adenocarcinoma Cell Line


title: HCC4066

source_name: HCC4066 Adenocarcinoma Cell Line

tag: HCC4066 Adenocarcinoma Cell Line


title: 7.5 dyn/cm^2 Physiological Rep 3

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2 3 Hz Rep 3

description: Amplification with Message AMP II kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 3 Hz.

tag: Cultured porcine aortic endothelial cells

source_name: reference


title: 7.5 dyn/cm^2 1 Hz Rep 1

description: Amplified with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was pulsatile with a sinusoidal frequency of 1 Hz.

tag: Cultured porcine aortic endothelial cells.


title: 7.5 dyn/cm^2 3 Hz Rep 2

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2  2 Hz Rep 3

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2 0 Hz Rep 3

description: Amplified with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 7.5 dyn/cm^2 in a parallel plate flow chamber. The flow was steady, laminar.


title: 7.5 dyn/cm^2 2 Hz Rep 2

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 1 Hz Rep 3

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 Physiological Rep 2

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2 2 Hz Rep 1

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 Physiological Rep 1

description: Amplification with Message AMP II kit


title: 7.5 dyn/cm^2 0 Hz Rep 1

description: Amplified with Message Amp II kit

source_name: Sheared Endothelial Cells

tag: Passage 1-6.


title: 7.5 dyn/cm^2 1 Hz Rep 2

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 physiological Rep 3

description: Amplified with Message Amp II kit

extract_protocol: Ambion PARIS kit

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was pulsatile, with a physiological waveform.

tag: Passage 1-5

treatment_protocol: static culture


title: 7.5 dyn/cm^2 1 Hz Rep 4

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 0 Hz Rep 4

description: Amplified with Message Amp II kit

tag: Passages 1-6.


title: 15 dyn/cm2 physiological Rep 4

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 physiological Rep 1

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 3 Hz Rep 2

description: Amplified with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was pulsatile, sinusoidal with a frequency of 3 Hz.


title: 15 dyn/cm2 2 Hz Rep 4

description: Amplified with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was pulsatile, sinusoidal with a frequency of 2 Hz.


title: 15 dyn/cm2 3 Hz Rep 1

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 3 Hz Rep 4

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 2 Hz Rep 3

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 physiological Rep 2

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 3 Hz Rep 3

description: Amplified with Message Amp II kit


title: 7.5 dyn/cm^2 3 Hz Rep 4

description: Amplification with Message AMP II kit


title: 15 dyn/cm2 2 Hz Rep 1

description: Amplified with Message Amp II kit


title: 15 dyn/cm2 2 Hz Rep 2

description: Amplified with Message Amp II kit


title: Cnidarian - algal symbiosis (Sym3_Cy5 vs Apo3_Cy3)_slide46

status: Public on Feb 21 2006

city: Corvallis

first: Mauricio

last: Rodriguez-Lanetty

address: 3029 Cordley Hall

department: Zoology

institute: Oregon State University

description: For statistical purposes, data was also normalized using the LOWESS transformation using the software MAANOVA (Bioconductor). But in this submission this transformation is not included. The value (Log Ratio) shown here has been normalized using only a global normalization method executed by GenePix Pro 6.0.

hyb_protocol: Array was pre-hybed  with the hybridization buffer (vial 7) from the Genisphere 3DNA 350 Kit with 0.1 mg/ml salmon sperm for 2 h at 50 degrees. cDNA hybridization was done using the same hybridization buffer (vial 7) plus blocker (supplied from Genisphere Kit). Hyb was carried out for 18h at 47 degrees. All washes were done as follow: 1) 2X SSC, 0.2% SDS at 60 degrees for 15 min; 2) 2X SSC at 23 degrees for 15 min; 3) 0.2X SSC at 23 degrees for 15 min; 4) Spin at 1000 rpm for 2 min. In the last wash after cDNA hybridization, array was dipped in Dye Saver 2 supplied from Genishere for 5 sec and spinned at 1000 rpm for 2 min.  Dye saver stops photobleaching of the dyes.

scan_protocol: Array scanned using Axon GenePix 4200  Software used GenePix Pro 6.0

organism: Anthopleura elegantissima

source_name: Symbiotic sea anemone (Sym 3)

label_protocol: Sample was labeled using genisphere 3DNA 350 labeling Kit

growth_protocol: This anemone was acclimatized in the lab after collection at 14 degrees for 5 days at a day/night cycle of 12:12 h

extract_protocol:
Trizol for total RNA and
Micro mRNA purist (Ambion) for PolyA RNA

treatment_protocol: This was a natural treatment. This anemone was found harboring algal symbionts naturally in the field (Oregon Coast)

tag: Sea anemone harboring intracellular algal symbionts (dinoflagellates

value: Symbiodinium sp)

source_name: Aposymbiotic sea anemone (Apo3)

treatment_protocol: This was a natural treatment. This anemone was found aposymbiotic (lacking algal symbionts) naturally in the field (Oregon Coast)

tag: Sea anemone (lacking intracellular algal symbionts)


title: Cnidarian - algal symbiosis (Sym5_Cy5 vs Apo5_Cy3)_slide06

data_processing: The value (Log Ratio) shown here has been normalized using only a global normalization method executed by GenePix Pro 6.0.

source_name: Symbiotic sea anemone (Sym 5)

source_name: Aposymbiotic sea anemone (Apo5)


title: Cnidarian - algal symbiosis (Apo4_Cy5 vs Sym4_Cy3) slide 18

scan_protocol: Array scanned using Axon GenePix 4200  Software used GenePix Pro 6.0  Array scanned using Axon GenePix 4200  Software used GenePix Pro 6.0

source_name: Aposymbiotic sea anemone (Apo 4)

source_name: Symbiotic sea anemone (Sym4)


title: Cnidarian - algal symbiosis (Apo2_Cy5 vs Sym2_Cy3) slide 15

source_name: Aposymbiotic sea anemone (Apo 2)

source_name: Symbiotic sea anemone (Sym2)


title: 15 dyn/cm2 0 Hz Rep 4

description: Amplified with Message Amp II kit

source_name: Sheared endothelial cells

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was steady, laminar.

source_name: Reference

treatment_protocol: Static culture


title: 15 dyn/cm2 1 Hz Rep 2

description: Amplified with Message Amp II kit

treatment_protocol: Cells were sheared for 24 hours at 15 dyn/cm^2 in a parallel plate flow chamber.  The flow was pulsatile, sinusoidal waveform with a frequency of 1 Hz.


title: 15 dyn/cm2 1 Hz Rep 4

description: Amplified with Message Amp II kit