title: YAP6-TAP SC media replicate 2

status: Public on Feb 04 2008

city: La Jolla

first: Kai

last: Tan

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

description: yeast cells untreated, enriched DNA compared to input genoimc DNA.

hyb_protocol: Cy-3 and Cy-5 labeled samples were mixed with hybridization buffer (Agilent In Situ Hybridization Kit) and co-hybridized to the Yeast Whole Genome Tiling Array (G4486A, Agilent Technologies). Slides were hybridized for 17h at 60 degree Celcius in a rotating oven, and washed

scan_protocol: Scanned on an GenePix 4000A scanner (Axon Instruments) at a 10.0 um resolution Images were quantified using GenePix Pro 6.0 software (Axon Instruments)

data_processing: Background subtraction. Background-adjusted log ratios were then corrected for cyanine-dye dependent bias using Loess normalization

organism: Saccharomyces cerevisiae

source_name: YAP6-TAP, SC media, input DNA

label_protocol: non-antibody enriched DNA sample was amplified by LM-PCR using a Cy3 label.

extract_protocol: Cells were fixed with 1% formaldehyde, lysed, and sonicated to shear DNA.  DNA fragments bound by the tagged TF were enriched by immunoprecipitation with an anti-TAP antibody (Open Biosystems). Afer reversal of crosslinking, DNA fragments were purified by phenol chloroform extraction

tag: Yeast BY4741 strain with YAP6-TAP

source_name: YAP6-TAP, SC media, anti-TAP enriched

label_protocol: Enriched DNA was amplified and Cy5-labeled by ligation-mediated PCR (LM-PCR).


title: YAP6-TAP SC media replicate 1

type: genomic

state: CA

country: USA

molecule: genomic DNA


title: Inoc-T4_vs_T0 rep3 KA

status: Public on Feb 05 2008

type: RNA

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

description: Replicate 3

hyb_protocol: Hegde et al 2000 Biotechniques 29:548-56

scan_protocol: Scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix4.1
data cleaned and formatted with in-house PERL scripts
log2 transformed using R/MAANOVA
glowess normalization using R/MAANOVA
statistically analyzed by ANOVA in SAS to calculate p-values and fold-changes

molecule: total RNA

organism: Glycine max

source_name: Pooled roots from 4-6 plants 4 days post inoc

label_protocol: Indirect incorporation using aa-dUTP, detailed in Zou et al 2005 MPMI 18:1161-1174

growth_protocol:
Growth Chamber (30C)
16 hour daylength: 60% humidity

extract_protocol: Trizol Phase Lock Gel RNA Extraction

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
1 ml pipetted over 1:3 perlite:vermiculite growth medium
4 days post inoculation

tag: Cultivar

value: Supernodulating GmNARKmutant SS2-2

tag: 4 days post inoculation

tag: Age

value: 6 days

source_name: Pooled roots from 4-6 plants T0

treatment_protocol:
Bradyrhizobium japonicum strain USDA110
OD600: 0.01 in water
sprayed over roots
then immediately collected

value: 2 days


title: T0_vs_T16 mock rep2 KA

description: Replicate 2

source_name: Pooled roots from 4-6 plants 16 days post mock inoc

treatment_protocol: water

tag: 16 days post mock inoculation

value: 18 days


title: YAP6-TAP 0.4mM CDDP treatment replicate 1

description: yeast cells treated with 0.4mM CDDP, enriched DNA compared to input genomic DNA.

source_name: YAP6-TAP, 0.4mM CDDP, input DNA

source_name: YAP6-TAP, 0.4mM CDDP, anti-TAP enriched


title: YAP5-TAP SC media replicate 1

source_name: YAP5-TAP, SC media, input DNA

tag: Yeast BY4741 strain with YAP5-TAP

source_name: YAP5-TAP, SC media, anti-TAP enriched


title: YAP6-TAP 1.4mM CDDP treatment replicate 2

description: yeast cells treated with 1.4mM CDDP, enriched DNA compared to input genomic DNA.

source_name: YAP6-TAP, 1.4mM CDDP, input DNA

source_name: YAP6-TAP, 1.4mM CDDP, anti-TAP enriched


title: YAP6-TAP 7.1mM MMS treatment replicate 1

description: yeast cells treated with 7.1mM MMS, enriched DNA compared to input genoimc DNA.

source_name: YAP6-TAP, 7.1mM MMS, input DNA

source_name: YAP6-TAP, 7.1mM MMS, anti-TAP enriched


title: Wild type 4.7mM MMS treatment replicate 4

description: yeast cells treated with 4.7mM MMS compared to untreated cells

hyb_protocol: Cy-3 and Cy-5 labeled samples were mixed with hybridization buffer (Agilent In Situ Hybridization Kit) and co-hybridized to the Yeast Oligo Microarray (G4140A, Agilent Technologies). Slides were hybridized for 17h at 60 degree Celcius in a rotating oven, and washed

molecule: polyA RNA

source_name: Wild type grown in SC media for 60 min

label_protocol: Reverse transcription and Labeling of cDNA was performed by direct incorporation using a CyScribe First-Strand cDNA Labeling Kit (Amersham Biosciences)

extract_protocol: Hot acid phenol extraction, mRNA purified with Poly(A)Pure kit(Ambion)

tag: wild type yeast strain BY4741

source_name: Wild type grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP6-TAP 0.4mM CDDP treatment replicate 2


title: Inoc-T4_vs_T0 rep4 KA

description: Replicate 4


title: YAP6-TAP 1.4mM CDDP treatment replicate 1


title: YAP5-TAP 4.7mM MMS treatment replicate 2

description: yeast cells treated with 4.7mM MMS, enriched DNA compared to input genomic DNA.

source_name: YAP5-TAP, 4.7mM MMS, input DNA

source_name: YAP5-TAP, 4.7mM MMS, anti-TAP enriched


title: YAP5-TAP SC media replicate 2


title: YAP6-TAP 7.1mM MMS treatment replicate 2


title: YAP6-TAP 4.7mM MMS treatment replicate 1

source_name: YAP6-TAP, 4.7mM MMS, input DNA

source_name: YAP6-TAP, 4.7mM MMS, anti-TAP enriched


title: Inoc-T4_vs_T0 rep2 KA

description: Replicate 2

source_name: Pooled roots from 4-6 plants 4 days post inoc


title: YAP6-TAP 4.7mM MMS treatment replicate 2


title: Wild type 7.1mM MMS treatment replicate 4

description: yeast cells treated with 7.1mM MMS compared to untreated cells

source_name: Wild type grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP5-TAP 4.7mM MMS treatment replicate 1


title: YAP5-TAP 0.4mM CDDP treatment replicate 2

source_name: YAP5-TAP, 0.4mM CDDP, input DNA

source_name: YAP5-TAP, 0.4mM CDDP, anti-TAP enriched


title: YAP5-TAP 7.1mM MMS treatment replicate 2

source_name: YAP5-TAP, 7.1mM MMS, input DNA

source_name: YAP5-TAP, 7.1mM MMS, anti-TAP enriched


title: Wild type 4.7mM MMS treatment replicate 3


title: YAP6 deletion 7.1mM MMS treatment replicate 2

source_name: YAP6 deletion grown in SC media for 60 min

tag: Yeast BY4741 strain with YAP6 deletion

source_name: YAP6 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: Wild type 7.1mM MMS treatment replicate 1


title: YAP5-TAP 7.1mM MMS treatment replicate 1


title: Wild type 7.1mM MMS treatment replicate 3


title: T0_vs_T16 mock rep3 KA

description: Replicate 3

source_name: Pooled roots from 4-6 plants T0

source_name: Pooled roots from 4-6 plants 16 days post mock inoc


title: YAP2-TAP SC media replicate 2

source_name: YAP2-TAP, SC media, input DNA

tag: Yeast BY4741 strain with YAP2-TAP

source_name: YAP2-TAP, SC media, anti-TAP enriched


title: YAP6 deletion 4.7mM MMS treatment replicate 2

source_name: YAP6 deletion grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP2-TAP 4.7mM MMS treatment replicate 2

source_name: YAP2-TAP, 4.7mM MMS, input DNA

source_name: YAP2-TAP, 4.7mM MMS, anti-TAP enriched


title: Wild type 4.7mM MMS treatment replicate 2

source_name: Wild type grown in SC media for 60 min

source_name: Wild type grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP6 deletion 0.4mM CDDP treatment replicate 1

description: yeast cells treated with 0.4mM CDDP compared to untreated cells

source_name: YAP6 deletion grown in SC media supplemented with 0.4mM CDDP for 60min


title: YAP2-TAP SC media replicate 1


title: YAP6 deletion 7.1mM MMS treatment replicate 1


title: YAP2-TAP 4.7mM MMS treatment replicate 1


title: YAP2-TAP 0.4mM CDDP treatment replicate 2

source_name: YAP2-TAP, 0.4mM CDDP, input DNA

source_name: YAP2-TAP, 0.4mM CDDP, anti-TAP enriched


title: YAP2-TAP 7.1mM MMS treatment replicate 2

source_name: YAP2-TAP, 7.1mM MMS, input DNA

source_name: YAP2-TAP, 7.1mM MMS, anti-TAP enriched


title: YAP6 deletion 1.4mM CDDP treatment replicate 1

description: yeast cells treated with 1.4mM CDDP compared to untreated cells

source_name: YAP6 deletion grown in SC media supplemented with 1.4mM CDDP for 60min


title: YAP2-TAP 0.4mM CDDP treatment replicate 1


title: YAP6 deletion 4.7mM MMS treatment replicate 1

source_name: YAP6 deletion grown in SC media for 60 min


title: Wild type 4.7mM MMS treatment replicate 1


title: YAP6 deletion 1.4mM CDDP treatment replicate 2


title: YAP5 deletion 4.7mM MMS treatment replicate 1

source_name: YAP5 deletion grown in SC media supplemented with 4.7mM MMS for 60min

tag: Yeast BY4741 strain with YAP5 deletion

source_name: YAP5 deletion grown in SC media for 60 min


title: YAP5-TAP 1.4mM CDDP treatment replicate 2

source_name: YAP5-TAP, 1.4mM CDDP, input DNA

source_name: YAP5-TAP, 1.4mM CDDP, anti-TAP enriched


title: YAP6 deletion 0.4mM CDDP treatment replicate 2


title: YAP4 deletion 1.4mM CDDP treatment replicate 2

source_name: YAP4 deletion grown in SC media for 60 min

tag: Yeast BY4741 strain with YAP4 deletion

source_name: YAP4 deletion grown in SC media supplemented with 1.4mM CDDP for 60min


title: YAP5-TAP 1.4mM CDDP treatment replicate 1


title: Wild type 7.1mM MMS treatment replicate 2

source_name: Wild type grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP2-TAP 7.1mM MMS treatment replicate 1


title: YAP5 deletion 7.1mM MMS treatment replicate 2

source_name: YAP5 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP1-TAP SC media replicate 2

source_name: YAP1-TAP, SC media, input DNA

tag: Yeast BY4741 strain with YAP1-TAP

source_name: YAP1-TAP, SC media, anti-TAP enriched


title: YAP1-TAP 4.7mM MMS treatment replicate 1

source_name: YAP1-TAP, 4.7mM MMS, input DNA

source_name: YAP1-TAP, 4.7mM MMS, anti-TAP enriched


title: YAP2 deletion 4.7mM MMS treatment replicate 2

source_name: YAP2 deletion grown in SC media for 60 min

tag: Yeast BY4741 strain with YAP2 deletion

source_name: YAP2 deletion grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP4 deletion 1.4mM CDDP treatment replicate 1


title: YAP2 deletion 0.4mM CDDP treatment replicate 2

source_name: YAP2 deletion grown in SC media supplemented with 0.4mM CDDP for 60min


title: YAP4 deletion 7.1mM MMS treatment replicate 1

source_name: YAP4 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP5 deletion 7.1mM MMS treatment replicate 1


title: YAP4 deletion 4.7mM MMS treatment replicate 2

source_name: YAP4 deletion grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP2-TAP 1.4mM CDDP treatment replicate 2

source_name: YAP2-TAP, 1.4mM CDDP, input DNA

source_name: YAP2-TAP, 1.4mM CDDP, anti-TAP enriched


title: YAP1-TAP SC media replicate 1


title: YAP5 deletion 4.7mM MMS treatment replicate 2

source_name: YAP5 deletion grown in SC media for 60 min

source_name: YAP5 deletion grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP4 deletion 7.1mM MMS treatment replicate 2

source_name: YAP4 deletion grown in SC media for 60 min


title: YAP2 deletion 7.1mM MMS treatment replicate 2

source_name: YAP2 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP2 deletion 0.4mM CDDP treatment replicate 1


title: YAP2 deletion 1.4mM CDDP treatment replicate 1

source_name: YAP2 deletion grown in SC media supplemented with 1.4mM CDDP for 60min


title: YAP2 deletion 1.4mM CDDP treatment replicate 2


title: YAP1 deletion 7.1mM MMS treatment replicate 3

source_name: YAP1 deletion grown in SC media for 60 min

tag: Yeast BY4741 strain with YAP1 deletion

source_name: YAP1 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP4 deletion 4.7mM MMS treatment replicate 1


title: YAP4 deletion 0.4mM CDDP treatment replicate 2

source_name: YAP4 deletion grown in SC media supplemented with 0.4mM CDDP for 60min


title: YAP2 deletion 7.1mM MMS treatment replicate 1


title: YAP1-TAP 7.1mM MMS treatment replicate 2

source_name: YAP1-TAP, 7.1mM MMS, input DNA

source_name: YAP1-TAP, 7.1mM MMS, anti-TAP enriched


title: YAP2-TAP 1.4mM CDDP treatment replicate 1


title: YAP1-TAP 1.4mM CDDP treatment replicate 2

source_name: YAP1-TAP, 1.4mM CDDP, input DNA

source_name: YAP1-TAP, 1.4mM CDDP, anti-TAP enriched


title: YAP1 deletion 4.7mM MMS treatment replicate 4

source_name: YAP1 deletion grown in SC media supplemented with 4.7mM MMS for 60min


title: YAP1 deletion 4.7mM MMS treatment replicate 1


title: YAP4 deletion 0.4mM CDDP treatment replicate 1


title: YAP2 deletion 4.7mM MMS treatment replicate 1

source_name: YAP2 deletion grown in SC media supplemented with 4.7mM MMS for 60min

source_name: YAP2 deletion grown in SC media for 60 min


title: YAP1 deletion 7.1mM MMS treatment replicate 4


title: YAP1-TAP 4.7mM MMS treatment replicate 2

source_name: YAP1-TAP, 4.7mM MMS, input DNA

source_name: YAP1-TAP, 4.7mM MMS, anti-TAP enriched


title: YAP4-TAP SC media replicate 2

source_name: YAP4-TAP, SC media, input DNA

tag: Yeast BY4741 strain with YAP4-TAP

source_name: YAP4-TAP, SC media, anti-TAP enriched


title: YAP1-TAP 1.4mM CDDP treatment replicate 1


title: YAP1-TAP 7.1mM MMS treatment replicate 1


title: YAP1 deletion 7.1mM MMS treatment replicate 2


title: YAP1-TAP 0.4mM CDDP treatment replicate 1

source_name: YAP1-TAP, 0.4mM CDDP, input DNA

source_name: YAP1-TAP, 0.4mM CDDP, anti-TAP enriched


title: YAP1-TAP 0.4mM CDDP treatment replicate 2


title: YAP1 deletion 4.7mM MMS treatment replicate 2


title: YAP1 deletion 4.7mM MMS treatment replicate 3


title: YAP1 deletion 0.4mM CDDP treatment replicate 2

source_name: YAP1 deletion grown in SC media supplemented with 0.4mM CDDP for 60min


title: YAP1 deletion 1.4mM CDDP treatment replicate 2

source_name: YAP1 deletion grown in SC media for 60 min

source_name: YAP1 deletion grown in SC media supplemented with 1.4mM CDDP for 60min


title: YAP4-TAP SC media replicate 1


title: Wild type 1.4mM CDDP treatment replicate 4

source_name: Wild type grown in SC media for 60 min

source_name: Wild type grown in SC media supplemented with 1.4mM CDDP for 60min


title: YAP1 deletion 7.1mM MMS treatment replicate 1

source_name: YAP1 deletion grown in SC media supplemented with 7.1mM MMS for 60min


title: YAP1 deletion 1.4mM CDDP treatment replicate 1


title: T0_vs_T16 mock rep1 KA

description: Replicate 1

source_name: Pooled roots from 4-6 plants T0

source_name: Pooled roots from 4-6 plants 16 days post mock inoc


title: YAP1 deletion 1.4mM CDDP treatment replicate 3


title: YAP1 deletion 1.4mM CDDP treatment replicate 4


title: YAP1 deletion 0.4mM CDDP treatment replicate 4


title: YAP1 deletion 0.4mM CDDP treatment replicate 3


title: YAP4-TAP 4.7mM MMS treatment replicate 2

source_name: YAP4-TAP, 4.7mM MMS, input DNA

source_name: YAP4-TAP, 4.7mM MMS, anti-TAP enriched


title: YAP4-TAP 4.7mM MMS treatment replicate 1


title: Wild type 0.4mM CDDP treatment replicate 4

source_name: Wild type grown in SC media supplemented with 0.4mM CDDP for 60min


title: Wild type 0.4mM CDDP treatment replicate 1


title: YAP4-TAP 0.4mM CDDP treatment replicate 1

source_name: YAP4-TAP, 0.4mM CDDP, input DNA

source_name: YAP4-TAP, 0.4mM CDDP, anti-TAP enriched


title: Wild type 1.4mM CDDP treatment replicate 2


title: YAP5-TAP 0.4mM CDDP treatment replicate 1

source_name: YAP5-TAP, 0.4mM CDDP, input DNA

source_name: YAP5-TAP, 0.4mM CDDP, anti-TAP enriched


title: YAP4-TAP 7.1mM MMS treatment replicate 1

source_name: YAP4-TAP, 7.1mM MMS, input DNA

source_name: YAP4-TAP, 7.1mM MMS, anti-TAP enriched


title: YAP1 deletion 0.4mM CDDP treatment replicate 1

source_name: YAP1 deletion grown in SC media supplemented with 0.4mM CDDP for 60min


title: Wild type 0.4mM CDDP treatment replicate 3


title: YAP4-TAP 0.4mM CDDP treatment replicate 2


title: Whole ovary from 8 Month Old Wild Type mice_03, biological rep3

city: Montreal

first: JAYAPRAKASH

last: ARAVINDAKSHAN

address: 110 Ave des Pins Ouest

country: Canada

institute: Clinical Research Institute of Montreal

description: Wild Type mice was euthanized with CO2 and whole ovaries were collected and immediately preserved in liquid nitrogen before RNA isolation.

hyb_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

scan_protocol: GeneChips were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: MAS5-calculated Signal intensity

label: biotin

organism: Mus musculus

source_name: 8 Month Wild Type Ovary_03

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Wild Type ovaries were carefully disected and immediately flash frozen in liquid nitrogen before RNA isolation.

tag: Genotype

value: Wild Type


title: YAP4-TAP 7.1mM MMS treatment replicate 2


title: YAP4-TAP 1.4mM CDDP treatment replicate 2

source_name: YAP4-TAP, 1.4mM CDDP, input DNA

source_name: YAP4-TAP, 1.4mM CDDP, anti-TAP enriched


title: Wild type 0.4mM CDDP treatment replicate 2

source_name: Wild type grown in SC media for 60 min


title: testis_orl_GD17_E

status: Public on Feb 03 2008

city: Wilmington

first: Julia

middle: S.

last: Barthold

state: DE

address: 1600 Rockland Road

department: Urology

institute: Nemours/AI duPont Hospital for Children

hyb_protocol: Hybridization, washing and staining were performed according to the standard Affymetrix protocol with the Affymetrix Hybridization Oven 640 and GeneChip Fluidics Station.  This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.

scan_protocol: GeneChips were scanned with the Affymetix GeneArray Scanner.  This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.

data_processing: The GC-RMA algorithm was used within the AffylmGUI package of Bioconductor to calculate log2 expression values. CEL files from all samples from the same tissue in the series were input together.

organism: Rattus norvegicus

source_name: testis, LE/orl fetus at gestational day 17 - fetus E

label_protocol:
Biotinylated cRNA was prepared as follows.  1 ug total RNA was labeled with the Affymetrix GeneChip One-Cycle cDNA synthesis Kit, according to the manufacturer's instructions.
Performed according to the standard Affymetrix protocol.  This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and contaminating DNA was removed with the RNAse-free DNase Set (Qiagen), both according to the manufacturer's instructions.

treatment_protocol: The lower half of a fetus was placed in RNAlater.  After storage at 4'C for at least 24 hours, the gubernaculum was dissected and placed in lysis buffer from the RNeasy Mini Kit (Qiagen)

tag: Strain

value: LE/orl

tag: Gender

value: male

value: Gestational day 17

tag: Tissue

value: testis

tag: Side

value: left


title: Wild type 1.4mM CDDP treatment replicate 1

source_name: Wild type grown in SC media supplemented with 1.4mM CDDP for 60min


title: Wild type 1.4mM CDDP treatment replicate 3


title: Whole ovary from 8 Month Old FORKO mice_02, biological rep2

source_name: 8 Month FORKO Ovary_02

value: Genotype:FORKO (FSH Recptor Knock Out). FORKO mice was generated by deleting all variants of FSH-Receptor


title: Whole ovary from 8 Month Old FORKO mice_01, biological rep1

source_name: 8 Month FORKO Ovary_01

value: FORKO (FSH Recptor Knock Out). FORKO mice was generated by deleting all variants of FSH-Receptor


title: testis_orl_GD19_D

source_name: testis, LE/orl fetus at gestational day 19 - fetus D

tag: Age

value: Gestational day 19


title: testis_orl_GD17_A

source_name: testis, LE/orl fetus at gestational day 17 - fetus A


title: YAP4-TAP 1.4mM CDDP treatment replicate 1


title: Whole ovary from 8 Month Old FORKO mice_03, biological rep3

source_name: 8 Month FORKO Ovary_03


title: testis_orl_GD17_D

source_name: testis, LE/orl fetus at gestational day 17 - fetus D


title: testis_orl_GD19_C

source_name: testis, LE/orl fetus at gestational day 19 - fetus C


title: testis_orl_GD17_C

source_name: testis, LE/orl fetus at gestational day 17 - fetus C


title: testis_orl_GD19_B

source_name: testis, LE/orl fetus at gestational day 19 - fetus B


title: testis_orl_GD17_B

source_name: testis, LE/orl fetus at gestational day 17 - fetus B


title: testis_wt_GD17_E

source_name: testis, LE/wt fetus at gestational day 17 - fetus E

value: LE/wt


title: testis_wt_GD19_D

source_name: testis, LE/wt fetus at gestational day 19 - fetus D


title: testis_wt_GD17_B

source_name: testis, LE/wt fetus at gestational day 17 - fetus B


title: testis_wt_GD17_C

source_name: testis, LE/wt fetus at gestational day 17 - fetus C


title: testis_orl_GD19_E

source_name: testis, LE/orl fetus at gestational day 19 - fetus E


title: gubernaculum_orl_GD20_male_left_A

source_name: gubernaculum, LE/orl male fetus at gestational day 20 - fetus A

label_protocol:
Biotinylated cRNA was prepared as follows.  30 ng total RNA was amplified and labeled with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit, according to the manufacturer's instructions.
Performed according to the standard Affymetrix protocol.  This was performed at DuPont Haskell Laboratory for Health and Environmental Sciences.

value: Gestational day 20

value: gubernaculum


title: gubernaculum_orl_GD19_male_left_D

source_name: gubernaculum, LE/orl male fetus at gestational day 19 - fetus D


title: testis_wt_GD17_D

source_name: testis, LE/wt fetus at gestational day 17 - fetus D


title: testis_orl_GD19_A

source_name: testis, LE/orl fetus at gestational day 19 - fetus A


title: gubernaculum_orl_GD20_male_left_B

source_name: gubernaculum, LE/orl male fetus at gestational day 20 - fetus B


title: testis_wt_GD19_C

source_name: testis, LE/wt fetus at gestational day 19 - fetus C


title: gubernaculum_orl_GD20_male_left_C

source_name: gubernaculum, LE/orl male fetus at gestational day 20 - fetus C


title: gubernaculum_orl_GD19_male_left_C

source_name: gubernaculum, LE/orl male fetus at gestational day 19 - fetus C


title: testis_wt_GD19_A

source_name: testis, LE/wt fetus at gestational day 19 - fetus A


title: testis_wt_GD17_A

source_name: testis, LE/wt fetus at gestational day 17 - fetus A


title: gubernaculum_orl_GD20_male_right_A

value: right


title: Whole ovary from 8 Month Old Wild Type mice_02, biological rep2

source_name: 8 Month Wild Type Ovary_02


title: gubernaculum_orl_GD19_male_left_A

source_name: gubernaculum, LE/orl male fetus at gestational day 19 - fetus A


title: testis_wt_GD19_E

source_name: testis, LE/wt fetus at gestational day 19 - fetus E


title: gubernaculum_orl_GD20_male_right_C


title: gubernaculum_orl_GD20_male_left_D

source_name: gubernaculum, LE/orl male fetus at gestational day 20 - fetus D


title: gubernaculum_orl_GD18_male_left_C

source_name: gubernaculum, LE/rol male fetus at gestational day 18 - fetus C

value: Gestational day 18


title: gubernaculum_orl_GD18_male_left_A

source_name: gubernaculum, LE/orl male fetus at gestational day 18 - fetus A


title: Whole ovary from 8 Month Old Wild Type mice_01, biological rep1

source_name: 8 Month Wild Type Ovary_01


title: gubernaculum_orl_GD18_male_left_B

source_name: gubernaculum, LE/orl male fetus at gestational day 18 - fetus B


title: gubernaculum_wt_GD19_male_left_D

source_name: gubernaculum, LE/wt male fetus at gestational day 19 - fetus D


title: gubernaculum_wt_GD20_male_right_B

source_name: gubernaculum, LE/wt male fetus at gestational day 20 - fetus B


title: gubernaculum_wt_GD20_male_right_C

source_name: gubernaculum, LE/wt male fetus at gestational day 20 - fetus C


title: testis_wt_GD19_B

source_name: testis, LE/wt fetus at gestational day 19 - fetus B


title: gubernaculum_orl_GD20_male_right_B

source_name: gubernaculum, LE/orl male fetus at gestational day 20 - fetus B


title: gubernaculum_wt_GD20_male_left_D

source_name: gubernaculum, LE/wt male fetus at gestational day 20 - fetus D


title: gubernaculum_wt_GD20_male_left_B


title: gubernaculum_orl_GD19_male_left_B

source_name: gubernaculum, LE/orl male fetus at gestational day 19 - fetus B


title: gubernaculum_wt_GD20_male_right_A

source_name: gubernaculum, LE/wt male fetus at gestational day 20 - fetus A


title: gubernaculum_wt_GD20_male_left_A


title: gubernaculum_wt_GD18_male_left_D

source_name: gubernaculum, LE/wt male fetus at gestational day 18 - fetus D


title: gubernaculum_wt_GD20_male_left_C


title: gubernaculum_wt_GD19_male_left_C

source_name: gubernaculum, LE/wt male fetus at gestational day 19 - fetus C


title: gubernaculum_orl_GD18_male_left_D

source_name: gubernaculum, LE/orl male fetus at gestational day 18 - fetus D


title: gubernaculum_wt_GD18_male_left_C

source_name: gubernaculum, LE/wt male fetus at gestational day 18 - fetus C


title: gubernaculum_wt_GD19_male_left_A

source_name: gubernaculum, LE/wt male fetus at gestational day 19 - fetus A


title: gubernaculum_wt_GD18_male_left_A

source_name: gubernaculum, LE/wt male fetus at gestational day 18 - fetus A


title: gubernacula_wt_GD18_female_B

source_name: gubernacula, LE/wt female fetus at gestational day 18 - fetus B

value: female

value: right and left


title: gubernacula_wt_GD18_female_C

source_name: gubernacula, LE/wt female fetus at gestational day 18 - fetus C


title: gubernacula_wt_GD18_female_A

source_name: gubernacula, LE/wt female fetus at gestational day 18 - fetus A


title: gubernaculum_wt_GD18_male_left_B

source_name: gubernaculum, LE/wt male fetus at gestational day 18 - fetus B


title: gubernaculum_wt_GD19_male_left_B

source_name: gubernaculum, LE/wt male fetus at gestational day 19 - fetus B


title: patient PV18 - hyb 2

status: Public on Feb 01 2008

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: Cirrhotic liver taken away from a Hepatocellular Carcinoma

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

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

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

organism: Homo sapiens

source_name: HCV-associated peritumoral cirrhosis liver

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

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

tag: 68 years old woman with hepatitis C


title: patient PV20 - hyb 2

tag: 79 years old woman with hepatitis C


title: patient PV17 - hyb 2

tag: 74 years old woman with hepatitis C


title: patient PV17 - hyb 3


title: patient PV17 - hyb 1


title: patient PV20 - hyb 1


title: patient PV18 - hyb 3


title: gubernacula_wt_GD18_female_D

source_name: gubernacula, LE/wt female fetus at gestational day 18 - fetus D


title: patient PV19 - hyb 2

tag: 80 years old man with hepatitis C


title: patient PV19 - hyb 3


title: patient PV19 - hyb 1


title: patient PV16 - hyb 3

tag: 73 years old woman with hepatitis C


title: patient PV16 - hyb 1


title: patient PV15 - hyb 2

tag: 69 years old man with hepatitis C


title: patient PV16 - hyb 2


title: patient PV15 - hyb 1


title: patient PV14 - hyb 3

tag: 66 years old man with hepatitis C


title: patient PV15 - hyb 3


title: patient PV12 - hyb 3

tag: 70 years old man with hepatitis C


title: patient PV13 - hyb 3

tag: 71 years old man with hepatitis C


title: patient PV13 - hyb 1


title: patient PV14 - hyb 1


title: patient PV11 - hyb 2

tag: 65 years old man with hepatitis C


title: patient PA9 - hyb 2

source_name: alcoholism-associated peritumoral cirrhosis liver

tag: 62 years old man with alcoholic liver disease


title: patient PV11 - hyb 1


title: patient PA8 - hyb 3

tag: 74 years old man with alcoholic liver disease


title: patient PA10 - hyb 2

tag: 55 years old man with alcoholic liver disease


title: patient PA9 - hyb 3


title: patient PA7 - hyb 3

tag: 73 years old woman with alcoholic liver disease


title: patient PA10 - hyb 3


title: patient PV12 - hyb 2


title: patient PV13 - hyb 2


title: patient PA9 - hyb 1


title: patient PV11 - hyb 3


title: patient PA6 - hyb 1

tag: 76 years old woman with alcoholic liver disease


title: patient PV12 - hyb 1


title: patient PV20 - hyb 3


title: patient PA5 - hyb 1

tag: 66 years old man with alcoholic liver disease


title: patient PV18 - hyb 1


title: patient PA7 - hyb 2


title: patient PA5 - hyb 3


title: patient PA8 - hyb 1


title: patient PA4 - hyb 1

tag: 70 years old man with alcoholic liver disease


title: patient PA7 - hyb 1


title: patient PA8 - hyb 2


title: patient PA2 - hyb 1

tag: 53 years old man with alcoholic liver disease


title: patient PA4 - hyb 3


title: patient PA6 - hyb 3


title: patient PA3 - hyb 2


title: patient PA5 - hyb 2


title: patient PA3 - hyb 1


title: patient PA1 - hyb 3

tag: 72 years old man with alcoholic liver disease


title: patient PA1 - hyb 1


title: patient PA3 - hyb 3


title: patient PA6 - hyb 2


title: patient PA2 - hyb 3


title: patient PA1 - hyb 2


title: patient V14 - hyb 1

description: cirrhosis without HCC

source_name: HCV-associated cirrhosis liver

tag: 49 years old man with hepatitis C


title: patient V14 - hyb 2

description: cirrhosis without HCC


title: patient V13 - hyb 3

description: cirrhosis without HCC


title: patient PA2 - hyb 2


title: patient V13 - hyb 1

description: cirrhosis without HCC


title: patient PA4 - hyb 2


title: patient PA10 - hyb 1


title: patient V14 - hyb 3

description: cirrhosis without HCC


title: patient V12 - hyb 3

description: cirrhosis without HCC

tag: 57 years old man with hepatitis C


title: patient V13 - hyb 2

description: cirrhosis without HCC


title: patient V12 - hyb 2

description: cirrhosis without HCC


title: patient V12 - hyb 1

description: cirrhosis without HCC


title: patient V10 - hyb 3

description: cirrhosis without HCC


title: patient A6 - hyb 2

description: cirrhosis without HCC

source_name: alcoholism-associated cirrhosis liver

tag: 50 years old man with alcoholic liver disease


title: patient V9 - hyb 1

description: cirrhosis without HCC


title: patient V8 - hyb 2

description: cirrhosis without HCC

tag: 48 years old woman with hepatitis C


title: patient V8 - hyb 3

description: cirrhosis without HCC


title: patient A6 - hyb 3

description: cirrhosis without HCC


title: patient V11 - hyb 1

description: cirrhosis without HCC

tag: 69 years old man with hepatitis C


title: patient V11 - hyb 3

description: cirrhosis without HCC


title: patient A6 - hyb 1

description: cirrhosis without HCC


title: patient V8 - hyb 1

description: cirrhosis without HCC


title: patient V11 - hyb 2

description: cirrhosis without HCC


title: patient V9 - hyb 2

description: cirrhosis without HCC


title: patient V10 - hyb 2

description: cirrhosis without HCC


title: patient V10 - hyb 1

description: cirrhosis without HCC


title: patient A7 - hyb 2

description: cirrhosis without HCC

tag: 47 years old man with alcoholic liver disease


title: patient A7 - hyb 1

description: cirrhosis without HCC


title: patient A5 - hyb 1

description: cirrhosis without HCC

tag: 44 years old woman with alcoholic liver disease


title: patient V9 - hyb 3

description: cirrhosis without HCC

tag: 65 years old man with hepatitis C


title: patient A5 - hyb 3

description: cirrhosis without HCC


title: patient A5 - hyb 2

description: cirrhosis without HCC


title: patient A3 - hyb 2

description: cirrhosis without HCC

tag: 50 years old woman with alcoholic liver disease


title: patient A4 - hyb 3

description: cirrhosis without HCC

tag: 53 years old woman with alcoholic liver disease


title: patient A2 - hyb 2

description: cirrhosis without HCC

tag: 45 years old man with alcoholic liver disease


title: patient A2 - hyb 3

description: cirrhosis without HCC


title: patient A4 - hyb 2

description: cirrhosis without HCC


title: patient CL7 - hyb 3

description: control wihout any histological abnormality

source_name: control liver

tag: 54 years old woman


title: patient CL8 - hyb 3

tag: 30 years old woman


title: patient A1 - hyb 1

description: cirrhosis without HCC


title: patient A1 - hyb 3

description: cirrhosis without HCC


title: patient A3 - hyb 3

description: cirrhosis without HCC


title: patient A3 - hyb 1

description: cirrhosis without HCC


title: patient CL7 - hyb 2


title: patient A1 - hyb 2

description: cirrhosis without HCC


title: patient CL8 - hyb 2


title: patient CL4 - hyb 3

tag: 45 years old woman


title: patient A4 - hyb 1

description: cirrhosis without HCC


title: patient CL6 - hyb 3

tag: 62 years old man


title: patient CL5 - hyb 3

tag: 74 years old man


title: patient CL3 - hyb 3

tag: 68 years old woman


title: patient CL5 - hyb 1


title: patient CL4 - hyb 1


title: patient CL7 - hyb 1


title: patient CL6 - hyb 1


title: patient CL5 - hyb 2


title: patient CL6 - hyb 2


title: patient CL8 - hyb 1


title: patient CL2 - hyb 3

tag: 75 years old woman


title: patient CL2 - hyb 2


title: patient CL2 - hyb 1


title: patient CL1 - hyb 1

tag: 71 years old man


title: patient CL4 - hyb 2


title: patient A2 - hyb 1

description: cirrhosis without HCC


title: patient CL1 - hyb 2


title: patient CL3 - hyb 1


title: patient CL3 - hyb 2


title: Day 14 (T3+4)

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: Biological replicate VEEV treated 2 of 6

hyb_protocol: Oligoarray control targets and hybridization buffer for 16 hrs at 60 degree celcius

scan_protocol: Scanned on Genpix Pro 4000B scanner

data_processing: Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.3.1 (Agilent Tech., CA)

organism: Macaca fascicularis

source_name: Total RNA from Monkey PBMC labeled with cyanine-5 (red)

label_protocol: Microarray labeling was performed using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., MA)

extract_protocol: Trizol procedure

tag: PBMC

tag: Age

value: day 14

source_name: Total RNA labeled with cyanine-3 (green)

extract_protocol: TriZol procedure

tag: Tissue

value: PBMC


title: patient CL1 - hyb 3


title: Day 4 (T29)

description: Biological replicate VEEV treated 5 of 6

value: day 4


title: Day 4 (T34)

description: Biological replicate VEEV treated 6 of 6


title: Control (C83)

description: Experimental replicate control 10 of 25


title: Control (C62)

description: Experimental replicate control 5 of 25


title: Control (C54)

description: Experimental replicate control 2 of 25


title: Control (C56)

description: Experimental replicate control 3 of 25


title: Control (C70)

description: Experimental replicate control 8 of 25


title: Day 14 (T1+2)

description: Biological replicate VEEV treated 1 of 6


title: Control (C66)

description: Experimental replicate control 7 of 25


title: Control (C88)

description: Experimental replicate control 12 of 25


title: Control (C50)

description: Experimental replicate control 1 of 25


title: Control (C85)

description: Experimental replicate control 11 of 25


title: Control (C80)

description: Experimental replicate control 9 of 25


title: Day 3 (T21)

description: Biological replicate VEEV treated 4 of 6

value: day 3


title: Day 3 (T12)

description: Biological replicate VEEV treated 3 of 6


title: Control (C64)

description: Experimental replicate control 6 of 25


title: Control (C276)

description: Experimental replicate control 18 of 25


title: Control (C282)

description: Experimental replicate control 22 of 25


title: Control (C285)

description: Experimental replicate control 24 of 25


title: Control (C284)

description: Experimental replicate control 23 of 25


title: Control (C270)

description: Experimental replicate control 15 of 25


title: Control (C278)

description: Experimental replicate control 20 of 25


title: Control (C277)

description: Experimental replicate control 19 of 25


title: Control (C280)

description: Experimental replicate control 21 of 25


title: Control (C267)

description: Experimental replicate control 13 of 25


title: Control (C60)

description: Experimental replicate control 4 of 25


title: Control (C268)

description: Experimental replicate control 14 of 25


title: Control (C286)

description: Experimental replicate control 25 of 25


title: 22A_460_replicate8

status: Public on Jan 31 2008

city: Winnipeg

first: stephanie

last: booth

address: 1015 Arlington St

institute: PHAC

description: uninfected, age-matched mice used for control

hyb_protocol: Labelled cDNA was dried down and resuspended in 60 µl DIG Easy Hyb hybridization buffer (Roche) containing calf thymus DNA (Sigma) and yeast tRNA (Life Technologies).  The labelled cDNAs were applied to arrays that contained 11,136 cDNAs from the Brain Molecular Anatomy Project (BMAP).  Arrays were constructed in-house as previously described [2].  Hybridization was performed under M Series Lifter Slips (Erie Scientific Company) and the slides incubated in a hybridization chamber at 42oC for 16 hours. Following hybridization lifter slips were removed and the arrays washed a total of 3 times for 5 minutes each in 1 X SSC, 0.2% SDS then 0.1 X SSC, 0.2% SDS pre-warmed to 42C.  A final wash in 0.1 X SSC at room temperature was performed and slides spun to dry.

scan_protocol: Spots were quantitated and background signals removed using Array-Pro® Analyser software (Media Cybernetics, Inc).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. GeneTraffic software was used.

label_protocol: A quantity of 10 µg of total RNA was used as a template for oligo dT primed reverse transcription which incorporated amino allyl -dUTP (Sigma) into the cDNA.  The remaining RNA template was hydrolyzed and the cDNA product purified using the QIAquick PCR purification system (Qiagen).  PCR products were dried down, then resuspended in 0.1 M Na2CO3 buffer, and incubated for 1 hour in either an Alexa Fluor555 (AF555) or Alexa Fluor647 (AF647) mono-functional reactive dye (Molecular Probes) made up in DMSO.  Labelled cDNA was also purified using QIAquick PCR purification columns.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol:
C57BL/6 or VM mice were inoculated intracerebrally with 20 µl of 1% brain homogenate from mice infected with scrapie strains 22A, ME7, or 79a.
At the onset of clinical symptoms 8 to 10 mice per sample group were sacrificed and the whole brains used for RNA extraction

tag: infected

source_name: Total RNA from pooled 460 day old C57 mice

tag: uninfected


title: RML_150_m138_swap

description: All procedures done using standard Agilent protocols

hyb_protocol: Following Agilent protocol

scan_protocol: Agilent scanner and feature extraction software, standard protocol

data_processing: Log ratio calculated using Agilent feature extraction software and standard procedures

source_name: brain RML-infected mouse 138

label_protocol: Following Agilent protocol

extract_protocol: RNA was isolated from brain tissue by disruption in Trizol reagent (Invitrogen) and was further purified using RNeasy columns (Qiagen) according to the manufacturer’s instructions.  Total RNA was QC'd using Agilent Bioanalyser and then processed as per Agilent array standard protocols

tag: brain female RML-infected 150 days

source_name: brain mock-infected mouse 65

tag: brain female mock-infected 150 days


title: 22A_460_replicate6


title: Control (C275)

description: Experimental replicate control 17 of 25


title: Control (C272)

description: Experimental replicate control 16 of 25


title: 22A_460_replicate3


title: RML_150_m137_swap

source_name: brain RML-infected mouse 137

source_name: brain mock-infected mouse 64


title: 22A_460_replicate5


title: 22A_460_replicate7


title: RML_150_m139_swap

source_name: brain RML-infected mouse 139

source_name: brain mock-infected mouse 66


title: RML_150_m138

tag: C57BL/6 female mock-infected 150 days

tag: C57BL/6 female RML-infected 150 days


title: RML_150_m139


title: 22AVM_200_replicate4

source_name: Total RNA from pooled 200 day old VM mice


title: 22A_460_replicate2


title: 22A_460_replicate4


title: RML_150_m137

extract_protocol: RNA was isolated from brain tissue by disruption in Trizol reagent (Invitrogen) and was further purified using RNeasy columns (Qiagen) according to the manufacturer’s instructions.  A quantity of 10 µg of total RNA was used as a template for oligo dT primed reverse transcription which incorporated amino allyl -dUTP (Sigma) into the cDNA.  The remaining RNA template was hydrolyzed and the cDNA product purified using the QIAquick PCR purification system (Qiagen).

tag: C57bl/6, female age 150 days


title: 22AVM_200_replicate6


title: 22AVM_200_replicate7


title: 22AVM_200_replicate5


title: 22AVM_200_replicate2


title: 22AVM_200_replicate3


title: 22AVM_200_replicate8


title: 22A_460_replicate1


title: 22AVM_200_replicate1


title: Me7_160_replicate2

source_name: Total RNA from pooled 160 day old C57 mice


title: 446_TaqMan

status: Public on Jan 29 2008

city: Foster City

first: Catalin

last: Barbacioru

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: Gene expression data from peripheral blood of TAA/normal individuals using TaqMan real-time PCR assays

data_processing: Data was processed using SDS 2.2 software (Applied Biosystems, Foster City, CA)

label: FAM

source_name: Peripheral blood

label_protocol: Each TaqMan(R) Assay was run in four replicates for each RNA sample using 10 ng total cDNA (measured as total input RNA) in a 10 ul final volume. Assays were run with 2X Universal Master Mix (without UNG) on Applied Biosystems 7900 Fast Real-Time PCR System using universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

extract_protocol: PAXgene tube and Qiagen Preanalytics Blood RNA kit

tag: Control; training set


title: Me7_160_replicate7

source_name: 160 dpi ME7


title: 470_TaqMan


title: 475_TaqMan


title: 476_TaqMan


title: 79a_160_replicate8


title: Me7_160_replicate8


title: 521_TaqMan


title: 474_TaqMan


title: 427_TaqMan


title: 499_TaqMan

tag: Control; testing set


title: Me7_160_replicate6


title: 444_TaqMan


title: Me7_160_replicate4


title: 441_TaqMan


title: 442_TaqMan


title: 443_TaqMan


title: Me7_160_replicate5


title: Me7_160_replicate1


title: 79a_160_replicate6


title: 79a_160_replicate4

tag: FEMALE

tag: INFECTED

tag: UNINFECTED

tag: AGE-MATCHED


title: 79a_160_replicate9


title: 79a_160_replicate10


title: 423_TaqMan


title: Me7_160_replicate3


title: 399_TaqMan

tag: TAA; testing set


title: 79a_160_replicate7


title: 342_TaqMan

tag: TAA; training set


title: 389_TaqMan


title: 351_TaqMan


title: 338_TaqMan


title: 340_TaqMan


title: 350_TaqMan


title: 374_TaqMan


title: 400_TaqMan


title: 394_TaqMan


title: 333_TaqMan


title: 377_TaqMan


title: 353_TaqMan


title: 329_TaqMan


title: 332_TaqMan


title: 330_TaqMan


title: 368_TaqMan


title: 360_TaqMan


title: 316_TaqMan


title: 327_TaqMan


title: 320_TaqMan


title: 416_TaqMan


title: 314_TaqMan


title: 79a_160_replicate5

source_name: Mus musculus


title: 312_TaqMan


title: 79a_160_replicate3

tag: 160 DAYS OLD

source_name: Total RNA from pooled 160 day old C57bl/6 mice

tag: UNINFECTED POOL


title: 319_TaqMan


title: 304_TaqMan


title: 263_TaqMan


title: 268_TaqMan


title: 264_TaqMan


title: 288_TaqMan


title: 294_TaqMan


title: 262_TaqMan


title: 267_TaqMan


title: 265_TaqMan


title: 301_TaqMan


title: 286_TaqMan


title: 278_TaqMan


title: 679_TaqMan


title: 310_TaqMan


title: 311_TaqMan


title: 683_TaqMan


title: 678_TaqMan


title: 282_TaqMan


title: 284_TaqMan


title: 685_TaqMan


title: 271_TaqMan


title: 269_TaqMan


title: 283_TaqMan


title: 270_TaqMan


title: 79a_160_replicate1

tag: Age:160 days

tag: Pool:8 mice


title: 676_TaqMan


title: 672_TaqMan


title: 677_TaqMan


title: 668_TaqMan


title: 664_TaqMan


title: 657_TaqMan


title: 652_TaqMan


title: 638_TaqMan


title: 658_TaqMan


title: 660_TaqMan


title: 541_TaqMan


title: 675_TaqMan


title: 564_TaqMan


title: 563_TaqMan


title: 522_TaqMan


title: 544_TaqMan


title: 547_TaqMan


title: 545_TaqMan


title: 661_TaqMan


title: 543_TaqMan


title: 548_TaqMan


title: MAA28

status: Public on Jan 10 2008

city: Ottawa

first: Mike

middle: G

last: Wade

state: Ontario

address: 50 Columbine Driveway

department: Environmental Health Science & Research Bureau

institute: Health Canada

hyb_protocol: Cy5- sample cRNA and Cy3-labelled common reference cRNA (rat universal reference total RNA (BD Biosciences Clontech, Palo Alto, CA, USA)  were hybridized to Agilent rat oligo microarrays (containing ~20,000 unique 60 mer oligonucleotides; Agilent Tech. Inc.) at 60║C overnight with Agilent hybridization solution and washed according to the Agilent's instructions.

scan_protocol: Arrays were scanned on a ScanArray Express (Perkin Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, Inc. El Segundo, CA).

data_processing: The data were normalized by lowess curve (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002; 30: e15.) using SAS/STAT software, Version 8.2 of the SAS System for Windows (1999 2001 SAS Institute Inc., Cary, NC, USA).  Data used to estimate foldchanges were adjusted for variation due to date of hybridization using the least square estimates.

source_name: 650 mg methoxyacetic acid/kg body weight_12 hr

label_protocol: Individual total RNA samples of testis from each animal or universal rat RNA were labelled with Cyanine 5-CTP or Cyanine 3-CTP, respectively (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc.) following the manufacturerÆs instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ╡g total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl, yielding 25 ~35 ╡g labelled cRNA-target. Three micrograms of labelled cRNA were fragmented at 60║C for 30 min with fragmentation solution.

extract_protocol: Total RNA was extracted from a portion of the right testis (about 30 mg) using the Qiagen RNeasy mini kit (Qiagen, Mississauga, ON) following the manufacturerÆs directions, and quantified using Quant-iT RiboGreen RNA assay kit (Invitrogen, Burlington, ON).  Total RNA quality was assessed using the RNA 6000 Nano LabChips with the 2100 Bioanalyzer system (Agilent Technologies Inc., Mississauga, ON, Canada).  Only samples with the ratios of 18s/28s ribosomal RNA intensity ratios of between 1.65 and 2.0 were used for microarray analyses.

tag: Tissue

value: Testis parenchyma

tag: Age

value: 90 days

tag: Strain

value: Sprague-Dawley

tag: Exposure=650 mg methoxyacetic acid/kg body weight i.p.

tag: Time Post treatment

value: 12 hr

tag: Method of termination

value: CO2 asphyxiation

tag: Microarray ID

tag: Hyb Date

extract_protocol: Unknown: Material was purchased as total RNA (universal rat reference total RNA (Catalog #740200; Stratagene, La Jolla, CA, USA))

tag: Total RNA derived from 14 rat cell lines


title: Con41

source_name: saline_24 hr

tag: Exposure=saline i.p.

value: 24 hr

source_name: universal rat reference total RNA (Catalog #740200; Stratagene, La Jolla, CA, USA)


title: MAA8

source_name: 650 mg methoxyacetic acid/kg body weight_4 hr

value: 4 hr


title: MAA20

source_name: 650 mg methoxyacetic acid/kg body weight_8 hr

value: 8 hr


title: Con34

source_name: saline_12 hr


title: Con6

source_name: saline_4 hr


title: Con29


title: MAA32


title: Con30


title: MAA19


title: MAA40

source_name: 650 mg methoxyacetic acid/kg body weight_24 hr


title: Con38


title: Con26


title: MAA47


title: Con17

source_name: saline_8 hr


title: MAA16


title: MAA31


title: Con45


title: MAA35


title: Con42


title: Con18


title: MAA48


title: Con14


title: MAA36


title: Con46


title: Con9


title: Con10


title: MAA43


title: MAA44


title: Ovarian tumor AM429

status: Public on Dec 31 2007

first: Jaroslav

middle: Petr

last: Novak

state: Quebec

address: 740, Dr Penfield Avenue

department: Microarray Platform

institute: McGill University and Genome Quebec Innovation Centre

description: invasive

hyb_protocol: 15 ug of total RNA was reverse-transcribed with oligo-dT primer containing a T7 RNA polymerase-binding site. An in vitro transcription was performed on this cDNA. DNA from the samples was fragmented in 40 mM Tris acetate, 100 mM potassium acetate, and 30 mM MgCl2 (pH 8.1) at 95°C to reduce secondary structures. 15 ug of cRNA were hybridized to an Affymetrix HuGeneFL microarray, washed and stained.

scan_protocol: Scanned with a Hewlett Packard Gene Array Scanner

data_processing: Raw values assigned by MAS 4

label: Biotin

source_name: epithelian ovarian tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 microg total RNA.

value: epithelial ovarian tumor, Tumor type:clear cell, Tumor stage:invasive grade 3, xenograft of an EOC cell line


title: MAA4


title: Ovarian tumor AM398

description: invasive

value: epithelial ovarian tumor, Tumor type:endometrioid, Tumor stage:invasive grade 3, xenograft of an EOC cell line


title: MAA23


title: Con22


title: MAA12


title: Ovarian tumor AM381

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 3


title: Con21


title: MAA7


title: Con25


title: MAA24


title: Con5


title: Con49


title: Ovarian tumor AM438

description: invasive

value: epithelial ovarian tumor, Tumor type:mixed, Tumor stage:invasive grade 3


title: Con37


title: Ovarian tumor AM367

description: invasive


title: MAA39


title: Ovarian tumor AM431

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 2


title: Con2


title: MAA3


title: Ovarian tumor AM368

description: invasive


title: MAA27


title: Ovarian tumor AM364

description: low malignant potential

value: epithelial ovarian tumor, Tumor type:mucinous, Tumor stage:borderline


title: Ovarian tumor AM382

description: invasive


title: MAA11


title: MAA15


title: Con13


title: Ovarian tumor AM344

description: low malignant potential

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:benign


title: Ovarian tumor AM268

description: invasive


title: Ovarian tumor AM333

description: invasive

value: epithelial ovarian tumor, Tumor type:clear cell, Tumor stage:invasive grade 2


title: Ovarian tumor AM294

description: invasive


title: Ovarian tumor AM313

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 2/3


title: Ovarian tumor AM345

description: invasive


title: Ovarian tumor AM341

description: invasive

value: epithelial ovarian tumor, Tumor type:mixed, Tumor stage:invasive grade 2/3


title: Ovarian tumor AM263

description: invasive


title: Ovarian tumor AM315

description: invasive


title: Ovarian tumor AM292

description: invasive

value: epithelial ovarian tumor, Tumor type:undetermined, Tumor stage:invasive, small foci of grade 3 tumor


title: Ovarian tumor AM290

description: invasive


title: Ovarian tumor AM289

description: invasive


title: Ovarian tumor AM339

description: invasive


title: Ovarian tumor AM348

description: invasive


title: Ovarian tumor AM317

description: invasive


title: Ovarian tumor AM354

description: invasive


title: Ovarian tumor AM293

description: invasive


title: Ovarian tumor AM269

description: invasive


title: Ovarian tumor AM259

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:microinvasion of grade 3


title: Ovarian tumor AM255

description: invasive


title: Ovarian tumor AM311

description: invasive

value: epithelial ovarian tumor, Tumor type:endometrioid, Tumor stage:invasive grade 1


title: Ovarian tumor AM256

description: invasive


title: Ovarian tumor AM349

description: invasive


title: Ovarian tumor AM335

description: invasive


title: Ovarian tumor AM287

description: invasive


title: Ovarian tumor AM347

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 2, post-chemotherapy sample


title: Ovarian tumor AM261

description: invasive


title: Ovarian tumor AM288

description: invasive


title: Ovarian tumor AM253

description: low malignant potential

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:borderline


title: Ovarian tumor AM233

description: low malignant potential


title: Ovarian tumor AM226

description: low malignant potential


title: Ovarian tumor AM252

description: invasive

value: epithelial ovarian tumor, Tumor type:endometrioid, Tumor stage:invasive grade 2


title: Ovarian tumor AM203

description: invasive

value: epithelial ovarian tumor, Tumor type:endometrioid, Tumor stage:invasive grade 3


title: Ovarian tumor AM204

description: invasive


title: Ovarian tumor AM228

description: low malignant potential


title: Ovarian tumor AM250

description: invasive


title: Ovarian tumor AM198

description: invasive


title: Ovarian tumor AM209

description: invasive

value: epithelial ovarian tumor, Tumor type:clear cell, Tumor stage:invasive grade 3


title: Ovarian tumor AM179

description: low malignant potential


title: Ovarian tumor AM201

description: invasive


title: Ovarian tumor AM200

description: invasive


title: Ovarian tumor AM208

description: invasive


title: Ovarian tumor AM207

description: invasive


title: Ovarian tumor AM133

description: invasive


title: Ovarian tumor AM202

description: invasive


title: Ovarian tumor AM144

description: invasive


title: Ovarian tumor AM182

description: invasive


title: Ovarian tumor AM137

description: low malignant potential


title: Ovarian tumor AM138

description: low malignant potential


title: Ovarian tumor AM195

description: invasive


title: Ovarian tumor AM196

description: low malignant potential


title: Ovarian tumor AM053

description: invasive


title: Ovarian tumor AM076

description: invasive


title: Ovarian tumor AM125

description: invasive


title: Ovarian tumor AM122

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 3, potentially from extra-ovarian origin


title: Ovarian tumor AM025

description: low malignant potential


title: Ovarian tumor AM127

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 3, post-chemotherapy sample


title: Ovarian tumor AM178

description: invasive

value: epithelial ovarian tumor, Tumor type:serous, Tumor stage:invasive grade 3


title: Ovarian tumor AM225

description: low malignant potential


title: Ovarian tumor AM124

description: invasive


title: Ovarian tumor AM027

description: low malignant potential


title: Ovarian tumor AM131

description: invasive


title: Ovarian tumor AM030

description: low malignant potential


title: Ovarian tumor AM029

description: low malignant potential


title: HK-2 GF HSA

status: Public on Jun 28 2007

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

country: United Kingdom

institute: University of Liverpool

description: Proteinuria is pathogenic to proximal tubular cells (PTC) and linked with progression to renal failure. Angiotensin II (AngII) is also independently involved in the pathogenesis of progressive renal injury in varied kidney disease. The effects of human serum albumin (HSA) overload and AngII on the changes in gene protein expression stimulated by oxidative stress in PTC were assesed using cDNA microarrays.

hyb_protocol: According to user manual for Nylon Atlas cDNA Expression Arrays available at www.clontech.com

scan_protocol: The arrays were exposed to Storage Phosphor Screens (Amersham Pharmacia Biotech, Little Chalfont, UK). The phosphor screens were scanned using a Biorad Personal Molecular Imager FX (Biorad, Hercules, CA, USA).

data_processing: Values were normalized using Global normalization

source_name: Human renal proximal tubular epithelial cells

growth_protocol: Cells were cultured until 90-95% confluent in DMEM/Ham s F12 medium supplemented with 5.5 mM glucose, 2 mM L-glutamine, 5 ug/ml insulin, 5 ug/ml transferrin, 5 ng/ml sodium selenite, 0.4 ug/ml hydrocortisone, 5 ng/ml epidermal growth factor, 100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes, and 10% FCS.

extract_protocol: Total RNA was isolated from HK-2 cells using Tri-reagent (Sigma, UK) as recommended by the manufacturer s protocol. The RNA content of the samples was measured using RiboGreen RNA Quantitation Reagent (Molecular Probes, Invitrogen, UK). The integrity of the total RNA was verified on a denaturing agarose-formaldehyde gel.

treatment_protocol: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Medium was refreshed and supplemented with 30 mg/ml GF HSA. After further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.

tag: Immortalised human renal proximal tubular epithelial cells


title: HSA-2

status: Public on Jul 01 2007

city: Baltimore

first: Tetsuo

last: Ito

address: 1503 E Jefferson St Rm 106

department: Medicine

institute: Johns Hopkins University

description: The labeling, hybridization, and scanning were performed at Johns Hopkins Bayview Medical Center Genomics Core, Baltimore, Maryland.

hyb_protocol: Each sample was hybridized with the Illumina Human RefSeq8 version 2 BeadChip with 20,589 transcript probes comprised of optimized 50 mer-oligonucleotides (Illumina, San Diego, CA), washed, and stained with Cy3-streptavidin (GE Healthcare) as per the manufactures’ instructions.

scan_protocol: The arrays were scanned with the Illumina Beadarray Reader confocal scanner (Illumina).

data_processing: The data were processed using the Illumina BeadStudio software (Illumina), were subjected to intensity-dependent normalization. Differentially expressed genes by PTTG1 downregulation were identified by the Significance Analysis of Microarrays (SAM) program.

label_protocol: After the RNA quality measurement by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), each RNA sample (100 ng) was amplified and labeled with the Illumina TotalPrep RNA Amplification kit (Ambion, Austin, TX).

extract_protocol: Total RNAs were extracted by the RNeasy kit (Qiagen) from the eight samples.

treatment_protocol: HSA/c and KYSE140 cells were transfected with three siRNA oligos (NTC, P1, P2) separately or without oligos (LF+) at day 0 and harvested at day 3.

tag: HSA/c (human esophageal squamous cell carcinoma cell line)

tag: HSA-NTC

tag: transfected with NTC (non-targeting control) siRNA oligo


title: Ovarian tumor AM132

description: invasive


title: HSA-1

source_name: human esophageal squamous cell carcinoma cell line

tag: HSA-LF+

tag: transfected without siRNA oligo with Lipofectamine

tag: normalized, logarithmic


title: HK-2 control

label_protocol: According to user manual for Nylon Atlas cDNA Expression Arrays available at www.clontech.com

treatment_protocol: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Medium was refreshed and after further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.


title: HK-2 AngII

extract_protocol: Total RNA was isolated from HK-2 cells using Tri-reagent (Sigma, UK) as recommended by the manufacturer?s protocol. The RNA content of the samples was measured using RiboGreen RNA Quantitation Reagent (Molecular Probes, Invitrogen, UK). The integrity of the total RNA was verified on a denaturing agarose-formaldehyde gel.

treatment_protocol: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Medium was refreshed and supplemented with 1 uM AngII. After further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.

tag: Human renal proximal tubular epithelial cells


title: HK-2 GF/FAF HSA

treatment_protocol: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Medium was refreshed and supplemented with 30 mg/ml GF/FAF HSA. After further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.


title: 5Aza_vs_mock_2

status: Public on Aug 08 2007

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufecturer's recommended protocol

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: log ratio of red signal to green signal was calculated after background subtraction and loess normalization as implemented in the Limma package from Bioconductor

source_name: 5Aza-treated HCT116

label_protocol: Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy clean-up with on-column DNase treatment

treatment_protocol: 5 micromolar 5Aza for 96 hours

tag: HCT116 human colorectal cancer cell line

source_name: mock-treated HCT116

treatment_protocol: 1x PBS for 96 hours


title: TSA_vs_mock_2

source_name: TSA treated HCT116

treatment_protocol: 300 nanomolar TSA for 18 hours


title: Wt_+/- bile_16-35

status: Public on Dec 09 2006

city: Lebanon

first: Francisca

middle: A

last: Cerda-Maira

state: NH

address: 16 Cavendish Court

department: Microbiology and Immunology

institute: Dartmouth College

hyb_protocol: 25% formamide 42 degrees O/N

scan_protocol: Scanned at 550 and 650 nm at 70-90% laser power using a GMS418 Scanner. Image saved as tif and imported into Scanalyze (Michael Eisen ver. 2.50, Stanford University)

data_processing: Data uploaded into Gene Traffic software (Stratagene ver. 3.2-12). Intensities normalized using global intensity method. Spot flagged if less than 2X background. Ratios represent Cy5/Cy3 (channel 2/channel1)

organism: Vibrio cholerae

source_name: Vibrio cholerae

label_protocol: Reverse transcription using aadUTP followed by coupling to Alexa555

growth_protocol: Bacteria was grown in AKI media in virulence genes inducing conditions (standing and shaking) in the abscence of bile

extract_protocol: Trizol extraction and RNAesy purification column from Qiagen

treatment_protocol: Bacteria was grown in the abscence of bile for 5.5 hours

tag: Wt Vibrio cholerae

label_protocol: Reverse transcription using aadUTP followed by coupling to Alexa647

growth_protocol: Bacteria was grown in AKI media in virulence genes inducing conditions (standing and shaking) in the presence of 0.4% bile

treatment_protocol: Bacteria was grown in the presence of 0.4% bile for 5.5 hours


title: Wt_+/- bile_16-36


title: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, biological repeat #2

status: Public on Mar 31 2006

city: Rehovot

first: Naama

last: Barkai

address: Hertzel

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

description: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, repeat #2

hyb_protocol: none provided

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using Aginlet's DNA microarray scanner and image intensity data were extracted and analyzed with SpotReader (Niles Scientific) analysis software.

data_processing: Background intensity was subtracted using a Bayesian correction, and the ratios of the two dyes were log2-transformed. Log2 ratios were then corrected for intensity-dependant and spatial-dependant biases by subtracting a Lowess curve followed by a median filter. The two spots corresponding to each gene were then averaged, and genes for which the two spots were significantly different were declared as 'missing values' (along with other genes which were flagged by the image analysis software or removed by manual inspection).

organism: Saccharomyces kudriavzevii

label_protocol: The cDNA from heat shock treated and untreated cells was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

growth_protocol: Cells were grown on YPD to log phase at 24oC and then transferred to YP-glycerol

extract_protocol: 5 O.D. units of cells were collected, pelleted and immediately frozen. Total RNA was obtained using MasterPure yeast RNA purification kit (Epicenter).

tag: Strain

value: IFO 1815 wild type, diploid

source_name: S. kudriavzevii grown in YPD at 24oC

label_protocol: cDNA was synthesized from total RNA using M-MLV Reverse Transcriptase RNase H Minus (Promega) and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method.

extract_protocol: The RNA (20 µg) was annealed with 4 µg oligo dT12-18, and reverse-transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2h at 45°C in the presence of 2.5mM MgCl2,  0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. After hydrolysis of RNA in 0.2 M NaOH (30min, 65oC), Tris was removed from the reaction with a Microcon-30 concentrator.

tag: For reference we used the same culture prior to pertubation in which cells were grown to log phase in YPD at 24oC.


title: HSA-3

tag: transfected with PTTG1 siRNA oligo 1


title: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, biological repeat #2

description: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, repeat #2

organism: Saccharomyces paradoxus

growth_protocol: Cells were grown on YPD to log phase at 30oC and then transferred to YP-glycerol

value: NRRL Y-17217 wild type, diploid

source_name: S. paradoxus2 grown in YPD at 30oC

tag: For reference we used the same culture prior to pertubation in which cells were grown to log phase in YPD at 30oC.


title: 140-1

tag: KYSE140 (human esophageal squamous cell carcinoma cell line)


title: i4-094B-680750_Hho1B

status: Public on Aug 21 2006

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

description:
Strains were grown in YPD media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC for 15 min. ( by adding an equal volume of heated media for the heat shocked set), or mock treated at 25ûC for 15 min. (by adding an equal volume of 25ûC media for the mock treated set).  After 15 min. incubation, cells were brought back to 25ûC and simultaneously cross-linked with 1% formaldehyde for 2 hours.  Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC.  See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae

source_name: Hho1-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Hho1-TAP Heat Shocked Purified ChIP DNA (CH2)


title: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, biological repeat #3

description: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, repeat #3


title: HSA-4

tag: transfected with PTTG1 siRNA oligo 2


title: Wt_+/- bile_16-34


title: i4-094A-750730_Hho1A

source_name: Hho1-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Hho1-TAP Mock Treated Purified ChIP DNA (CH2)


title: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, biological repeat #3

description: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, repeat #3


title: 140-3


title: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, biological repeat #1

description: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, repeat #1


title: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, biological repeat #4

description: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, repeat #4


title: 140-2


title: i4-028B-680710_Rpb2B

source_name: Rpb2-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Rpb2-TAP Heat Shocked Purified ChIP DNA (CH2)


title: i4-029A-700700_Rpb7A

source_name: Rpb7-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Rpb7-TAP Mock Treated Purified ChIP DNA (CH2)


title: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, biological repeat #4

description: S. paradoxus2, transfer from glucose to glycerol, 30 minutes, repeat #4


title: TP_S2_A

status: Public on Oct 03 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description: Biological replicate 1 of 2

hyb_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).

organism: Drosophila melanogaster

growth_protocol: Schneider´s Drosophila line 2 cells (ATCC CRL-1963) grown at 25°C in Erlenmeyer-flasks to a density of 0.5-1.5x107 cells/ml in Drosophila SFM medium (Invitrogen) supplemented with 100U/ml of Penicillin G, 100 μg/ml of Streptomycin sulfate and 2 mM of L-glutamine.

extract_protocol: For transcript profiling experiments, poly(A)+RNA was isolated using DynabeadsOligo (dT)25 (Dynal). Two biological replicates were used of both salivary glands (300 pairs per replicate) and S2 cells. The cells or tissue were frozen at -70C and homogenized in 0.1 M TRIS-HCl (pH 8.0), 0.5 M LiCl, 10 mM EDTA, 1% SDS and 5 mM DTT. Dynal’s recommendations were then followed. The poly(A)+RNA was converted to cDNA using an ImPromII first strand synthesis kit (Promega) according to the supplier’s recommendations. The cDNA was then used as a template for forming double-stranded cDNA using a Superscript double stranded cDNA synthesis kit (Invitrogen). The double-stranded cDNA was purified by phenol-chloroform extraction followed by passage through S200HR columns (GE Healthcare) and 4µg of the double-stranded cDNA from each sample was sent to Nimblegen for labeling and hybridization using the same array design as for the ChIP-chip.

tag: Schneider 2 embryonic cell-line, Wild type, male


title: S. mikatae, transfer from glucose to glycerol, 30 minutes, biological repeat #3

description: S. mikatae, transfer from glucose to glycerol, 30 minutes, repeat #3

organism: Saccharomyces mikatae

source_name: S. mikatae grown in YPD at 30oC


title: S. mikatae, transfer from glucose to glycerol, 30 minutes, biological repeat #4

description: S. mikatae, transfer from glucose to glycerol, 30 minutes, repeat #4


title: S. mikatae, transfer from glucose to glycerol, 30 minutes, biological repeat #2

description: S. mikatae, transfer from glucose to glycerol, 30 minutes, repeat #2


title: S. mikatae, transfer from glucose to glycerol, 30 minutes, biological repeat #1

description: S. mikatae, transfer from glucose to glycerol, 30 minutes, repeat #1


title: i4-029B-680730_Rpb7B

source_name: Rpb7-TAP Mock Treated Purified ChIP DNA (CH1)

source_name: Rpb7-TAP Heat Shocked Purified ChIP DNA (CH2)


title: S. paradoxus2 Heat shock (37oC) 30 minutes, biological repeat #3

description: S. paradoxus Heat shock (37oC) 30 minutes, repeat #3

growth_protocol: Cells were grown on YPD to log phase at 30oC prior to heat shock and then transferred to 37oC

source_name: S. paradoxus grown in YPD at 30oC


title: TP_S2_B

description: Biological replicate 2 of 2

scan_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).


title: S. cerevisiae, transfered from glucose to glycerol, 30 minutes, biological repeat #3

description: S. cerevisiae, transfer from glucose to glycerol, 30 minutes, repeat #3

value: BY4743 wild type, diploid

source_name: S. cerevisiae grown in YPD at 30oC


title: 140-4

source_name: human esophageal squamous cell carcinoma cell line


title: TP_SG_B

description: Biological replicate 2 of 2

label_protocol: NimbleGen standard protocol (http://www.nimblegen.com/products/lit/lit.html).

tag: Salivary gland, Wild type, mixed sex


title: TP_SG_A

description: Biological replicate 1 of 2


title: i4-028A-700700_Rpb2A

source_name: Rpb2-TAP Heat Shocked Purified ChIP DNA (CH1)

source_name: Rpb2-TAP Mock Treated Purified ChIP DNA (CH2)


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes, biological repeat #2

description: S. paradoxus, transfer from glucose to glycerol, 30 minutes, repeat #2

value: CBS432 wild type, diploid


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes, biological repeat #1

description: S. paradoxus, transfer from glucose to glycerol, 30 minutes, repeat #1


title: S. cerevisiae, transfered from glucose to glycerol, 30 minutes, biological repeat #4

description: S. cerevisiae, transfer from glucose to glycerol, 30 minutes, repeat #4


title: S. mikatae Heat shock (37oC) 30 minutes, biological repeat #3

description: S. mikatae Heat shock (37oC) 30 minutes, repeat #3

source_name: S. mikatae Heat shock (37oC) 30 minutes


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes, biological repeat #4

description: S. paradoxus, transfer from glucose to glycerol, 30 minutes, repeat #4


title: S. mikatae Heat shock (37oC) 30 minutes, biological repeat #2

description: S. mikatae Heat shock (37oC) 30 minutes, repeat #2


title: S. paradoxus2 Heat shock (37oC) 30 minutes, biological repeat #4

description: S. paradoxus Heat shock (37oC) 30 minutes, repeat #4


title: S. mikatae Heat shock (37oC) 30 minutes, biological repeat #4

description: S. mikatae Heat shock (37oC) 30 minutes, repeat #4


title: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, biological repeat #1

description: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes, repeat #1

source_name: S. kudriavzevii grown in YPD at 24oC


title: S. paradoxus Heat shock (37oC) 30 minutes, biological repeat #2

description: S. paradoxus Heat shock (37oC) 30 minutes, repeat #2


title: S. paradoxus Heat shock (37oC) 30 minutes, biological repeat #3


title: S. kudriavzevii Heat shock (37oC) 30 minutes, biological repeat #4

description: S. kudriavzevii Heat shock (37oC) 30 minutes, repeat #4

growth_protocol: Cells were grown on YPD to log phase at 24oC prior to heat shock and then transferred to 37oC

value: IFO 1802 wild type, diploid


title: S. cerevisiae, transfered from glucose to glycerol, 30 minutes, biological repeat #1

description: S. cerevisiae, transfer from glucose to glycerol, 30 minutes, repeat #1


title: S. kudriavzevii Heat shock (37oC) 30 minutes, biological repeat #1

description: S. kudriavzevii Heat shock (37oC) 30 minutes, repeat #1


title: S. paradoxus Heat shock (37oC) 30 minutes, biological repeat #4


title: S. cerevisiae, transfered from glucose to glycerol, 30 minutes, biological repeat #2

description: S. cerevisiae, transfer from glucose to glycerol, 30 minutes, repeat #2


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes, biological repeat #3

description: S. paradoxus, transfer from glucose to glycerol, 30 minutes, repeat #3


title: S. cerevisiae Heat shock (37oC) 30 minutes, biological repeat #3

description: S. cerevisiae Heat shock (37oC) 30 minutes, repeat #3


title: S. paradoxus2 Heat shock (37oC) 30 minutes, biological repeat #1

description: S. paradoxus Heat shock (37oC) 30 minutes, repeat #1


title: S. paradoxus, MMS (0.02%), 90 minutes 2

description: S. paradoxus, MMS (0.02%), 90 minutes

source_name: S. paradoxus, MMS (0.02%), 90 minutes

growth_protocol: Cells were grown on YPD to log phase at 30oC and then MMS was adeed to a final concentration of 0.02%

extract_protocol: The RNA (20 ?g) was annealed with 4 ?g oligo dT12-18, and reverse-transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2h at 45?C in the presence of 2.5mM MgCl2,  0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. After hydrolysis of RNA in 0.2 M NaOH (30min, 65oC), Tris was removed from the reaction with a Microcon-30 concentrator.


title: S. mikatae Heat shock (37oC) 30 minutes, biological repeat #1

description: S. mikatae Heat shock (37oC) 30 minutes, repeat #1


title: S. paradoxus Heat shock (37oC) 30 minutes, biological repeat #1


title: S. paradoxus, MMS (0.02%), 45 minutes 2

description: S. paradoxus, MMS (0.02%), 45 minutes

source_name: S. paradoxus, MMS (0.02%), 45 minutes


title: S. paradoxus, MMS (0.02%), 30 minutes 2

description: S. paradoxus, MMS (0.02%), 30 minutes

source_name: S. paradoxus, MMS (0.02%), 30 minutes


title: S. paradoxus2 Heat shock (37oC) 30 minutes,biological repeat #2


title: S. kudriavzevii Heat shock (37oC) 30 minutes, biological repeat #2

description: S. kudriavzevii Heat shock (37oC) 30 minutes, repeat #2


title: S. kudriavzevii Heat shock (37oC) 30 minutes, biological repeat #3

description: S. kudriavzevii Heat shock (37oC) 30 minutes, repeat #3


title: S. cerevisiae Heat shock (37oC) 30 minutes, biological repeat #1

description: S. cerevisiae Heat shock (37oC) 30 minutes, repeat #1


title: S. cerevisiae Heat shock (37oC) 30 minutes, biological repeat #4

description: S. cerevisiae Heat shock (37oC) 30 minutes, repeat #4


title: S. paradoxus, MMS (0.02%), 20 minutes 2

description: S. paradoxus, MMS (0.02%), 20 minutes

source_name: S. paradoxus, MMS (0.02%), 20 minutes


title: S. paradoxus, MMS (0.02%), 60 minutes 2

description: S. paradoxus, MMS (0.02%),) 60 minutes

source_name: S. paradoxus, MMS (0.02%), 60 minutes


title: S. cerevisiae Heat shock (37oC) 30 minutes, biological repeat #2

description: S. cerevisiae Heat shock (37oC) 30 minutes, repeat #2


title: S. kudriavzevii, MMS (0.02%), 60 minutes

growth_protocol: Cells were grown on YPD to log phase at 24oC and then MMS was adeed to a final concentration of 0.02%


title: S. kudriavzevii, MMS (0.02%),45 minutes

description: S. kudriavzevii, MMS (0.02%), 45 minutes


title: S. mikatae, MMS (0.02%), 30 minutes

description: S. mikate, MMS (0.02%), 30 minutes

source_name: S. mikatae, MMS (0.02%), 30 minutes


title: S. kudriavzevii, MMS (0.02%), 90 minutes


title: S. paradoxus, MMS (0.02%), 45 minutes

description: S. paradoxu, MMS (0.02%), 45 minutes


title: S. paradoxus, MMS (0.02%), 10 minutes

description: S. paradoxus, MMS (0.02%), 10 minutes

source_name: S. paradoxus Heat shock (37oC) 10 minutes


title: S. cerevisiae, MMS (0.02%), 60 minutes

description: S. cerevisiae, MMS (0.02%), 60 minutes

source_name: S. cerevisiae, MMS (0.02%), 60 minutes


title: S. kudriavzevii, MMS (0.02%), 20 minutes


title: S. mikataes, MMS (0.02%), 45 minutes

description: S. mikate, MMS (0.02%), 45 minutes

source_name: S. mikataes, MMS (0.02%), 45 minutes

source_name: S. mikatae grown in YPD at 30oC


title: S. mikatae, MMS (0.02%), 90 minutes

description: S. mikate, MMS (0.02%), 90 minutes

source_name: S. mikatae, MMS (0.02%), 90 minutes


title: S. paradoxus, MMS (0.02%), 30 minutes

description: S. paradoxus, MMS (0.02%), 30 minutes

source_name: S. paradoxus grown in YPD at 30oC


title: S. mikatae, MMS (0.02%), 60 minutes

description: S. mikate, MMS (0.02%), 60 minutes

source_name: S. mikatae, MMS (0.02%), 60 minutes


title: S. cerevisiae, MMS (0.02%), 30 minutes

description: S. cerevisiae, MMS (0.02%), 30 minutes

source_name: S. cerevisiae, MMS (0.02%), 30 minutes

source_name: S. cerevisiae grown in YPD at 30oC


title: S. cerevisiae, MMS (0.02%), 90 minutes

description: S. cerevisiae, MMS (0.02%), 90 minutes

source_name: S. cerevisiae, MMS (0.02%), 90 minutes


title: S. kudriavzevii, MMS (0.02%), 30 minutes

source_name: S. kudriavzevii grown in YPD at 24oC


title: S. mikatae, MMS (0.02%), 20 minutes

description: S. mikate, MMS (0.02%), 20 minutes

source_name: S. mikatae, MMS (0.02%), 20 minutes


title: S. kudriavzevii, MMS (0.02%), 10 minutes


title: S. paradoxus, MMS (0.02%), 60 minutes

description: S. paradoxus, MMS (0.02%), 60 minutes


title: S. mikatae, nitrogen starvation, 2 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

growth_protocol: Cells were grown to log-phase in complete minimal medium (SCD) and harvested. A sample was removed for reference and immediately frozen and the rest of the cells were resuspended in minimal medium with limiting concentration of ammonium sulfate (YNB ?AA, -AS, 0.05M ammonium sulfate, 2% glucose, 20mg/L uracil, 100mg/L leucine, 20mg/L histidin) for additional growth.

source_name: S. mikatae grown in complete minimal medium (SCD) at 30oC


title: S. cerevisiae, MMS (0.02%), 10 minutes

description: S. cerevisiae, MMS (0.02%), 10 minutes

source_name: S. cerevisiae, MMS (0.02%), 10 minutes


title: S. paradoxus, MMS (0.02%), 90 minutes

description: S. paradoxus, MMS (0.02%), 90 minutes

source_name: S. paradoxus, MMS (0.02%), 90 minutes


title: S. cerevisiae, MMS (0.02%), 45 minutes

description: S. cerevisiae, MMS (0.02%), 45 minutes

source_name: S. cerevisiae, MMS (0.02%), 45 minutes


title: S. mikatae, nitrogen starvation, 8 hours


title: S. kudriavzevii, nitrogen starvation, 20 minutes

source_name: S. kudriavzevii grown in complete minimal medium (SCD) at 24oC


title: S. paradoxus, MMS (0.02%), 10 minutes 2

description: S. paradoxus, MMS (0.02%), 10 minutes

source_name: S. paradoxus, MMS (0.02%), 10 minutes


title: S. paradoxus, nitrogen starvation, 8 hours 2

source_name: S. paradoxus grown in complete minimal medium (SCD) at 30oC


title: S. cerevisiae, MMS (0.02%),) 20 minutes

description: S. cerevisiae, MMS (0.02%), 20 minutes

source_name: S. cerevisiae, MMS (0.02%), 20 minutes


title: S. paradoxus, nitrogen starvation, 4 hours 2


title: S. kudriavzevii, nitrogen starvation, 2 hours


title: S. kudriavzevii, nitrogen starvation, 45 minutess


title: S. kudriavzevii, nitrogen starvation, 10 minutes


title: S. paradoxus, nitrogen starvation, 45 minutes 2

source_name: S. paradoxus, nitrogen starvation,45 minutes


title: S. mikatae, MMS (0.02%), 10 minutes

description: S. mikatae, MMS (0.02%), 10 minutes

source_name: S. mikatae, MMS (0.02%), 10 minutes

source_name: S. mikatae grown in YPD at 30oC


title: S. kudriavzevii, nitrogen starvation, 8 hours


title: S. paradoxus, nitrogen starvation, 20 minutes 2


title: S. paradoxus, nitrogen starvation, 2 hours 2

source_name: S. paradoxuse, nitrogen starvation, 2 hours


title: S. mikatae, nitrogen starvation, 45 minutess


title: S. mikatae, nitrogen starvation, 4 hours

description: S. mikatae, nitrogen starvation,4 hours


title: S. mikatae, nitrogen starvation, 10 minutes


title: S. paradoxus, nitrogen starvation, 10 minutes 2


title: S. paradoxus, MMS (0.02%), 20 minutes

description: S. paradoxus, MMS (0.02%), 20 minutes

source_name: S. paradoxus, MMS (0.02%), 20 minutes

source_name: S. paradoxus grown in YPD at 30oC


title: S. paradoxus, transfer from glucose to glycerol, 45 minutes 2


title: S. mikatae, nitrogen starvation, 20 minutes


title: S. paradoxus, nitrogen starvation, 1 day


title: S. paradoxus, nitrogen starvation, 10 minutes


title: S. cerevisiae, nitrogen starvation, 8 hours

source_name: S. cerevisiae grown in complete minimal medium (SCD) at 30oC


title: S. paradoxus, transfer from glucose to glycerol, 60 minutes 2


title: S. kudriavzevii, nitrogen starvation, 4 hours


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes 2


title: S. paradoxus, nitrogen starvation, 4 hours


title: S. cerevisiae, nitrogen starvation, 10 minutes


title: S. paradoxus, nitrogen starvation, 20 minutes


title: S. paradoxus, nitrogen starvation, 45 minutes

description: S. paradoxus, nitrogen starvation,45 minutes


title: S. paradoxus, nitrogen starvation, 8 hours

description: S. paradoxus, nitrogen starvation, 8 houra


title: S. paradoxus, transfer from glucose to glycerol, 90 minutes 2


title: S. paradoxus, nitrogen starvation, 2 hours


title: S. cerevisiae, nitrogen starvation, 2 hours


title: S. cerevisiae, nitrogen starvation, 20 minutes


title: S. cerevisiae, nitrogen starvation, 1 day


title: S. cerevisiae, nitrogen starvation, 45 minutes

source_name: S. cerevisiae, nitrogen starvation,45 minutes


title: S. cerevisiae, nitrogen starvation, 4 hours


title: S. paradoxus, transfer from glucose to glycerol, 10 minutes 2


title: S. kudriavzevii, transfer from glucose to glycerol, 60 minutes

source_name: S. kudriavzevii grown in YPD at 24oC


title: S. mikatae, transfer from glucose to glycerol, 90 minutes


title: S. paradoxus, transfer from glucose to glycerol, 20 minutes 2


title: S. paradoxus, transfered from glucose to glycerol, 90 minutes

description: S. paradoxus, transfer from glucose to glycerol, 90 minutes


title: S. mikatae, transfer from glucose to glycerol, 30 minutes


title: S. mikatae, transfer from glucose to glycerol, 20 minutes


title: S. mikatae, transfer from glucose to glycerol, 10 minutes


title: S. mikatae, transfer from glucose to glycerol, 60 minutes


title: S. mikatae, transfer from glucose to glycerol, 45 minutes


title: S. cerevisiae, transfer from glucose to glycerol, 45 minutes

source_name: S. cerevisiae, transfered from glucose to glycerol, 45 minutes

source_name: S. cerevisiae grown in YPD at 30oC


title: S. cerevisiae, transfer from glucose to glycerol, 30 minutes

source_name: S. cerevisiae, transfered from glucose to glycerol, 30 minutes


title: S. cerevisiae, transfer from glucose to glycerol, 20 minutes

source_name: S. cerevisiae, transfered from glucose to glycerol, 20 minutes


title: S. paradoxus, transfer from glucose to glycerol, 45 minutes


title: S. cerevisiae, transfered from glucose to glycerol, 10 minutes

description: S. cerevisiae, transfer from glucose to glycerol, 10 minutes


title: S. kudriavzevii, transfer from glucose to glycerol, 45 minutes


title: S. cerevisiae, transfer from glucose to glycerol, 60 minutes

source_name: S. cerevisiae, transfered from glucose to glycerol, 60 minutes


title: S. paradoxus H2O2 (0.3mM) 60 minutes 2

description: S. paradoxus H2O2 (0.3mM) 60 minutes

source_name: S. paradoxus H2O2 (0.3mM) 60 minutes


title: S. paradoxus, transfer from glucose to glycerol, 60 minutes


title: S. paradoxus H2O2 (0.3mM) 90 minutes 2

description: S. paradoxus H2O2 (0.3mM) 90 minutes

source_name: S. paradoxus H2O2 (0.3mM) 90 minutes


title: S. kudriavzevii, transfer from glucose to glycerol, 10 minutes


title: S. kudriavzevii, transfer from glucose to glycerol, 20 minutes


title: S. cerevisiae, transfer from glucose to glycerol, 90 minutes

source_name: S. cerevisiae, transfered from glucose to glycerol, 90 minutes


title: S. paradoxus H2O2 (0.3mM) 45 minutes 2

description: S. paradoxus H2O2 (0.3mM) 45 minutes

source_name: S. paradoxus H2O2 (0.3mM) 45 minutes


title: S. mikatae H2O2 (0.3mM) 90 minutes

description: S. mikate H2O2 (0.3mM) 90 minutes

source_name: S. mikatae H2O2 (0.3mM) 90 minutes


title: S. kudriavzevii H2O2 (0.3mM) 30 minutes

description: S. kudriavzevii H2O2 (0.3mM) 30 minutes

source_name: S. kudriavzevii H2O2 (0.3mM) 30 minutes


title: S. kudriavzevii, transfer from glucose to glycerol, 90 minutes


title: S. kudriavzevii H2O2 (0.3mM) 10 minutes

description: S. kudriavzevii H2O2 (0.3mM) 10 minutes

source_name: S. kudriavzevii H2O2 (0.3mM) 10 minutes


title: S. paradoxus, transfer from glucose to glycerol, 20 minutes


title: S. paradoxus, transfer from glucose to glycerol, 10 minutes


title: S. mikatae H2O2 (0.3mM) 60 minutes

description: S. mikate H2O2 (0.3mM) 60 minutes

source_name: S. mikatae H2O2 (0.3mM) 60 minutes

source_name: S. mikatae grown in YPD at 30oC


title: S. kudriavzevii, transfer from glucose to glycerol, 30 minutes


title: S. kudriavzevii H2O2 (0.3mM) 45 minutes

description: S. kudriavzevii H2O2 (0.3mM) 45 minutes

source_name: S. kudriavzevii H2O2 (0.3mM) 45 minutes


title: S. mikatae H2O2 (0.3mM) 10 minutes

description: S. mikatae H2O2 (0.3mM) 10 minutes

source_name: S. mikatae H2O2 (0.3mM) 10 minutes


title: S. mikatae H2O2 (0.3mM) 20 minutes

description: S. mikate H2O2 (0.3mM) 20 minutes

source_name: S. mikatae H2O2 (0.3mM) 20 minutes


title: S. paradoxus H2O2 (0.3mM) 30 minutes 2

description: S. paradoxus H2O2 (0.3mM) 30 minutes

source_name: S. paradoxus H2O2 (0.3mM) 30 minutes

source_name: S. paradoxus grown in YPD at 30oC


title: S. kudriavzevii H2O2 (0.3mM) 60 minutes

description: S. kudriavzevii H2O2 (0.3mM) 60 minutes

source_name: S. kudriavzevii H2O2 (0.3mM) 60 minutes

source_name: S. kudriavzevii grown in YPD at 24oC


title: S. kudriavzevii H2O2 (0.3mM) 20 minutes

description: S. kudriavzevii H2O2 (0.3mM) 20 minutes

source_name: S. kudriavzevii H2O2 (0.3mM) 20 minutes


title: S. paradoxus H2O2 (0.3mM) 20 minutes

description: S. paradoxus H2O2 (0.3mM) 20 minutes

source_name: S. paradoxus H2O2 (0.3mM) 20 minutes


title: S. paradoxus H2O2 (0.3mM) 30 minutes

description: S. paradoxus H2O2 (0.3mM) 30 minutes


title: S. paradoxus H2O2 (0.3mM) 45 minutes

description: S. paradoxus H2O2 (0.3mM) 45 minutes


title: S. paradoxus H2O2 (0.3mM) 10 minutes 2

description: S. paradoxus H2O2 (0.3mM) 10 minutes

source_name: S. paradoxus H2O2 (0.3mM) 10 minutes


title: S. paradoxus H2O2 (0.3mM) 20 minutes 2

description: S. paradoxus H2O2 (0.3mM) 20 minutes


title: S. paradoxus Heat shock (37oC) 20 minutes 2


title: S. paradoxus H2O2 (0.3mM) 90 minutes

description: S. paradoxus H2O2 (0.3mM) 90 minutes

source_name: S. paradoxus H2O2 (0.3mM) 90 minutes


title: S. mikatae H2O2 (0.3mM) 30 minutes

description: S. mikate H2O2 (0.3mM) 30 minutes

source_name: S. mikatae H2O2 (0.3mM) 30 minutes


title: S. paradoxus Heat shock (37oC) 30 minutes 2


title: S. paradoxus H2O2 (0.3mM) 60 minutes

description: S. paradoxus H2O2 (0.3mM) 60 minutes

source_name: S. paradoxus H2O2 (0.3mM) 60 minutes


title: S. paradoxus Heat shock (37oC) 60 minutes 2


title: S. cerevisiae H2O2 (0.3mM) 90 minutes

description: S. cerevisiae H2O2 (0.3mM) 90 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 90 minutes

source_name: S. cerevisiae grown in YPD at 30oC


title: S. kudriavzevii Heat shock (37oC) 30 minutes


title: S. kudriavzevii Heat shock (37oC) 45 minutes


title: S. paradoxus H2O2 (0.3mM) 10 minutes

description: S. paradoxus H2O2 (0.3mM) 10 minutes


title: S. paradoxus, transfer from glucose to glycerol, 30 minutes


title: S. kudriavzevii Heat shock (37oC) 60 minutes


title: S. cerevisiae H2O2 (0.3mM) 20 minutes

description: S. cerevisiae H2O2 (0.3mM) 20 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 20 minutes


title: S. paradoxus Heat shock (37oC) 10 minutes 2


title: S. cerevisiae H2O2 (0.3mM) 30 minutes

description: S. cerevisiae H2O2 (0.3mM) 30 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 30 minutes


title: S. mikatae Heat shock (37oC) 10 minutes

description: S. mikatae Heat shock (37oC) 10 minutes

source_name: S. mikatae Heat shock (37oC) 10 minutes

source_name: S. mikatae grown in YPD at 30oC


title: S. cerevisiae H2O2 (0.3mM) 60 minutes

description: S. cerevisiae H2O2 (0.3mM) 60 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 60 minutes


title: S. paradoxus Heat shock (37oC) 90 minutes


title: S. mikatae Heat shock (37oC) 60 minutes

description: S. mikate Heat shock (37oC) 60 minutes

source_name: S. mikatae Heat shock (37oC) 60 minutes


title: S. mikatae Heat shock (37oC) 20 minutes

description: S. mikate Heat shock (37oC) 20 minutes

source_name: S. mikatae Heat shock (37oC) 20 minutes


title: S. mikatae Heat shock (37oC) 30 minutes

description: S. mikate Heat shock (37oC) 30 minutes

source_name: S. mikatae Heat shock (37oC) 30 minutes


title: S. mikataes Heat shock (37oC) 45 minutes

description: S. mikate Heat shock (37oC) 45 minutes


title: S. paradoxus Heat shock (37oC) 45 minutes 2

source_name: S. paradoxus grown in YPD at 30oC


title: S. cerevisiae Heat shock (37oC) 30 minutes


title: S. cerevisiae Heat shock (37oC) 60 minutes


title: S. mikataes H2O2 (0.3mM) 45 minutes

description: S. mikate H2O2 (0.3mM) 45 minutes

source_name: S. mikataes H2O2 (0.3mM) 45 minutes


title: S. mikatae Heat shock (37oC) 90 minutes

description: S. mikate Heat shock (37oC) 90 minutes

source_name: S. mikatae Heat shock (37oC) 90 minutes


title: S. cerevisiae H2O2 (0.3mM) 10 minutes

description: S. cerevisiae H2O2 (0.3mM) 10 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 10 minutes


title: S. kudriavzevii Heat shock (37oC) 90 minutes

source_name: S. kudriavzevii grown in YPD at 24oC


title: S. cerevisiae Heat shock (37oC) 10 minutes


title: S. cerevisiae Heat shock (37oC) 20 minutes


title: S. paradoxus Heat shock (37oC) 45 minutes


title: S. paradoxus Heat shock (37oC) 60 minutes


title: S. kudriavzevii Heat shock (37oC) 10 minutes


title: S. cerevisiae Heat shock (37oC) 45 minutes


title: S. kudriavzevii Heat shock (37oC) 20 minutes


title: S. cerevisiae Heat shock (37oC) 90 minutes


title: S. paradoxus Heat shock (37oC) 30 minutes


title: S. paradoxus Heat shock (37oC) 10 minutes


title: S. cerevisiae H2O2 (0.3mM) 45 minutes

description: S. cerevisiae H2O2 (0.3mM) 45 minutes

source_name: S. cerevisiae H2O2 (0.3mM) 45 minutes


title: S. paradoxus Heat shock (37oC) 20 minutes


title: MicMa185_Agilent

status: Public on Nov 30 2005

first: Yulei

last: Wang

description: biopsy of breast carcinoma

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: MicMa185_Agilent with Cy5

label_protocol: Amplified and labeled according to standard Agilent protocols

extract_protocol: not provided

tag: early stage, breast carcinoma

source_name: Universal Human Reference (Stratagene) with Cy3

tag: Common Reference

value: Universal Human Reference RNA sample (Stratagene)