title: HU_IFN_A5

status: Public on Dec 28 2006

type: RNA

city: Genova

first: Ulrich

last: Pfeffer

address: L. Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

description: endothelial cells isoltaed from human umbilical cord veins, primary culture

data_processing: GCRMA

label: biotin - SAPE

molecule: total RNA

organism: Homo sapiens

source_name: human endothelial cells

tag: 1000 IU interferon alpha treated, 5hrs.


title: FH_con_3

description: fibroblasts isolated from human umbilical cord veins, primary culture

source_name: human fibroblasts

tag: untreated control


title: FH_IFN_A2


title: HU_IFN_A4


title: HU_IFN_G3

tag: 1000 IU interferon gamma treated, 5 hrs.


title: FH_IFN_G2


title: rpb1-E1230K-N2

status: Public on Dec 21 2006

city: Aarhus

first: Francisco

last: Malagon

address: C.F. Mollers Alle, Bldg. 130

department: Department of Molecular Biology

country: Denmark

institute: Aarhus University

description:
Total RNA from rpb1-E1230K mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

hyb_protocol: As described previously: Nuwaysir EF, et all. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:1749-55.

data_processing: RMA (Robust Multichip Average) applied to seven samples of day B (N2)

label: bio-11-CTP and bio-16 UTP

organism: Saccharomyces cerevisiae

source_name: rpb1-E1230K; 30C-YPED; BY series strain

growth_protocol: Rich Media (YPED) at 30C with shaking. As described previously (Malagon F and Aguilera A. 2001. Yeast spt6-140 mutation, affecting chromatin and transcription, preferentially increases recombination in which Rad51p-mediated strand exchange is dispensable. Genetics. 158:597-611).

extract_protocol: Hot acid phenol extraction as described previously (Kohrer K and Domdey H. 1991. Preparation of high molecular weight RNA. Methods Enzymol. 194:398-405).

tag: BY series strain of the Yeast Knock-Out collection. rpb1-E1230K mutant strain.


title: HU_IFN_B2

description: endothelial cells isolated from human umbilical cord veins, primary culture

tag: 1000 IU interferon beta treated, 5hrs.


title: HU_con_5


title: HU_IFN_G1

tag: 1000 IU interferon gamma treated, 5hrs.


title: FH_con_1


title: HU_IFN_A2


title: FH_IFN_G1


title: HU_IFN_G2


title: HU_con_1


title: FH_IFN_A1

tag: 1000 IU interferon treated, 5hrs.


title: HU_IFN_A3

tag: 1000 IU interferon alpha treated, 5 hrs.


title: HU_con_4


title: rpb1-N488D-N2

description:
Total RNA from rpb1-N488D mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-N488D; 30C-YPED; BY series strain

label_protocol: As described previously: Nuwaysir EF, et all. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:1749-55.

tag: BY series strain of the Yeast Knock-Out collection. rpb1-N488D mutant strain.


title: HU_con_2


title: FH_con_2


title: HU_IFN_B1


title: FH_IFN_A3


title: HU_IFN_A1


title: HU_con_3


title: rpb1-D261N-N1

description:
Total RNA from rpb1-D261N mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

data_processing: RMA (Robust Multichip Average) applied to seven samples of day A (N1)

source_name: rpb1-D261N mutant; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-D261N mutant.


title: rpb1-R320C-N2

description:
Total RNA from rpb1-R320C mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-R320C-N2; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. Wild type RPB1.rpb1-R320C-N2 strain.


title: rpb1-E1103G-N1

description:
Total RNA from rpb1-E1103G mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-E1103G; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-E1103G mutant strain.


title: RPB1-N2

description:
Total RNA from RPB1 wild type strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: Wild type RPB1; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. Wild type RPB1.


title: rpb1-D261N-N2

description:
Total RNA from rpb1-D261N mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-D261N; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-D261N strain.


title: rpb1-D260N-N1

description:
Total RNA from rpb1-D260N mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-D260N mutant; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-D260N mutant


title: rpb1-R320C-N1

description:
Total RNA from rpb1-R320C mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-R320C; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-R320C mutant strain.


title: rpb1-E1230K-N1

description:
Total RNA from rpb1-E1230K mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).


title: LacZ-2

status: Public on Dec 19 2006

city: University of OULU

first: Jaana

last: Rysä

address: PO BOX 5000

department: Pharmacology and toxicology

country: Finland

institute: University of Oulu

description: Gene expression profiles three days after MKK3bE + WT p38α gene transfer were compared with those of Lac Z –treated animals by screening Affymetrix Rat Expression Set 230_2.0 Arrays (there are 5 samples in both group).

hyb_protocol: Wash A1 Recovery Mixes:		0 Wash A1 Temperature (C):		30 Number of Wash A1 Cycles:		10 Mixes per Wash A1 Cycle:		2 Wash B Recovery Mixes:		0 Wash B Temperature (C):		50 Number of Wash B Cycles:		6 Mixes per Wash B Cycle:		15 Stain Temperature (C):		35 First Stain Time (seconds):		300 Wash A2 Recovery Mixes:		0 Wash A2 Temperature (C):		30 Number of Wash A2 Cycles:		10 Mixes per Wash A2 Cycle:		4 Second Stain Time (seconds):		300 Third Stain Time (seconds):		300 Wash A3 Recovery Mixes:		0

data_processing: GCOS 1.2

label: Biotin

organism: Rattus norvegicus

source_name: LacZ-injected rat left ventricle

tag: Strain:Sprague-Dawley rats Gender:male Weight

value: 250-300 g Tissue:left ventricle


title: p38-5

source_name: p38-injected rat left ventricle


title: BMAL-/- replicate F08

status: Public on Dec 16 2006

city: Philadelphia

first: Radu

middle: Daniel

last: Rudic

state: PA

address: 421 Curie Boulevard

department: Center of Experimental Therapeutics

country: USA

institute: University of Pennsylvania

description: After 2 week acclimation to 12 hr/12 hr light/dark regimen, mice were placed in constant darkness for at least 30 hours before sacrifice under anesthesia at ZT14. Thoracic aortae were harvested and the RNA extracted and hybridized to Affymetrix MOE 430V2 chips.

hyb_protocol: Target cRNA was prepared from total RNA and hybridized using 20ug of cRNA onto Affymetrix MOE 430V2 chips in accordance with protocols described in the Affymetrix Gene-Chip Expression Analysis Technical Manual.

data_processing: GCRMA normalization; Affymetrix Microarray Suite 5.0 normalization

organism: Mus musculus

source_name: Aorta, male BMAL-/-, ZT14

extract_protocol: Mice were anesthetized at the time of sacrifice. The abdomen and thorax were opened and a blood sample was taken from the vena cava. The animal was then perfused via the left ventricle with 10mls of phosphate buffered saline (PBS) (Fisher Scientific) followed by 5mls of DEPC treated water (Fischer Scientific). The aorta was exposed as close to the heart as possible at the aortic arch and to just beyond the femoral artery bifurcation, using a dissection microscope. It was then removed and immediately flash-frozen in liquid Nitrogen. Aortae were pulverized on dry ice with a Plattner’s diamond mortar and pestle set (Fisher Scientific). Total RNA was extracted using RNAqueous (Ambion, TX) and Trizol (Invitrogen, CA) and quantified by spectrophotometer.

treatment_protocol: Mice were initially acclimatized for at least 2 weeks to a 12 hour light/dark cycle (light 7:00-19:00h or ZT0-ZT12; dark 19:00-7:00h or ZT12-ZT24). Mice were placed in constant darkness for at least 30 hours before sacrifice

tag: Strain

value: BMAL-/- partially backcrossed onto C57Bl/6J

tag: Sex

value: male

tag: Tissue

value: aorta

tag: Circadian time


title: p38-1


title: p38-4


title: BMAL-/- replicate F03


title: BMAL-/- replicate F02


title: BMAL+/+ replicate F01

treatment_protocol: Mice were initially acclimatized for at least 2 weeks to a 12 hour light/dark cycle (light 7:00-19:00h or ZT0-ZT12; dark 19:00-7:00h or ZT12-ZT24). Mice were placed in constant darkness for at least 30 hours before sacrifice.

value: BMAL+/+ partially backcrossed onto C57Bl/6J


title: LacZ-4


title: BMAL+/+ replicate F10

source_name: Aorta, male BMAL+/+, ZT14


title: LacZ-3


title: LacZ-1

tag: Strain:Sprague-Dawley rats

tag: Weight

tag: Tissue:left ventricle


title: BMAL+/+ replicate F07


title: BMAL-/- replicate F05


title: BMAL+/+ replicate F09


title: p38-3


title: p38-2


title: BMAL+/+ replicate F04


title: NPAS2 mutant replicate F19

source_name: Aorta, male NPAS2 mutant, ZT14

value: NPAS2 mutant on C57Bl/6J background


title: NPAS2 mutant replicate F13


title: NPAS2 mutant replicate F20


title: NPAS2 mutant replicate F12


title: NPAS2 mutant replicate F18


title: LacZ-5


title: P.aeruginosa_+40µMPQS_11h_2

status: Public on Dec 12 2006

city: Braunschweig

first: Florian

last: Bredenbruch

address: Mascheroderweg 1

department: Cellbiology

country: Germany

institute: GBF-Braunschweig

description: · Threshold of Signal Log ratio: -1/1; change is I (increased), MI (marginally increased), D (decreased), MD (marginally decreased); change p-value >0.999 or <0.001; only genes that are present (Detection=P) in at least one of the compared chipsets.

hyb_protocol: Hybridization of the probes was carried out according to the manufacturer’s “Expression Analysis Protocol (p. 25: Modified Fluidic Protocol for P. aeruginosa cDNA Assay)”, see http://www.affymetrix.com:

data_processing: MAS 5.0

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa total RNA after 11 h growth with 40 µM PQS

growth_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 11 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 11 h of growth

tag: In order to evaluate the influence of 40µM PQS on the global Pseudomonas aeruginosa gene expression, we performed a comparative gene expression analysis of PQS-treated versus untreated P. aeruginosa PAO1 cultures after 5, 11 and 20 h of incubation.


title: P.aeruginosa_-PQS_11h_2

source_name: P. aeruginosa total RNA after 11 h growth without PQS

growth_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 11 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 11 h of growth


title: P.aeruginosa_+40µMPQS_20h_2

source_name: P. aeruginosa total RNA after 20 h growth with 40 µM PQS

growth_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 20 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 20 h of growth


title: Wild Type replicate F17

source_name: Aorta, male WT, ZT14


title: P.aeruginosa_-PQS_5h_1

description:
· Threshold of Signal Log ratio: -1/1; change is I (increased), MI (marginally increased), D (decreased), MD (marginally decreased); change p-value >0.999 or <0.001; only genes that are present (Detection=P) in at least one of the compared chipsets.
· Only following genes were considered: Minimal threshold of regulation ±2 fold; minimal change p-values of 0.999 and 0.001, respectively; minimal difference of signal intensities of 200.
· The final gene expression data table used by the authors to make their conclusions after data selection and transformation will be published as supplementary data.

hyb_protocol: Hybridization of the probes was carried out according to the manufacturer’s “Expression Analysis Protocol (p. 25: Modified Fluidic Protocol for P. aeruginosa cDNA Assay)”, see http://www.affymetrix.com:  Hybridization for 16 h at 50°C and 60 rpm.  - Post Hyb Wash 1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C - Post Hyb Wash 2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C - Stain: Stain the probe array for 10 minutes in Streptavidin Solution Mix at 25°C - Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C - 2nd Stain Wash: Stain the probe array for 10 minutes in antibody solution at 25°C - 3rd Stain Wash: Stain the probe array for 10 minutes in SAPE solution at 25°C - Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C.

source_name: P. aeruginosa total RNA after 5 h growth without PQS

growth_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 5 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 5 h of growth


title: P.aeruginosa_-PQS_20h_2

source_name: P. aeruginosa total RNA after 20 h growth without PQS

growth_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 20 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures without addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 20 h of growth


title: P.aeruginosa_-PQS_20h_1


title: P.aeruginosa_+40µMPQS_20h_1


title: P.aeruginosa_-PQS_11h_1


title: Wild Type replicate F16


title: P.aeruginosa_+40µMPQS_5h_2

source_name: P. aeruginosa total RNA after 5 h growth with 40 µM PQS

growth_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in 10 ml BHI medium in a 50 ml flask shaking culture (180 rpm, 37°C) and total RNA was extracted after 5 h of growth

treatment_protocol: P. aeruginosa PAO1 cultures with addition of 40 µM PQS were grown in BHI medium and total RNA was extracted after 5 h of growth


title: Wild Type replicate F11


title: P.aeruginosa_-PQS_5h_2


title: Wild Type replicate F14_2


title: Wild Type replicate F15


title: P.aeruginosa_+40µMPQS_5h_1


title: EtOH-160-3

status: Public on Dec 03 2006

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

hyb_protocol: standard Affymetrix recommended protocol

data_processing: Value column are raw signal intensity generated from MAS 5.0.

label: R-pycoerythin streptavadin

source_name: Kartik Shankar-UAMS/ACNC

tag: Pregnant rats fed either control or EtOH containing diets through 15 days of gestation at 220 kcal/kg0.75/d or 160 kcal/kg0.75/d. Hepatic gene expression in the dams were analyzed at gestation day 15


title: EtOH-160-4

scan_protocol: standard Affymetrix recommended protocol


title: EtOH-160-2

label_protocol: standard Affymetrix recommended protocol


title: EtOH-160-1


title: P.aeruginosa_+40µMPQS_11h_1


title: TEN-160-2


title: EtOH-220-3


title: EtOH-220-2


title: rpb1-E1103G-N2

description:
Total RNA from rpb1-E1103G mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-E1103G; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. Wild type RPB1.rpb1-E1103G mutant strain.


title: TEN-220-3


title: TEN-220-1


title: EtOH-220-1


title: TEN-220-2


title: RPB1-N1

description:
Total RNA from RPB1 wild type strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: Wild type RPB1; 30C-YPED; BY series strain


title: TEN-160-1


title: R7E 5

status: Public on Nov 18 2006

city: ILLKIRCH

first: Gretta

last: ABOU-SLEYMANE

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing: MAS 5.0 algorithms - Global data normalization

label: Biotinylated cRNA

source_name: Retina

tag: Gender

value: Male

tag: Age

value: 3 weeks (Onset stage)

tag: Transgene

value: Mutant ataxin-7


title: R7E 9

value: 9 weeks (Moderate stage)


title: R7E 6

value: Female


title: R7E 7


title: R7E 10


title: R7N 9

value: Normal ataxin-7


title: R7E 2


title: R7N 11


title: R7N 10


title: R7E 8


title: R7N 4


title: R7N 7


title: R7E 1


title: R7E 4


title: R7E 3


title: R7N 6


title: R7N 5


title: R7N 8


title: R7N 3


title: R7E 11


title: WT 4

tag: WILD  TYPE


title: R7N 1


title: R7N 2


title: R6 1

value: 9 weeks (Moderate Stage)

value: Mutant huntingtin


title: WT 2

tag: WILD TYPE


title: WT 3


title: 022xbl7k_liver_Wcaf_TP4215

status: Public on Jul 01 2006

city: Maastricht

first: Marten H.

last: Hofker

address: P.O. Box 616

department: Molecular Genetics

country: Netherlands

institute: University Maastricht

description: Experiments were performed in duplicate: the same RNAs were labeled, divided into two different pools and hybridized onto two different GEMs 2.03 (Incyte Genomics, Palo Alto, CA).

data_processing: cDNA arrays were scanned for both fluorescent signals (Cy5, Cy3) and the data were analyzed using the GEMTools software version 2.5.1 (Incyte Genomics, Palo Alto, CA). To determine if the signal was sufficiently high above background and was not the result of non-uniform noise on spotted DNA sites, a spot was included in the analysis if it showed a signal to background ratio of minimal 2.5, a signal intensity above 250 arbitrary units for one or both dyes, and a spot size of at least 40% of the spotted area.

molecule: polyA RNA

source_name: liver_E3L_diet W_4 wks

label_protocol: Poly (A)+ RNA was labeled for microarray hybridization as described by DeRisi JL et.al (1997) Science 278(5338):680-686.

extract_protocol: Total RNA was isolated using RNA STAT-60 (Tel-Test, Inc., Friendswood, TX) according to manufacturer's protocol. Subsequently, poly (A)+ RNA was isolated from total RNA using the poly (A) Tract mRNA isolation systems (Promega, Madison, WI)

value: APOE3Leiden (E3L); Gender:females; Diet:Western type diet (diet W), for 4 weeks; Tissue:liver

source_name: liver_E3L_diet W + caf_4 wks

value: APOE3Leiden (E3L), mouse TP4215; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022jbl7i_liver_Wcaf_TP4205

value: APOE3Leiden (E3L), mouse TP4205; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022ybl7f_liver_Wcaf_TP4163

value: APOE3Leiden (E3L), mouse TP4163; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022uc3zc_liver_Wcaf_SY521RL

value: APOE3Leiden (E3L), mouse SY521RL; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022fc3zf_liver_Wcaf_SY524ROB+L

value: APOE3Leiden (E3L), mouse SY524ROB+L; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022qbl7j_liver_Wcaf_TP4205


title: 022tc3zh_liver_Wcaf_SY522ROB

value: APOE3Leiden (E3L), mouse SY522ROB; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 022mc3zg_liver_Wcaf_SY522ROB


title: 0221c3zd_liver_Wcaf_SY521RL

value: APOE3Leiden (E3L);

value: females;

tag: Diet

value: Western type diet (diet W), for 4 weeks;

value: liver

value: APOE3Leiden (E3L), mouse SY521RL;

value: female;

value: Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks;


title: 0228c3ze_liver_Wcaf_SY524ROB+L


title: 022cbl7h_liver_Wcaf_TP4168

value: APOE3Leiden (E3L), mouse TP4168; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 0224bl7l_liver_Wcaf_TP4215


title: 022nc3zb_liver_Wcaf_SY518Z

value: APOE3Leiden (E3L), mouse SY518Z; Gender:female; Diet:Western type diet (diet W) supplemented with 0.04% (wt/wt) cafestol and 0.02% (wt/wt) kahweol, for 4 weeks; Tissue:liver


title: 0223bl7q_liver_Wcaf_SY518Z


title: rpb1-D260N-N2

description:
Total RNA from rpb1-D260N mutant strain growing at 30C in rich media in day B (N2).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-D260N mutant; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-D260N mutant


title: 0225bl7g_liver_Wcaf_TP4168

tag: Strain


title: O377 homozygotes brains 12

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: Homozygous O377 mutant mouse line versus wildtype mice

hyb_protocol: Total RNA from individual samples was obtained according to manufacturer's protocols using RNeasy Midi kits (Qiagen). 15 µg total RNA was used for treverse transcription and indirectly labelled with Cy3 or Cy5 fluorescent dye according the TIGR protocol. Labelled cDNA was dissolved in 30 µl hybridisation buffer and mixed with 30µl of reference cDNA solution labelled with the second dye. The hybridisation mix is placed on a pre-hybridised microarray, cover with coverslip and incubated at 42°C for 16-20 h.

scan_protocol: Slides were scanned for both CY3 and Cy5 signal with a GenePix 4000A

data_processing: Images were  processed by GenePixPro 6.0. Mean intensities with subtracted background were normalised so that the median of there rations has become 1.

source_name: RNA pool of 4 WT mouse brains

tag: C3HeB/FeJEL and C3H/EL, male, 4 weeks

source_name: RNA of 5 O377 homo mutant mouse brains 1-5


title: O377 homozygotes brains 11


title: O377 homozygotes brains 10


title: WT 1

value: Female

value: 9 weeks (Moderate stage)


title: O377 homozygotes brains 9


title: O377 homozygotes brains 8


title: O377 homozygotes brains 5


title: O377 homozygotes brains 7


title: O377 homozygotes brains 13


title: Unstaged Head Hair Follicles Plucked from woman (33F)

status: Public on Jun 30 2006

city: RTP

first: David

middle: J

last: Dix

state: NC

address: E. HWY54  US EPA

department: NHEERL

institute: US EPA

description: Healthy adult female

hyb_protocol: Each labeled cRNA was then fragmented, added to a hybridization solution, and hybridized for 16 hours to a HG-Focus genechip (Affymetrix, Santa Clara, CA) in an Affymetrix Fluidics Station 400.

scan_protocol: The chips were washed, stained with phycoerythrin-conjugated streptavidin and amplified by biotinylated anti-streptavidin.  After a final wash the arrays were scanned in a GCS3000 (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin: double amplication using MessageAmp aRNA Kit (Ambion)

source_name: Human Unstaged Head Hair Follicles

label_protocol: Briefly, first and second strand cDNA were synthesized.  Unlabelled aRNA was generated by in vitro transcription with unbiotinylated NTPs.  For probe preparation, aRNA was reverse transcribed with second round primers.  Second-strand cDNA was synthesized with T7 Oligo(dT) primer and purified.  Biotin-labeled cRNA was generated by in vitro synthesis transcription, and purified with Qiagen RNeasy kit.

extract_protocol: Total RNA was extracted on the day of collection or following storage at 4oC for 1-9 days in RNAlater.  The hair follicle samples from each individual were removed from RNALater and, without verifying their stage, placed directly into a 2 ml microcentrifuge tube containing 1 ml Trizol™. RNA extraction was then conducted according to manufacturer’s instructions (Invitrogen Life Technologies, CA); a handheld homogenizer (Fisher Scientific, Hampton NH) was used to break up the samples.  At the isopropanol precipitation step, RNA was pelleted either immediately or following storage at -80oC for up to seven months.  After centrifugation, the pellet was washed with 70% ethanol, air dried and resuspended in 10 µl RNA free water (Gibco-BRL, Gaithersburg, MD).  Concentration of the eluted RNA was quantified using GeneQuant spectrophotometer (Pharmacia Biotech, now Amersham Pharmacia Biotech, Piscataway, NJ) by absorbance readings at 260 and 280nm.

tag: Individual hairs were grasped as near to the scalp as possible and then yanked quickly out.  The bottom centimeter of each hair, containing the hair follicle, was trimmed off into a 5ml specimen jar filled to the top with RNALater (Ambion, Austin, Texas).  Samples were stored at ambient temperature until reaching the analytical laboratory, a period of 1-4 hr.


title: Unstaged Head Hair Follicles Plucked from woman (34F)

description: Healthy adult female


title: Unstaged Head Hair Follicles Plucked from woman (30F)

description: Healthy adult female


title: Unstaged Head Hair Follicles Plucked from woman (24F)

description: Healthy adult female


title: Unstaged Head Hair Follicles Plucked from woman (32F)

description: Healthy adult female


title: O377 homozygotes brains 6


title: O377 homozygotes brains_3


title: Unstaged Head Hair Follicles Plucked from man (5M)

description: Healthy adult male


title: Unstaged Head Hair Follicles Plucked from woman (27F)

description: Healthy adult female


title: Unstaged Head Hair Follicles Plucked from man (16M)

description: Healthy adult male


title: O377 homozygotes brains

scan_protocol: Slides were scanned for both CY3 and Cy5 signal with a GenePix 4000A..

data_processing: images were  processed by GenePixPro 6.0. Mean intensities with subtracted background were normalised so that the median of there rations has become 1.


title: Unstaged Head Hair Follicles Plucked from man (3M)

description: Healthy adult male


title: Unstaged Head Hair Follicles Plucked from woman (26F)

description: Healthy adult female


title: O377 homozygotes brains_2


title: O377 homozygotes brains_0


title: O377 homozygotes brains_1


title: 022rbl7e_liver_Wcaf_TP4163

value: APOE3Leiden (E3L); Gender:females; Diet:Western type diet (diet W), for 4 weeks; Tissue:liver


title: cDNA scc 11

city: Berlin

first: Ingo

last: Nindl

address: Schumannstr. 20/21

department: Dermatology

institute: Skin Cancer Center Charite

description:
sample of squamous cell carcinoma of the skin (scc_11):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA no 18

description:
sample of normal skin (no_18):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA no 17

description:
sample of normal skin (no_17):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA scc 06

description:
sample of squamous cell carcinoma of the skin (scc_06):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA scc 01

description:
sample of squamous cell carcinoma of the skin (scc_01):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA no 02+05+08

description:
sample of normal skin (no_02+05+08):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyB mutant

status: Public on May 15 2006

city: Albany

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

description: phyB mutant seedlings

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

label: biotin

organism: Arabidopsis thaliana

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

extract_protocol: Total RNA was extracted from ~400 mg (fw) tissue using the method of Chang et al. (Chang, S., Puryear, J. & Cairney, J. (1993) Plant Mol. Biol. Rep. 11, 113-116) followed by further purification using Qiagen RNeasy columns.

tag: phyB mutant


title: cDNA scc 14

description:
sample of squamous cell carcinoma of the skin (scc_14):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyA mutant

description: phyA mutant seedlings

tag: phyA mutant


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyB mutant

description: phyB mutant seedlings


title: cDNA no 19

description:
sample of normal skin (no_19):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA scc 07

description:
sample of squamous cell carcinoma of the skin (scc_07):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA ak 09+15

description:
sample of actinic keratoses (ak_09+15):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: cDNA ak 12

description:
sample of actinic keratoses (ak_12):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyAphyB mutant

description: phyAphyB mutant seedlings

tag: phyAphyB mutant


title: cDNA ak 04

description:
sample of actinic keratoses (ak_04):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)

source_name: ak 04


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_wildtype

description: Wild type seedlings

tag: Wild type


title: cDNA ak 03

description:
sample of actinic keratoses (ak_03):

Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. The type and number of genes involved in non-melanoma skin cancer (NMSC) are still unclear. This study examined and identified different expressed genes in NMSC. Fifteen snap-frozen biopsies of five immunosuppressed organ-transplanted recipients each normal skin, actinic keratosis (AK) and invasive squamous cell carcinoma (SCC) were analysed. Total RNA was extracted reverse transcribed and biotin-labeled cRNA was used for hybridization with Affymetrix HG-U133A gene expression cDNA-microarrays containing 22,283 known genes. Confocal scanner evaluated the signals twice and data analysis was performed by predicition analysis of microarrays (PAM) using nearest shrunken centroids with the threshold 3.5 to identify genes best characterizing normal skin and skin cancer. ANOVA analysis was performed as a second independent method to identify differentially expressed genes (p<0.05, and p<0.15). Quantitative verification of 13 up- or down-regulated genes was performed by real-time RT-PCR and genes were confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. Some of the genes (e.g. annexin, lamin, and metalloproteinases) up-regulated in carcinomas in our study have previously reported as over-expressed in NMSC. In total 42 genes were up-regulated and 76 genes were down-regulated in non-melanoma skin cancer. The majority of genes identified have not been previously reported different expressed during non-melanoma skin carcinogenesis.
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)

source_name: ak 03


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_wildtype

description: Wild type seedlings


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyA mutant

description: phyA mutant seedlings


title: rpb1-N488D-N1

description:
Total RNA from rpb1-N488D mutant strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19: 185-193)  and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

source_name: rpb1-N488D; 30C-YPED; BY series strain

tag: BY series strain of the Yeast Knock-Out collection. rpb1-N488D strain.


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep3_phyAphyB mutant

description: phyAphyB mutant seedlings


title: cDNA no 22

description:
sample of normal skin (no_22):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyAphyB mutant

description: phyAphyB mutant seedlings


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_wildtype

description: Wild type seedlings


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep1_phyA mutant

description: phyA mutant seedlings


title: 4 day seedling dark rep3_phyAphyB mutant

description: phyAphyB mutant seedlings


title: 4 day seedling dark rep2_phyB mutant

description: phyB mutant seedlings


title: 4 day seedling dark rep1_phyB mutant

description: phyB mutant seedlings


title: 4 day seedling dark rep2_phyAphyB mutant

description: phyAphyB mutant seedlings


title: TEN-160-3

tag: Pregnant rats fed either control or EtOH containing diets through 15 days of gestation at 220 kcal/kg0.75/d or 160 kcal/kg0.75/d. Hepatic gene expression in the dams were analyzed at gestation day 15


title: 4 day seedling dark rep3_phyA mutant

description: phyA mutant seedlings


title: Wild type E13.5 kidney rep 2 (430A)

status: Public on May 01 2006

city: Cincinnati

first: Kristopher

middle: Robert

last: Schwab

state: OH

address: 3333 Burnett Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Research Foundation

description: Wildtype complete (whole) E13.5 kidney replicate 2

source_name: Wild type E13.5 kidneys replicate 2

label_protocol: 30 ng of total RNA underwent two round of in vitro transcription according to Baugh LR, Hill AA, Brown EL, Hunter CP: Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29:E2938, 2001

extract_protocol: Kidneys were cleanly dissected from an wild type CD-1 E13.5 embryo, rinsed in PBS, pooled, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Wild type embryonic kidney at E13.5, CD-1 strain, whole kidney


title: Hoxa11, Hoxd11 null E16.5 kidney rep 2 (430A)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E16.5 kidney replicate 2

source_name: Hoxa11, Hoxd11 null E16.5 kidneys replicate 2

extract_protocol: Both kidneys were cleanly dissected from an E16.5 HoxA11/D11 targeted null embryo, rinsed in PBS, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Hoxa11, Hoxd11 double null targeted embryonic kidney at E16.5, mixed C57, C3H and CF1 strain, whole kidney


title: 4 day seedling dark rep1_wildtype

description: Wild type seedlings


title: 4 day seedling dark rep3_phyB mutant

description: phyB mutant seedlings


title: 4 day seedling dark rep1_phyAphyB mutant

description: phyAphyB mutant seedlings


title: 4 day seedling dark rep1_phyA mutant

description: phyA mutant seedlings


title: 4 day seedling dark rep3_wildtype

description: Wild type seedlings


title: Wild type E16.5 kidney rep 1 (430A)

description: Wildtype complete (whole) E16.5 kidney replicate 1

source_name: Wild type E16.5 kidneys replicate 1

extract_protocol: Kidneys were cleanly dissected from an wild type CD-1 E16.5 embryo, rinsed in PBS, pooled, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Wild type embryonic kidney at E16.5, CD-1 strain, whole kidney


title: Wild type E16.5 kidney rep 2 (430A)

description: Wildtype complete (whole) E16.5 kidney replicate 2

source_name: Wild type E16.5 kidneys replicate 2


title: Wild type E13.5 kidney rep 1 (430A)

description: Wildtype complete (whole) E13.5 kidney replicate 1

source_name: Wild type E13.5 kidneys replicate 1


title: Adult kidney rep 2 (430A)

description: Wild type adult complete (whole) kidney replicate 1

source_name: Adult kidney replicate 2

label_protocol: 100 ng of total RNA underwent two round of in vitro transcription according to Baugh LR, Hill AA, Brown EL, Hunter CP: Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29:E2938, 2001

extract_protocol: Both kidneys were removed from a sacrificed adult mouse, rinsed in PBS, total RNA was prepared using RNAzol (Tel-Test, Friendwood, TX, USA)

tag: Wild type, CD-1 strain, greater than 10 week old (Adult), whole kidney


title: 4 day seedling dark rep2_phyA mutant

description: phyA mutant seedlings


title: Wild type E12.5 kidney rep 1 (430A)

description: Wildtype complete (whole) E12.5 kidney replicate 1

source_name: Wild type E12.5 kidneys replicate 1

extract_protocol: Kidneys were cleanly dissected from an wild type CD-1 E12.5 embryo, rinsed in PBS, pooled, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Wild type embryonic kidney at E12.5, CD-1 strain, whole kidney


title: Wild type E12.5 kidney rep 2 (430A)

description: Wildtype complete (whole) E12.5 kidney replicate 2

source_name: Wild type E12.5 kidneys replicate 2


title: Hoxa11, Hoxd11 null E13.5 kidney rep 2 (430A)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E13.5 kidney replicate 2

source_name: Hoxa11, Hoxd11 null E13.5 kidneys replicate 2

extract_protocol: Both kidneys were cleanly dissected from an E13.5 HoxA11/D11 targeted null embryo, rinsed in PBS, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Hoxa11, Hoxd11 double null targeted embryonic kidney at E13.5, mixed C57, C3H and CF1 strain, whole kidney


title: 4 day seedling dark rep2_wildtype

description: Wild type seedlings


title: Hoxa11, Hoxd11 null E16.5 kidney rep 1 (430A)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E16.5 kidney replicate 1

source_name: Hoxa11, Hoxd11 null E16.5 kidneys replicate 1


title: Hoxa11, Hoxd11 null E12.5 kidney rep 2 (430A)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E12.5 kidney replicate 2

source_name: Hoxa11, Hoxd11 null E12.5 kidneys replicate 2

extract_protocol: Both kidneys were cleanly dissected from an E12.5 HoxA11/D11 targeted null embryo, rinsed in PBS, total RNA was prepared using the Stratagene Absolutely RNA Nanoprep Kit (La Jolla, CA)

tag: Hoxa11, Hoxd11 double null targeted embryonic kidney at E12.5, mixed C57, C3H and CF1 strain, whole kidney


title: Hoxa11, Hoxd11 null E16.5 kidney rep 1 (430B)


title: Wild type E16.5 kidney rep 2 (430B)


title: Wild type E13.5 kidney rep 1 (430B)


title: Wild type E16.5 kidney rep 1 (430B)


title: Hoxa11, Hoxd11 null E12.5 kidney rep 1 (430A)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E12.5 kidney replicate 1

source_name: Hoxa11, Hoxd11 null E12.5 kidneys replicate 1


title: Wild type E12.5 kidney rep 2 (430B)


title: Wild type E13.5 kidney rep 2 (430B)


title: Hoxa11, Hoxd11 null E16.5 kidney rep 2 (430B)


title: Wild type E12.5 kidney rep 1 (430B)


title: Hoxa11, Hoxd11 null E13.5 kidney rep 2 (430B)


title: Adult kidney rep 1 (430A)

source_name: Adult kidney replicate 1


title: Hoxa11, Hoxd11 null E13.5 kidney rep 1 (430B)

description: Hoxa11, Hoxd11 double null targeted complete (whole) E13.5 kidney replicate 1

source_name: Hoxa11, Hoxd11 null E13.5 kidneys replicate 1


title: Adult kidney rep 1 (430B)


title: Livers from fat line chickens, pool 9, replicate 3

city: Rennes cedex

first: Christian

last: Diot

address: 65, rue de saint-Brieuc, CS 84215

department: Animal Genetics

institute: INRA

hyb_protocol: Test sample labelled with Cy5 and reference sample labelled with Cy3 solutions (10 µl) were mixed and incubated 2 min at 100°C, and 30 min at 37°C before hybridization. Hybridizations were performed in hybridization chambers (Corning Life Sciences) overnight at 42°C and slides were washed in 2X SSC, 0.1 % SDS, then in 1X SSC and finally twice in 0.2X SSC.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with ScanArray 4000 XL (Packard Biochip Technologies) fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0.1.17 analysis software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were normalized by lowess fitness using Madtools.

organism: Gallus gallus

source_name: Livers from fat line chickens

label_protocol: Poly(A)+ RNA (500 ng) were reverse-transcribed with amino-allyl-dUTPs (CyScribe Post-Labeling Kit, Amersham Biosciences). The amino-allyl modified cDNAs were purified on GFX columns (GFX Purification Kit, Amersham Biosciences) and further labelled by incubation with cyanine dyes (Cy3 or Cy5). Labeled cDNAs were also purified on GFX columns and mixed with hybridization buffer (5X Denhardt’s, 3.5X SSC, 0.3 % SDS, 0.5 µg/µl yeast RNA, 0.5 µg/µl poly(A) RNA and 50 % formamide)

extract_protocol: Total RNA were extracted with TRIzol Reagent (Invitrogen) from 4 chickens. Poly(A)+ RNA was extracted from a pool of the 4 total RNA preparations with PolyATtract® mRNA isolation system III (Promega)

tag: Livers from four fat line chickens with 3.6 % (mean) of adipose tissue content per live body weight

source_name: Livers from all lean and fat line chickens

extract_protocol: pooling of poly(A)+ RNA prepared from ten lean and fat line chicken liver total RNA pools

tag: As a reference sample, poly(A)+ RNA preparations from all lean and fat line chickens (10) were mixed in a superpool.


title: Livers from fat line chickens, pool 10, replicate 1

tag: Livers from four fat line chickens with 4.6 % (mean) of adipose tissue content per live body weight


title: Livers from fat line chickens, pool 9, replicate 1


title: Livers from fat line chickens, pool 10, replicate 2


title: Livers from fat line chickens, pool 10, replicate 3


title: Livers from fat line chickens, pool 8, replicate 1

tag: Livers from four fat line chickens with 3.2 % (mean) of adipose tissue content per live body weight


title: Hoxa11, Hoxd11 null E12.5 kidney rep 1 (430B)


title: Livers from fat line chickens, pool 9, replicate 2


title: Hoxa11, Hoxd11 null E12.5 kidney rep 2 (430B)


title: Livers from fat line chickens, pool 8, replicate 2


title: Livers from fat line chickens, pool 7, replicate 3

tag: Livers from four fat line chickens with 2.7 % (mean) of adipose tissue content per live body weight


title: O377 homozygotes brains 4

description: Homozygous O377 mutant mouse line versus wildtype mice

source_name: RNA pool of 4 WT mouse brains

tag: C3HeB/FeJEL and C3H/EL, male, 4 weeks

source_name: RNA of 5 O377 homo mutant mouse brains 1-5


title: Livers from fat line chickens, pool 7, replicate 2


title: Livers from lean line chickens, pool 4, replicate 3

source_name: Livers from lean line chickens

tag: Livers from four lean line chickens with 1.2 % (mean) of adipose tissue content per live body weight


title: Livers from lean line chickens, pool 4, replicate 1


title: Livers from lean line chickens, pool 5, replicate 2

tag: Livers from four lean line chickens with 1.8 % (mean) of adipose tissue content per live body weight


title: Livers from lean line chickens, pool 3, replicate 2

tag: Livers from four lean line chickens with 1 % (mean) of adipose tissue content per live body weight


title: Livers from lean line chickens, pool 5, replicate 3


title: Livers from fat line chickens, pool 6, replicate 3

tag: Livers from four fat line chickens with 2.3 % (mean) of adipose tissue content per live body weight


title: Livers from fat line chickens, pool 6, replicate 1


title: Livers from lean line chickens, pool 3, replicate 1


title: Livers from lean line chickens, pool 4, replicate 2


title: Livers from lean line chickens, pool 5, replicate 1


title: Livers from lean line chickens, pool 2, replicate 3

tag: Livers from four lean line chickens with 0.9 % (mean) of adipose tissue content per live body weight


title: Adult kidney rep 2 (430B)


title: Livers from lean line chickens, pool 2, replicate 2


title: affymetrix slide 3

status: Public on Mar 30 2006

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

institute: Animal Sciences Group

description: n.a.

data_processing: Rosetta Luminator

label: biotine

source_name: jejunum fast salmonella d1

tag: tissue

value: jejunum

tag: infection

value: salmonella


title: Livers from lean line chickens, pool 1, replicate 1

tag: Livers from four lean line chickens with 0.6 % (mean) of adipose tissue content per live body weight


title: Livers from lean line chickens, pool 1, replicate 3


title: Livers from lean line chickens, pool 2, replicate 1

tag: Livers from four lean line chickens with 0.9 % (mean)  of adipose tissue content per live body weight


title: Livers from lean line chickens, pool 1, replicate 2


title: affymetrix slide 4

description: n.a.

source_name: jejunum slow salmonella d1

value: control


title: diabetic muscle from vanadyl sulfate treated rats replicate 5

status: Public on Mar 05 2006

city: Buffalo

first: Gail

middle: R

last: Willsky

state: NY

address: 140 Farber Hall

department: Biochemistry

institute: University at Buffalo

source_name: rear leg muscle

label_protocol: Approximately 1 ug of mRNA processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was obtained from approximately 100 mg of rear leg skeletal muscle stored in RNAlater® Qiagen (Valencia, CA) at -80oC using Qiagen RNeasy Maxi kits. Homogenates were made using a Brinkman/Kinetmatica Model PT-2100 polytron (Westbury, NY) for tissue dispersal. Total RNA samples were further processed for poly(A)+ mRNA isolation using Qiagen oligotex mRNA kit.

tag: Diabetic Male Wistar rat after 7 days of diabetes induced with streptozotocin and subsequent treatment with oral vanadyl sulfate for 20 days.


title: normal muscle from vanadyl sulfate treated rats replicate 1

tag: Normal Male Wistar rat treated with oral vanadyl sulfate for 28 days.


title: normal muscle from vanadyl sulfate treated rats replicate 5


title: HOXA10_rep2_0.1

status: Public on Mar 20 2006

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

description: We cultured the cells in three different conc. of doxycycline (0, 0.1 and 0.5). Then we compered the expression levels between 0 - 0.1 and 0 - 0.5.

data_processing: dChip intensity normalized PM/MM model-based expression value

label: Affymetrix Biotin

source_name: LSK Bone Marrow cells

growth_protocol: The cells were cultured for 72 hours in serum free medium, SCF, FLT-3 and TPO.

tag: Sorted LSK cells from double transgenic tetOHOXA10/Rosa26rtTA


title: HOXA10_rep2_0


title: Livers from fat line chickens, pool 7, replicate 1

tag: As a reference sample, poly(A)+ RNA preparations from all lean and fat line chickens (10) were mixed in a superpool.


title: normal muscle from vanadyl sulfate treated rats replicate 3


title: normal muscle from vanadyl sulfate treated rats replicate 4


title: affymetrix slide 2

description: n.a.

data_processing: Rosetta luminator

source_name: jejunum slow control d1

tag: infection control


title: HOXA10_rep2_0.5


title: HOXA10_rep1_0.5


title: normal muscle from vanadyl sulfate treated rats replicate 2


title: diabetic muscle from vanadyl sulfate treated rats replicate 4


title: 4 day seedling treated with red light (680nm, 8 µmol m-2 s-1) for 1 hr rep2_phyB mutant

description: phyB mutant seedlings

tag: phyB mutant


title: HOXA10_rep1_0

tag: Sorted LSK cells from double transgenic tetOHOXA10/Rosa26rtTA mice


title: HOXA10_rep1_0.1


title: diabetic muscle from vanadyl sulfate treated rats replicate 2


title: diabetic muscle replicate 4

tag: Diabetic Male Wistar rat  after 28 days of diabetes induced with streptozotocin


title: diabetic muscle replicate 3


title: diabetic muscle from vanadyl sulfate treated rats replicate 1


title: diabetic muscle replicate 1


title: diabetic muscle from vanadyl sulfate treated rats replicate 3


title: affymetrix slide 1

description: n.a.

source_name: jejunum fast control d1


title: normal muscle replicate 5

tag: Normal male wistar rat


title: diabetic muscle replicate 2


title: normal muscle replicate 4


title: diabetic muscle replicate 5


title: normal muscle replicate 2


title: normal muscle replicate 1


title: normal muscle replicate 3


title: Myog 48h replicate 2

status: Public on Mar 01 2006

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

description: MDER cells induced for 48h in DMEM+1%HS+Insulin+Transferin

data_processing: Bioconductor RMA package

source_name: mouse embryonic fibroblast transduced with MDER+Myog

label_protocol: 6 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from 35mm plates using an RNeasy kit (Qiagen).

tag: cultured primary fibroblasts isolated from Myod-/- and Myf5-/- mice


title: CON 48h replicate 3

source_name: mouse embryonic fibroblast transduced with MDER


title: MDER 48h replicate 3

description: MDER cells induced for 48h in DMEM+1%HS+Insulin+Transferin+beta-estradiol


title: CON 48h replicate 1


title: MDER 48h replicate 2


title: CON 48h replicate 2


title: Myog 24h replicate 3

description: MDER+Myog cells induced for 24h in DMEM+1%HS+Insulin+Transferin


title: MDER 48h replicate 1


title: MDER 24h replicate 2

description: MDER cells induced for 24h in DMEM+1%HS+Insulin+Transferin+beta-estradiol


title: Myog 24h replicate 2


title: Myog 48h replicate 1


title: CON 24h replicate 2

description: MDER cells induced for 24h in DMEM+1%HS+Insulin+Transferin


title: Myog 24h replicate 1


title: CON 24h replicate 1


title: Myog 48h replicate 3


title: CON 24h replicate 3


title: MDER 24h replicate 3


title: Myog 12h replicate 2

description: MDER+Myog cells induced for 12h in DMEM+1%HS+Insulin+Transferin


title: cDNA no 21

description:
sample of normal skin (no_21):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)


title: Myog 12h replicate 1


title: MDER +Myog 12h replicate 1

description: MDER+Myog cells induced for 12h in DMEM+1%HS+Insulin+Transferin+beta-estradiol

source_name: mouse embryonic fibroblast transduced with MDER + Myog


title: MDER 24h replicate 1


title: MDER +Myog 12h replicate 3


title: CON 12h replicate 2

description: MDER cells induced for 12h in DMEM+1%HS+Insulin+Transferin


title: CON 12h replicate 3


title: Myog 12h replicate 3


title: MDER +Myog 12h replicate 2


title: Myog 0h replicate 1

description: MDER + Myog cells before induction

source_name: mouse embryonic fibroblast transduced with MDER and Myog


title: MDER 12h replicate 2

description: MDER cells induced for 12h in DMEM+1%HS+Insulin+Transferin+beta-estradiol


title: MDER 12h replicate 1


title: MDER 0h replicate 2

description: MDER cells before induction

source_name: mouse embryonic fibroblast transduced with a fusion protein between Myod and the activation domain of the human estrogen receptor


title: MDER 0h replicate 1

description: MDER cells before induction

source_name: mouse embryonic fibroblast transduced with a fusion protein between Myod and the activation domain of the human estrogen receptor (MDER)


title: CON 12h replicate 1


title: K562_AS5A3

city: Buenos Aires

first: Michele

last: Bianchini

address: Cramer 1180

department: Centro de Investigaciones Oncologicas

country: Argentina

institute: Instituto Alexander Fleming

description: high quality RNA with minimal degradation and clear 28S/18S ribosomal bands

data_processing: MIDAS (Microarray Data Analysis System)

tag: K562 cell line was co-treated during 40 h with AMI (0.75 mg/ml) added 15min before STI571 (1uM).

tag: K562 cell line was treated during 40 h with AMI at 0.75 mg/ml


title: MDER 12h replicate 3


title: K562_S5C3

tag: K562 cell line was treated during 40 h with STI571 at 1 µM

source_name: K562 untreated

tag: K562 cells were maintained in a 5% CO2 atmosphere at 37ºC in RPMI 1640 medium supplemented with 10% heat inactivated (30min, 65ºC) fetal bovine serum.


title: MDER 0h replicate 3

description: MDER cells before induction


title: Tumor_36

source_name: Normal Colon Tissue

tag: Pool of 13 colon mucosa:

tag: 4 right normal colon tissue

tag: 4 rectum normal tissue

tag: 5 left normal colon tissue

source_name: Tumor Rectum Colon Tissue

tag: Sex M

tag: Age 75

tag: TNM T1N0M0

tag: Dukes C

tag: AJCC 3


title: Tumor_34

source_name: Tumor Right Colon Tissue

tag: Sex F

tag: Age 77

tag: TNM T3N0M0

tag: Dukes B

tag: AJCC 2


title: K562_S3C5


title: Tumor_41

tag: Age 68

tag: TNM T3N2M0


title: Tumor_35

tag: Age 78


title: Tumor_37

tag: Pool of 13 colon mucosa:

tag: Age 56

tag: AJCC 1


title: Tumor_30

tag: 4 right normal colon tissue

tag: 4 rectum normal tissue

tag: 5 left normal colon tissue

tag: Age 86

tag: TNM T3N1M0


title: Hoxa11, Hoxd11 null E13.5 kidney rep 1 (430A)

source_name: Hoxa11, Hoxd11 null E13.5 kidneys replicate 1

tag: Hoxa11, Hoxd11 double null targeted embryonic kidney at E13.5, mixed C57, C3H and CF1 strain, whole kidney


title: Myog 0h replicate 2

description: MDER + Myog cells before induction

tag: cultured primary fibroblasts isolated from Myod-/- and Myf5-/- mice


title: Tumor_32

tag: Sex M

tag: Age 69


title: Tumor_40

source_name: Tumor Left Colon Tissue

tag: Age 76

tag: Dukes C

tag: AJCC 3


title: Myog 0h replicate 3

description: MDER + Myog cells before induction


title: K562_AS3A5

tag: K562 cell line was treated during 40 h with AMI at 0.75 mg/ml

tag: K562 cell line was co-treated during 40 h with AMI (0.75 mg/ml) added 15min before STI571 (1uM).


title: Tumor_31

tag: Pool of 13 colon mucosa:

tag: Sex F

tag: Age 81


title: Tumor_22

tag: Age 78

tag: TNM T3N0M0

tag: AJCC 2

tag: 4 right normal colon tissue


title: Tumor_33

tag: 4 rectum normal tissue

tag: 5 left normal colon tissue

tag: Age 89

tag: TNM T3N1M0


title: Tumor_28

tag: Sex M

tag: TNM T3N2M0


title: Tumor_12

tag: Age 73

tag: Dukes C


title: Tumor_5

tag: Age 50

tag: AJCC 3


title: Tumor_15

tag: Age 77

tag: TNM T1N0M0

tag: Dukes B

tag: AJCC 1

tag: Pool of 13 colon mucosa:


title: Tumor_1

source_name: Tumor right colon tissue

tag: Age 65

tag: AJCC stage 3

tag: 4 right normal colon tisues

tag: 4 rectum normal colon tissues

tag: 5 left normal colon tissues


title: Tumor_4

tag: Age 49

tag: Normal Colon Tissue

tag: 4 right normal colon tissue

tag: 4 rectum normal tissue

tag: 5 left normal colon tissue


title: Med13 ORF-3

type: genomic

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

description: IgG beads were used for ChIP of chromatin extracts from Med13-TAP cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: CHIP IP Med13-3 ORF

tag: IP sample med13-TAP

source_name: WCE

tag: WCE of Med13-TAP


title: Med13 ORF-6

source_name: CHIP IP Med13-6 ORF


title: Tumor_7

tag: Sex M

tag: Age 71

tag: TNM T3N2M0

tag: Dukes C

tag: AJCC 3


title: Med13 ORF-2

source_name: CHIP IP Med13-2 ORF


title: Med13 ORF-1

description:
IgG beads were used for ChIP of chromatin extracts from Med13-TAP cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was
labeled with Cy5. The wCE control ChIP DNA was labeled with Cy3 and imultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mediator occupancy profile.

source_name: CHIP IP Med13-1 ORF


title: Med13 IGR-5

description:
IgG beads were used for ChIP of chromatin

extracts from Med7-TAP cells. Cell cultures

were then grown to mid logarithmic growth

phase (5 x106 cells/ml) in rich medium before

fixation and ChIP. The resulting ChIP DNA was

labeled with Cy5. The wCE control ChIP DNA was

labeled with Cy3 and simultaneously hybridized

with the Cy5 labeled DNA to the IGR+ORF

microarrays to produce genome wide mediator

occupancy profile.

source_name: CHIP IP med13-5 IGR


title: Med7 ORF-6

source_name: CHIP IP Med7-6 ORF

tag: IP sample med7-TAP

tag: WCE of Med7-TAP


title: Med7 ORF-1

source_name: CHIP IP Med7-1 ORF


title: Med13 IGR-3

source_name: CHIP IP med13-3 IGR


title: Med7 ORF-3

source_name: CHIP IP Med7-3 ORF


title: Med7 ORF-5

source_name: CHIP IP Med7-5 ORF


title: Med13 ORF-5

source_name: CHIP IP Med13-5 ORF


title: Med7 ORF-4

source_name: CHIP IP Med7-4 ORF


title: Tumor_21

source_name: Tumor Right Colon Tissue

tag: Age 77

tag: TNM T3N1M0

source_name: Normal Colon Tissue

tag: Pool of 13 colon mucosa:


title: Med13 IGR-6

source_name: CHIP IP med13-6 IGR


title: Med13 IGR-2

source_name: CHIP IP med13-2 IGR


title: Med13 IGR-1

source_name: CHIP IP med13-1 IGR


title: Med7 IGR-6

source_name: CHIP IP Med7-6 IGR

source_name: WCE


title: Med7 IGR-4

source_name: CHIP IP Med7-4 IGR


title: Med13 ORF-4

source_name: CHIP IP Med13-4 ORF


title: Med7 IGR-1

description:
IgG beads were used for ChIP of chromatin

extracts from Med7-TAP cells.  Cell cultures

were then grown to mid logarithmic growth

phase (5 x106 cells/ml) in rich medium before

fixation and ChIP. The resulting ChIP DNA was

labeled with Cy5. The wCE control ChIP DNA was

labeled with Cy3 and simultaneously hybridized

with the Cy5 labeled DNA to the IGR+ORF

microarrays to produce genome wide mediator

occupancy profile.

source_name: CHIP IP Med7-1 IGR


title: Med7 IGR-3

source_name: IP sample med7-TAP


title: Med13 IGR-4

source_name: CHIP IP med13-4 IGR


title: Med7 IGR-2


title: Med7 ORF-2

source_name: CHIP IP Med7-2 ORF


title: Med13-2

description: IgG beads were used for ChIP of chromatin extracts from Med13-TAP cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA and WCE were labeled with biotin.

data_processing: IP/WCE

tag: Med13-TAP distribution on chr2 and 3.


title: Med7-2

description: IgG beads were used for ChIP of chromatin extracts from Med7-TAP cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA and WCE were labeled with biotin.

source_name: med7 -2

tag: Med7-TAP distribution on chr2 and 3.


title: Med7 IGR-5

source_name: CHIP IP Med7-5IGR


title: Med13-1


title: Med7-1

source_name: med7 -1


title: Tumor_29

source_name: Tumor Left Colon Tissue

tag: Sex F

tag: Age 61

tag: TNM T3N0M0

tag: AJCC 2

tag: 4 right normal colon tissue


title: Vd2 PBS rep2

status: Public on Feb 28 2006

city: Bozeman

first: Ellen

last: Kress

state: MT

department: Veterinary Molecular Biology

institute: Montana State University

description: expanded Vd2 cells, PBS treated, donor 2

hyb_protocol: 15mg of labelled RNA was hybridized to the arrays according to standart Affymetrix procedures, then arrays were washed and stained on the Affymetrix GeneChip Fluidics Station 450 using the Midi_euk2v3 protocol

scan_protocol: samples were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix GCOS

source_name: expanded peripheral blood Vd2 gd T lymphocytes

label_protocol: 1mg of total RNA was labelled using the Affymetrix One-Cycle labelling procedure

growth_protocol: 3 week culture with Vd1 mab 0.1mg/mL, pan gd mAb 0.1 mg/mL, and IL-15 10ng/mL

extract_protocol: cells were homogenized in TRIzol reagent, then RNA was extracted using a Quagen Rneasy column with no DNase treatment

treatment_protocol: PBS, 4hr

tag: healthy female, age 27


title: Vd2 LPS rep2

description: expanded Vd2 cells, LPS treated, donor 2

treatment_protocol: phenol extracted E. coli lipopolysaccharide, 10 mg/mL, 4hr


title: Vd1 PMA rep1

description: expanded Vd1 cells, PMA treated, donor 1

source_name: expanded peripheral blood Vd1 gd T lymphocytes

extract_protocol: cells were homogenized in TRIzol reagent, isopropanol precipitated, DNAse treated, then ethanol precipitated

treatment_protocol: PMA 20ng/mL, ionomycin 0.5mg/mL, 4hr

tag: healthy male, age 27


title: Vd2 PMA rep2

description: expanded Vd2 cells, PMA treated, donor 2


title: Vd2 PMA rep1

description: expanded Vd2 cells, PMA treated, donor 1


title: Vd2 PBS rep1

description: expanded Vd2 cells, PBS treated, donor 1


title: Vd1 PBS rep2

description: expanded Vd1 cells, PBS treated, donor 2


title: T60_repD_refcy5_HY2

status: Public on Feb 15 2006

city: Boston

first: XiaoYun

last: Qiu

state: MA

address: 200 longwood Ave

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

description: The hybridization image was acquired using GenePix 4000B scanner. The fluorescent intesity of Cy5 (635 nm) and Cy3 (532 nm) were obtained using GenePix Pro provided by Axon.

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm 532 nm PMTVolts=620 500 ScanPower=100 100 Software=GenePix Pro

data_processing: The gene expression rations of IR-irradiated sample and the respective nonirradiated control were normalized both per feature and per chip as described in Qiu et al 2006 (Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation. J. Bacteriol. Vol 188, No. 3.). The Value is the ratio (log2) of the IR-irradiated sample to the control.

organism: Shewanella oneidensis MR-1

source_name: Total RNA of the control (non-irradiated MR-1) at 60 min after irradiation.

label_protocol: Comparative analysis of differentially expressed genes in shewanella oneidensis MR-1 following UVC, UVB, and UVA radiation. J. Bacteriol. 187:3556-3564.

growth_protocol: Grown in Davis medium to 0.2 of OD600 (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).

treatment_protocol: Sit on ice for the same time as the IR-irradiated sample, then return to shaker for 60 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).

tag: strain

value: MR-1 (control)

source_name: Total RNA of the sample (IR-irradiated MR-1) at 60 min after irradiation.

treatment_protocol: Irradiated with 40Gy of gamma ray on ice, then return to shaker for 60 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).

value: MR-1 (sample)


title: Vd1 PMA rep2

description: expanded Vd1 cells, PMA treated, donor 2


title: Vd2 LPS rep1

description: expanded Vd2 cells, LPS treated, donor 1


title: Livers from fat line chickens, pool 6, replicate 2

source_name: Livers from fat line chickens

tag: Livers from four fat line chickens with 2.3 % (mean) of adipose tissue content per live body weight

source_name: Livers from all lean and fat line chickens

tag: As a reference sample, poly(A)+ RNA preparations from all lean and fat line chickens (10) were mixed in a superpool.


title: Vd1 LPS rep2

description: expanded Vd1 cells, LPS treated, donor 2


title: Vd1 PBS rep1

description: expanded Vd1 cells, PBS treated, donor 1


title: T60_repA_refcy5_HY2

extract_protocol: Comparative analysis of differentially expressed genes in shewanella oneidensis MR-1 following UVC, UVB, and UVA radiation. J. Bacteriol. 187:3556-3564.


title: T60_repB_refcy3_HY1

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm 532 nm PMTVolts=650 500 ScanPower=100 100 Software=GenePix Pro


title: T60_repD_refcy3_HY1


title: T60_repB_refcy5_HY2

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm 532 nm PMTVolts=600 500 ScanPower=100 100 Software=GenePix Pro


title: T20_repB_refcy5_HY4

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=620	500 ScanPower=100	100 Software=GenePix Pro

source_name: Total RNA of the control (non-irradiated MR-1) at 20 min after irradiation.

treatment_protocol: Sit on ice for the same time as the IR-irradiated sample, then return to shaker for 20 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).

source_name: Total RNA of the sample (IR-irradiated MR-1) at 20 min after irradiation.

treatment_protocol: Irradiated with 40Gy of gamma ray on ice, then return to shaker for 20 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).


title: Vd1 LPS rep1

description: expanded Vd1 cells, LPS treated, donor 1


title: T60_repA_refcy3_HY1

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm 532 nm PMTVolts=580 500 ScanPower=100 100 Software=GenePix Pro

tag: strai


title: T20_repD_refcy3_HY1

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=600	500 ScanPower=100	100 Software=GenePix Pro


title: T20_repB_refcy5_HY3


title: T20_repD_refcy5_HY2

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=650	500 ScanPower=100	100 Software=GenePix Pro


title: T5_repD_refcy5_HY2

source_name: Total RNA of the control (non-irradiated MR-1) at 5 min after irradiation.

treatment_protocol: Sit on ice for the same time as the IR-irradiated sample, then return to shaker for 5 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).

source_name: Total RNA of the sample (IR-irradiated MR-1) at 5 min after irradiation.

treatment_protocol: Irradiated with 40Gy of gamma ray on ice, then return to shaker for 5 min. (J. Bacteriol. vol 188, No. 3. Transcriptome analysis applied to survival of shewanella oneidensis MR-1 exposed to ionizing radiation).


title: Exp Pt 3(VTS1 )

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

description: The experiment was designed to look for genes up/downregulated in the absense of Vts1p compared to wild-type cells grown in steady state conditions.

data_processing: MAS5 Statistical Algorithm

source_name: vts1 deletion in BMA64

growth_protocol: Cells were grown in steady state conditions in SD media at 30 degrees. Cells were harvested at OD600=0.4.

treatment_protocol: VTS1 Chemical Transfection

tag: vts 1 deletion in BMA64


title: Exp Pt 2(dvts1-2 VTS1 )

tag: vts1 deletion in BMA64


title: T20_repB_refcy3_HY1

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=580	500 ScanPower=100	100 Software=GenePix Pro


title: T5_repB_refcy3_HY1


title: T5_repD_refcy3_HY1


title: Exp Pt 1(dvts1-1 VTS1 )


title: WT1


title: T5_repB_refcy5_HY2

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=650	550 ScanPower=100	100 Software=GenePix Pro


title: MGAS5305 replicate 2

status: Public on Feb 01 2006

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description: Early exponential phase THY growth

data_processing: GCOS

organism: Streptococcus pyogenes

label_protocol: Approximately 4 µg of cDNA was processed to produce biotinylated cDNA targets.

extract_protocol: Total RNA was extracted from GAS grown in THY to early exponential phase with the FastPrep FP 120 kit (Qbiogene, Carlsbad, CA).  RNAprotect (Qiagen, Valencia, CA) treated GAS were centrifuged and resuspended in 300 ul  5 mM ammonium aurintricarboxylate before transferring to FastPrep Blue tubes containing 450 ul CRSR-Blue(Qbiogene), and 450 ul acid phenol:chloroform (5:1, pH 4.5; Ambion, Austin, TX). The mixture was homogenized (11 sec at speed #4), heated at 65 oC for 15 min, and centrifuged at 16,000xg for 10 min. The aqueous phase was collected and concentrated to 100 ul with a vacuum concentrator (Eppendorf, Germany). The concentrate was purified using the Qiagen RNeasy 96 kit following the manufacturer's protocol (Qiagen, Valencia, CA).

tag: Pharyngeal clinical isolate


title: T20_repA_refcy3_HY1

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=640	500 ScanPower=100	100 Software=GenePix Pro


title: MGAS5005 replicate 1 invasive

description: Early exponential phase THY growth

tag: Invasive clinical isolate


title: T20_repB_refcy3_HY2

scan_protocol: Scanner=GenePix 4000B ImageName=635 nm	532 nm PMTVolts=580 500 ScanPower=100	100 Software=GenePix Pro

tag: stran


title: MGAS5005 replicate 2 invasive

description: Early exponential phase THY growth


title: MGAS5393 replicate 1

description: Early exponential phase THY growth


title: T5_repA_refcy5_HY2


title: MGAS5531 replicate 2

description: Early exponential phase THY growth


title: MGAS294 replicate 1

description: Early exponential phase THY growth


title: MGAS337 replicate 2

description: Early exponential phase THY growth


title: MGAS6413 replicate 1

description: Early exponential phase THY growth


title: MGAS5305 replicate 1

description: Early exponential phase THY growth


title: MGAS5456 replicate 2

description: Early exponential phase THY growth


title: MGAS294 replicate 2

description: Early exponential phase THY growth


title: WT2


title: MGAS5393 replicate 2

description: Early exponential phase THY growth


title: MGAS6413 replicate 2

description: Early exponential phase THY growth


title: 53SL2

description: Early exponential phase THY growth

label_protocol: Approximately 4 ?g of cDNA was processed to produce biotinylated cDNA targets.

tag: MGAS5005 mouse passaged ITP-derivative isolated from the spleen of mouse number 7


title: MGAS5475 replicate 2

description: Early exponential phase THY growth


title: MGAS5475 replicate 1

description: Early exponential phase THY growth


title: T20_repA_refcy5_HY2


title: 53SL1

description: Early exponential phase THY growth


title: 53PL2

description: Early exponential phase THY growth

tag: MGAS5005 mouse passaged ITP-derivative isolated from the skin lesion of mouse number 9


title: 53SL3

description: Early exponential phase THY growth


title: 53PL3

description: Early exponential phase THY growth


title: T5_repA_refcy3_HY1

description: The hybridization image was acquired using GenePix4000B scanner. The fluorescent intensity of Cy5(635 nm) and Cy3(532 nm) were obtained using GenePix Pro provided by Axon.

tag: Strain


title: 21PS1

description: Early exponential phase THY growth

tag: MGAS2221 mouse passaged PTP-derivative isolated from the skin lesion of mouse number 1


title: 26PS1

description: Early exponential phase THY growth

tag: MGAS2221 mouse passaged PTP-derivative isolated from the skin lesion of mouse number 6


title: 24SS2

description: Early exponential phase THY growth

tag: MGAS2221 mouse passaged ITP-derivative isolated from the spleen of mouse number 4


title: 53PL1

description: Early exponential phase THY growth


title: 26PS3

description: Early exponential phase THY growth


title: 24SS1

description: Early exponential phase THY growth


title: 24SL3

description: Early exponential phase THY growth


title: 24SS3

description: Early exponential phase THY growth


title: 26PL3

description: Early exponential phase THY growth

tag: MGAS2221 mouse passaged ITP-derivative isolated from the skin lesion of mouse number 6


title: 21PL3

description: Early exponential phase THY growth

tag: MGAS2221 mouse passaged ITP-derivative isolated from the skin lesion of mouse number 1


title: 26PL2

description: Early exponential phase THY growth


title: 26PS2

description: Early exponential phase THY growth


title: 26PL1

description: Early exponential phase THY growth


title: 24SL2

description: Early exponential phase THY growth


title: MGAS337 replicate 1

description: Early exponential phase THY growth


title: 21PL1

description: Early exponential phase THY growth


title: MGAS5005 replicate 1

description: Early exponential phase THY growth


title: MGAS5005 replicate 2

description: Early exponential phase THY growth


title: MGAS5005 replicate 3

description: Early exponential phase THY growth


title: MGAS2221 replicate 3

description: Early exponential phase THY growth


title: 21PS3

description: Early exponential phase THY growth


title: Tumor_16

description: high quality RNA with minimal degradation and clear 28S/18S ribosomal bands

source_name: Tumor Rectum Colon Tissue

tag: Sex F

tag: Age 83

tag: TNM T2N0M0

tag: Dukes B

tag: AJCC 1

source_name: Normal Colon Tissue

tag: Pool of 13 colon mucosa:

tag: 4 right normal colon tissue

tag: 4 rectum normal tissue

tag: 5 left normal colon tissue


title: MGAS2221 replicate 2

description: Early exponential phase THY growth

tag: Pharyngeal clinical isolate


title: MGAS2221 replicate 1

description: Early exponential phase THY growth


title: 21PS2

description: Early exponential phase THY growth


title: 21PL2

description: Early exponential phase THY growth


title: Hyperplastic gastric tumor of K19-C2mE transgenic mice_1

city: Sakyo-ku, Kyoto-shi

first: Akihiro

last: Matsunaga

state: Kyoto

address: Yoshida-konoe-cho

department: Medicine

country: Japan

institute: Kyoto University

description: K19-C2mE transgenic mice express cyclooxygenase-2 (COX-2) and microsomal prostaglandin E synthase (mPGES)-1 simultaneously in the gastric epithelial cells. The transgenic mice develop mucous metaplasia, hyperplasia and tumorous growth in the glandular stomach.

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide spotted with oligonucleotides (65mers) for 16h at 60ºC.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray microarray scanner (Perkin Elmer) and image intensity data were extracted and analyzed with ScanArray Express v3.1 software.

data_processing: Both Cy3 and Cy5 signals were normalizaed by Lowess method. VALUE is Log (base 10) of the ratio of the mean of Channel 2 (Cy5) to Channel 1 (Cy3).

source_name: control#1 glandular stomach

label_protocol: The mRNA was amplified and incorporated with 5-(3-aminoallyl)-UTP using AminoAllyl MessageAmp aRNA Amplification Kit (Ambion). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3.

extract_protocol: Total RNA was isolated by homogenizing normal glandular stomach in TriReagent (Sigma). The total RNA (150 µg) was treated with DNase I for 30 min at 37ºC and purified using RNeasy Mini Kit (Qiagen). The mRNA was then extracted from 100µg of total RNA using GenElute mRNA Miniprep Kit (Sigma).

value: C57BL/6, Gender:male, Age:30 weeks age, Tissue:normal glandular stomach

source_name: K19-C2mE#1 gastric hyperplastic tumor

label_protocol: The mRNA was amplified and incorporated with 5-(3-aminoallyl)-UTP using AminoAllyl MessageAmp aRNA Amplification Kit (Ambion). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy5.

extract_protocol: Total RNA was isolated by homogenizing hyperplastic tumors in the glandular stomach of K19-C2mE mouse in TriReagent (Sigma). The total RNA (150 µg) was treated with DNase I for 30 min at 37ºC and purified using RNeasy Mini Kit (Qiagen). The mRNA was then extracted from 100µg of total RNA using GenElute mRNA Miniprep Kit (Sigma).

value: C57BL/6, Gender:male, Age:30 weeks age, Tissue:hyperplastic tumor in glandular stomach


title: Hyperplastic gastric tumor of K19-C2mE transgenic mice_2

source_name: control#2 glandular stomach

value: C57BL/6, Gender:female, Age:30 weeks age, Tissue:normal glandular stomach

source_name: K19-C2mE#2 gastric hyperplastic tumor

value: C57BL/6, Gender:female, Age:30 weeks age, Tissue:hyperplastic tumor in glandular stomach


title: 1606038018 Ishikawa_Tamoxifen

city: Leicester

first: Jerry

middle: A

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

description: Ishikawa cells grown for 72h in RPMI medium with Gmax containing 10% charcoal stripped FBS then incubated for 24h with ethanol (control) or 10-6M 4OH-tamoxifen (treated)

label: Cy3 control

source_name: Uterus

tag: Ishikawa cell line derived from well differentiated human uterine carcinoma cells.

label: Cy5 treated

extract_protocol: Qiagen RNeasy Mini Kit

tag: Cell line derived from well differentiated uterine carcinoma cells


title: 1606038017 Ishikawa_Estradiol

description: Ishikawa cells grown for 72h in RPMI medium with Gmax containing 10% charcoal stripped FBS then incubated for 48h with ethanol (control) or 10-8M 17beta estradiol (treated)

label: Cy5 control

label: Cy3 treated


title: MGAS5456 replicate 1

description: Early exponential phase THY growth


title: 1606038013 Ishikawa_Estradiol

description: Ishikawa cells grown for 72h in RPMI medium with Gmax containing 10% charcoal stripped FBS then incubated for 24h with ethanol (control) or 10-8M 17beta estradiol (treated)


title: 1606038025 Ishikawa_Estradiol


title: 1606038021 Ishikawa_Estradiol


title: 1606038019 Ishikawa_Estradiol


title: 1606038024 Ishikawa_Tamoxifen

description: Ishikawa cells grown for 72h in RPMI medium with Gmax containing 10% charcoal stripped FBS then incubated for 48h with ethanol (control) or 10-6M 4OH-tamoxifen (treated)


title: 1606038011 Ishikawa_Estradiol


title: 1606038023 Ishikawa_Estradiol


title: 1606038022 Ishikawa_Tamoxifen


title: 1606038012 Ishikawa_Tamoxifen


title: 1606038016 Ishikawa_Tamoxifen


title: 1606038020 Ishikawa_Tamoxifen


title: 1606038006 Ishikawa_Tamoxifen


title: 1606038005 Ishikawa_Estradiol


title: 1606038007 Ishikawa_Estradiol


title: 1606038004 Ishikawa_Tamoxifen


title: 1606038014 Ishikawa_Tamoxifen


title: 1606038002 Ishikawa_Tamoxifen


title: 1606038003 Ishikawa_Estradiol


title: Hyperplastic gastric tumor of K19-C2mE transgenic mice_3

source_name: control#3 glandular stomach

tag: Strain

source_name: K19-C2mE#3 gastric hyperplastic tumor


title: 1606038010 Ishikawa_Tamoxifen


title: 1606038015 Ishikawa_Estradiol


title: 1606038008 Ishikawa_Tamoxifen


title: 501048030 Ishikawa_Estradiol


title: 501048028 Ishikawa_Estradiol


title: 501048027 Ishikawa_Tamoxifen


title: 501048031 Ishikawa_Estradiol


title: 501048014 Ishikawa_Estradiol


title: 501048013 Ishikawa_Tamoxifen


title: MGAS5531 replicate 1

description: Early exponential phase THY growth


title: 501048033 Ishikawa_Estradiol


title: 501048032 Ishikawa_Tamoxifen


title: 501048018 Ishikawa_Estradiol


title: 501048029 Ishikawa_Tamoxifen


title: 501048019 Ishikawa_Tamoxifen


title: 501048016 Ishikawa_Estradiol


title: 501048020 Ishikawa_Estradiol


title: 1606038009 Ishikawa_Estradiol


title: 24SL1

description: Early exponential phase THY growth


title: 501048011 Ishikawa_Tamoxifen


title: 501048015 Ishikawa_Tamoxifen


title: 501048017 Ishikawa_Tamoxifen


title: 501048008 Ishikawa_Tamoxifen


title: 501048004 Ishikawa_Estradiol


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, 76

status: Public on Jan 31 2006

city: Braunschweig

first: Susanne

last: Pfoertner

address: Mascheroder Weg 1

institute: German Research Centre for Biotechnology (GBF)

description: CD4+CD25+ regulatory T cells from human peripheral blood

hyb_protocol: 15 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre). Samples were hybridized to individual Human TReg Chips for 16 hours at 42°C using a Lucidea Slidepro (Amersham Biosciences). After hybridisation the microarrays were washed as recommended by the manufacturer’s instructions (CodeLink Expression Bioarray System, Amersham Biosciences) and stained with Cy5-streptavidin (Amersham Biosciences).

scan_protocol: Fluorescent array images were collected for Cy5 with an arrayWorX fluorescent scanner (Applied Precision, USA) and image intensity data were extracted and analyzed with Imagene analysis software (v5.5.2, Biodiscovery).

data_processing: Spots of poor quality (flag=3) or signal intensities lower than the background intensity were excluded from further analysis. After background correction, data normalization was carried out as proposed by MWG. Briefly, signal intensities were normalized by dividing each signal by exp(median of ln[signal intensities of housekeeping genes]).

label_protocol: Quality and integrity of the total RNA isolated from 1-2x10^5 CD4+CD25+ and CD4+CD25- T cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Samples were prepared by applying a double-linear amplification method according to the Eberwine protocol and modified by Affymetrix. Briefly, the first round of RNA-amplification was performed without biotinylated nucleotides using the Promega P1300 RiboMax Kit for T7 amplification (Promega, Mannheim, Germany). After clean-up of the precipitated aRNA synthesis of second round, first-strand cDNA was done using random hexamers (Pharmacia, Freiburg, Germany). Subsequent second-strand cDNA was prepared like in the first round but integrating an additional RNAse H incubation step to digest the aRNA before annealing of the T7T23V primer. The second round of RNA amplification was performed as an in vitro transcription assay in the presence of biotinylated UTP using the GeneChip® Expression 3’-Amplification Reagents Kit for IVT Labeling (Affymetrix, Santa Clara, CA). The concentration of the obtained biotin-labelled cRNA was determined by UV absorbance and its quality as means of product length distribution was again checked using the Agilent Bioanalyzer.

extract_protocol: Cells were lysed in RLT-buffer containing 1% beta-Mercaptoethanol. RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from freshly drawn blood by Ficoll density gradient centrifugation. For isolation of CD4+CD25+ regulatory and CD4+CD25- naive T cells, PBMCs were further separated using the regulatory human T cell isolation kit and an AutoMACS separation unit (Miltenyi Biotec).

tag: donor D, gender

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: 501048003 Ishikawa_Tamoxifen


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, A6

tag: donor K, gender

value: male, age:26 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, 80

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: 501048007 Ishikawa_Estradiol


title: 501048009 Ishikawa_Estradiol


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, A5

value: male, age:26 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: 501048010 Ishikawa_Tamoxifen


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, 82

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, A33A

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, C19

tag: donor I, gender

value: female, age:62 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, C17

tag: donor B, gender

value: female, age:57 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, A4

value: male, age:26 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, A12

value: male, age:26 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, C12

value: female, age:57 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, C18

value: female, age:62 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, C14

value: female, age:57 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: 501048005 Ishikawa_Tamoxifen


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, C2

value: female, age:62 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, A10

value: male, age:26 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: 501048006 Ishikawa_Estradiol


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, C16

value: female, age:57 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, 56

tag: donor E, gender

value: male, age:36 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, C1

value: female, age:62 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, 57

value: male, age:36 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, 52

value: male, age:36 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, 53

value: male, age:36 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, C6

tag: donor A, gender

value: male, age:58 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, 54

value: male, age:36 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, 63

tag: donor H, gender

value: female, age:26 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, B29

tag: donor F, gender

value: male, age:39 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, B31

value: male, age:39 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, C10

value: male, age:58 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, C4

value: male, age:58 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, B28

value: male, age:39 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, 81

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, B27

value: male, age:39 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, 74

tag: donor G, gender


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, B30

value: male, age:39 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, C11

value: male, age:58 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, 59

value: female, age:26 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, B26

value: male, age:39 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, 73


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, 72


title: AND-TCR transgenic mouse second hybridization_MG-U74Av2

city: Chuo-ku

first: Tsutomu

last: Ohta

state: Tokyo

address: 5-1-1 Tsukiji

department: Medical Genomics Center

institute: National Cancer Center Research Institute

description: Total adult thymocytes from AND-TCR transgenic mouse that were positively selected in the H-2b background

data_processing: Affymetrix Microarray Suite version 4

source_name: thymocytes

label_protocol: 5 micro g of total RNA was processed to produce biotinylated cRNA targets.

tag: H-2b AND-TCR-transgenic thymocytes


title: AND-TCR transgenic mouse first hybridization_MG-U74Av2


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, A37


title: C57BL/6 second hybridization_MG-U74Av2

description: Total adult thymocytes from C57BL/6 mouse

tag: Wild type thymocytes


title: C57BL/6 first hybridization_MG-U74Av2


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, A38


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, B5

tag: donor J, gender

value: female, age:54 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, A34

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, B1

value: female, age:54 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, 71


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, 62

value: female, age:26 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, B4

value: female, age:54 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3, B2

value: female, age:54 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3

tag: donor C, gender

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1, B16

value: female, age:54 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: C57BL/6 first hybridization_MG-U74Bv2


title: AND-TCR transgenic mouse second hybridization_MG-U74Bv2

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