title: KS15R02

status: Public on Nov 24 2007

type: RNA

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

country: USA

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = rice
Keyword = submergence stress response

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: 15 min_IR24_Replication 2

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in Growth chambers and leaf samples were harvested on 14 DAS.

extract_protocol: Qiagen Rneasy Plant Maxi Kit and according to manufacturers protocol.

treatment_protocol: 14 days old plants were submerged in transparent polythene bags in growth chamber

tag: Leaf samples from submerged plants of IR24 collected after 15 min of submergence

source_name: 15 min_FR13A_Replication 2

tag: Leaf samples from submerged plants of FR13A collected after 15 min of submergence


title: T. rubrum PHS11A rep-3

status: Public on Nov 30 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

description: Signals were normalized using a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.

hyb_protocol: Labeled cDNA was purified using QIAquick columns and mixed with 2μl polyA; 5× Denharts; 3× SSC; yeast tRNA 24 μg; 25 mM HEPES, pH 7.0; 0.25% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization.

data_processing: Genes were considered to be differentially expressed if (i) average expression changed by at least 2-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

molecule: polyA RNA

organism: Trichophyton rubrum

source_name: T.rubrum_PHS11A, labelled with Cy5

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime? DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy? Plant Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions. Poly(A)+ mRNA was isolated with Oligotex mRNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: T.rubrum treated with PHS11A

source_name: T.rubrum_DMSO, labelled with Cy3

tag: T.rubrum treated with DMSO


title: T. rubrum PHS11A rep-1


title: T. rubrum PHS11A rep-2


title: KS24R01

source_name: 24 h_IR24_Replication1

growth_protocol: Plants were grown in Growth chambers and leaf samples were harvested on 15 DAS.

tag: Leaf samples from submerged plants of IR24 collected after 24 h of submergence

source_name: 24 h_FR13A_Replication1

tag: Leaf samples from submerged plants of FR13A collected after 24 h of submergence


title: KS15R01

source_name: 15 min_IR24_Replication1

growth_protocol: Plants were grown under Growth chambers and leaf samples were harvested on 14 DAS.

source_name: 15 min_FR13A_Replication1


title: Blue catfish Liver control 3d replicate 1

status: Public on Nov 22 2007

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

description: During the challenge, symptomatic treatment fish and control fish were collected and confirmed to be infected with E. ictaluri and pathogen-free, respectively, at the Fish Disease Diagnostic Laboratory, Auburn University.

hyb_protocol: The microarrays were prehybridized with a solution of 2x MES hybridization buffer (100 mM 2-morpholinoethanesulfonic acid, 1.0 M Na+, 20 mM EDTA, 0.01% Tween 20), 50 µg of herring sperm DNA, and 250 µg of acetylated bovine serum albumin (BSA) at 45°C for 15 min followed by hybridization with 10 µg of denatured and fragmented cRNA per microarray, 3.5 µl of CPK6 control oligo, 35 µg of herring sperm DNA, 175 µg of acetylated BSA, and 2X MES buffer at 45°C for 16–20 h with constant rotation. After hybridization, the microarrays were washed twice with nonstringent buffer (6x SSPE, 0.01% Tween 20) at room temperature followed by two stringent washes (100 mM MES salt and free acid solution, 0.1 M Na+, 0.01% Tween 20) at 45°C for 15 min each. After a final one minute rinse with nonstringent buffer, the arrays were placed into a 1x stain solution (100 mM MES, 1 M Na+, 0.05% Tween 20, 50 mg/ml BSA, and 1 µg/µl Cy3-streptavidin) at room temperature for 15 min, agitating every few minutes. The microarrays were removed from the stain solution and placed in fresh nonstringent wash buffer for one minute. They were then placed into Nimblegen’s proprietary final wash buffer for 30 s, and then immediately dried under a stream of argon gas.

scan_protocol: The microarrays were scanned with an Axon GenePix 4000B scanner (Molecular Devices Corp., Union City, CA) at 5 µM resolution.

data_processing: After extraction of data from raw images using the NimbleScan software (Nimblegen, Inc.), gene calls were generated using the Robust Multichip Average (RMA) algorithm (Irizarry et al. 2003) which takes into account only the PM oligos. RMA takes a background adjustment on the raw intensity scale, carries out quantile normalization (Bolstad et al. 2003), takes the log2 of the normalized background adjusted PM values, and then uses a linear model to estimate expression values on the log scale.

label: Biotin

organism: Ictalurus furcatus

source_name: Blue catfish liver 3d control

label_protocol: Total RNA was converted to double-stranded cDNA using a SuperScript II cDNA synthesis kit (Invitrogen) and an oligo-dT primer containing the T7 RNA polymerase promoter. In vitro transcription (IVT) was carried out to produce biotin-labeled cRNA from cDNA using the MEGAscript T7 kit (Ambion). Briefly, 3 μL double-stranded cDNA was incubated with 7.5 mM ATP and GTP, 5.6 mM UTP and CTP, 1.875 mM bio-11-CTP and bio-16 UTP (Enzo) and 1x T7 enzyme mix in 1x reaction buffer for 16 h at 37˚C. The cRNA was then purified using an RNeasy mini kit (Qiagen, ). Before hybridization, cRNA was fragmented to an average size of 50 to 200 bp by incubation in a buffer of 100 mM potassium acetate, 30 mM magnesium acetate, and 40mM tris-acetate for 35 min at 94˚C. Fragmentation was measured using a Bioanalyzer 1000 (Agilent Technologies).

growth_protocol:
Fish were moved to challenge aquaria at least two weeks prior to
challenge and 30 channel catfish and 30 blue catfish were added to
each aquaria. Fish were fed a commercial diet to satiation prior to
challenge and all fish were fed lightly during the course of the
challenge. Continuous water flowthrough and supplemental aeration
were provided. At 3 d fish were killed by anesthesia overdose and
their livers dissected. The livers of 25 fish were pooled for each
replicate, flash frozen in liquid nitrogen, and stored at -80°C until
RNA extraction.

extract_protocol: The livers for each replicate were ground in liquid nitrogen by mortar and pestle to a fine powder and thoroughly mixed. Approximately 30 mg of tissue powder was homogenized in Buffer RLT Plus by passing the lysate several times through a 20-gauge needle fitted to a syringe according to the protocol of the RNeasy Plus Mini Kit (Qiagen). Following the manufacturer’s instructions, approximately 35 μg of total RNA was obtained from each extraction. RNA quality and concentration was checked by spectrophotometer analysis and gel electrophoresis. All extracted samples had an A260/280 ratio of greater than 1.8, and were diluted to 1 μg/μL.

treatment_protocol:
Fish were mock challenged for 2 h by adding sterile BHI media in 30 L
aquaria with water turned off. Water flowthrough was resumed after
challenge.

tag: Livers from ~15 cm long D&B strain blue catfish


title: Blue catfish Liver ESC-infection 3d replicate1

source_name: Blue catfish Liver 3d post ESC infection

treatment_protocol: Edwardsiella ictaluri bacteria were cultured from a single isolate (MS-S97-773) and used in a small test infection of several channel catfish. Bacteria were re-isolated from a single symptomatic fish and biochemically confirmed to be E. ictaluri, before being inoculated into brain heart infusion (BHI) medium and incubated in a shaker incubator at 28 °C overnight. The bacterial concentration was determined using colony forming unit (CFU) per ml by plating 10 μl of 10-fold serial dilutions onto BHI agar plates. At the time of challenge, the bacterial culture was added to the aquaria to a concentration of 4X108 CFU/ml. Water was turned off in the aquaria for 2 h of immersion exposure, and then continuous water flow-through resumed for the duration of the challenge.


title: KSCR001

treatment_protocol: No treatment

tag: Leaf samples from control plants of IR24

tag: Leaf samples from un-inoculated control plants of FR13A


title: Blue catfish liver control 3d replicate3


title: KSCR002

tag: Leaf samples from control plants of FR13A


title: w1118 muscle 45 days set 2

status: Public on Nov 19 2007

city: Baltimore

first: Haruyoshi

last: Yamaza

state: MD

address: 6200 Seaforth Street

department: Laboratory of Experimental Gerontology

institute: National Institute on Aging

description: w1118 45 days muscle

hyb_protocol: Equal amount of sample and reference probes (one or two micrograms) were co-hybridized to microarrays at 42oC using cDNA Hyb Buffer (Full Moon Biosystems).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner (Axon Instruments) and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software (Axon Instruments).

data_processing: Raw microarray data were first processed by conducting within-slide normalization of signal intensities using the LOWESS curve-fitting method followed by between-slide scaling using Median Absolute Deviation method. Only genes with at most 4 missing values in the 10 time course samples for each tissue were included for further analysis. Remaining missing values were imputed using k-nearest neighbor algorithm.

organism: Drosophila melanogaster

source_name: w1118 3 days muscle

label_protocol: Two to four micrograms of amplified RNAs were labeled with fluorescent dye Cy5 and purified using the PowerScript labeling kit (Clontech)

extract_protocol: Tissues or organs from four males of the same age were pooled together and used for each RNA sample preparation. Total RNA was extracted using miniRNA preparation kit (Zymo Research).  RNA was then amplified as described in PMID: 12186645.

tag: Drosophila w1118 male 3 days muscle

source_name: w1118 45 days muscle

label_protocol: Two to four micrograms of amplified RNAs were labeled with fluorescent dye Cy3 and purified using the PowerScript labeling kit (Clontech)

tag: Drosophila w1118 male 45 days muscle


title: w1118 testis 45 days set 2

description: w1118 45 days testis

source_name: w1118 3 days testis

tag: Drosophila w1118 male 3 days testis

source_name: w1118 45 days testis

tag: Drosophila w1118 male 45 days testis


title: w1118 testis 60 days set 1

description: w1118 60 days testis

source_name: w1118 60 days testis

tag: Drosophila w1118 male 60 days testis


title: w1118 testis 15 days set 1

description: w1118 15 days testis

source_name: w1118 15 days testis

tag: Drosophila w1118 male 15 days testis


title: Blue catfish Liver ESC-infection 3d replicate3


title: KS24R02

source_name: 24 h_IR24_Replication 2

source_name: 24 h_FR13A_Replication 2


title: w1118 testis 20 days set 2

description: w1118 20 days testis

source_name: w1118 20 days testis

tag: Drosophila w1118 male 20 days testis


title: w1118 muscle 60 days set 2

description: w1118 60 days muscle

source_name: w1118 60 days muscle

tag: Drosophila w1118 male 60 days muscle


title: Blue catfish Liver control 3d replicate2

source_name: Blue catfish Liver 3d control


title: w1118 testis 30 days set 2

description: w1118 30 days testis

source_name: w1118 30 days testis

tag: Drosophila w1118 male 30 days testis


title: Blue catfish Liver ESC-infection 3d replicate2


title: w1118 muscle 30 days set 2

description: w1118 30 days muscle

source_name: w1118 30 days muscle

tag: Drosophila w1118 male 30 days muscle


title: w1118 muscle 60 days set 1

description: w1118 60 days muscle


title: w1118 testis 45 days set 1

description: w1118 45 days testis


title: w1118 muscle 45 days set 1

description: w1118 45 days muscle


title: w1118 testis 30 days set 1

description: w1118 30 days testis


title: w1118 testis 20 days set 1

description: w1118 20 days testis


title: w1118 testis 15 days set 2

description: w1118 15 days testis


title: w1118 testis 60 days set 2

description: w1118 60 days testis


title: w1118 muscle 15 days set 2

description: w1118 15 days muscle

source_name: w1118 15 days muscle

tag: Drosophila w1118 male 15 days muscle


title: w1118 fat 45 days set 1

description: w1118 45 days fat

source_name: w1118 3 days fat

tag: Drosophiola w1118 male 3 days fat

source_name: w1118 45 days fat

tag: Drosophila w1118 male 45 days fat


title: w1118 fat 60 days set 1

description: w1118 60 days fat

source_name: w1118 60 days fat

tag: Drosophila w1118 male 60 days fat


title: w1118 muscle 15 days set 1

description: w1118 15 days muscle

source_name: w1118 3 days muscle


title: w1118 fat 30 days set 2

description: w1118 30 days fat

source_name: w1118 30 days fat

tag: Drosophila w1118 male 30 days fat


title: w1118 fat 15 days set 1

description: w1118 15 days fat

tag: Drosophila w1118 male 3 days fat

source_name: w1118 15 days fat

tag: Drosophila w1118 male 15 days fat


title: w1118 fat 45 days set 2

description: w1118 45 days fat


title: w1118 muscle 30 days set 1

description: w1118 30 days muscle

tag: Drosophila w1118 male 3 days muscle


title: w1118 fat 20 days set 1

description: w1118 20 days fat

tag: Drosophila w1118 3 male days fat

source_name: w1118 20 days fat

tag: Drosophila w1118 male 20 days fat


title: w1118 muscle 20 days set 2

description: w1118 20 days muscle

source_name: w1118 20 days muscle

tag: Drosophila w1118 male 20 days muscle


title: w1118 fat 15 days set 2

description: w1118 15 days fat


title: w1118 fat 20 days set 2

description: w1118 20 days fat


title: w1118 malpighian tubule 60 days set 1

description: w1118 60 days malpighian tubule

source_name: w1118 3 days malpighian tubule

tag: Drosophila w1118 male 3 days malpighian tubule

source_name: w1118 60 days malpighian tubule

tag: Drosophila w1118 male 60 days malpighian tubule


title: w1118 fat 60 days set 2

description: w1118 60 days fat


title: w1118 malpighian tubule 20 days set 1

description: w1118 20 days malpighian tubule

source_name: w1118 20 days malpighian tubule

tag: Drosophila w1118 male 20 days malpighian tubule


title: w1118 malpighian tubule 45 days set 1

description: w1118 45 days malpighian tubule

source_name: w1118 45 days malpighian tubule

tag: Drosophila w1118 male 45 days malpighian tubule


title: w1118 fat 30 days set 1

description: w1118 30 days fat


title: w1118 malpighian tubule 20 days set 2

description: w1118 20 days malpighian tubule


title: w1118 gut 60 days set 2

description: w1118 60 days gut

source_name: w1118 3 days gut

tag: Drosophila w1118 male 3 days gut

source_name: w1118 60 days gut

tag: Drosophila w1118 male 60 days gut


title: w1118 malpighian tubule 30 days set 1

description: w1118 30 days malpighian tubule

source_name: w1118 30 days malpighian tubule

tag: Drosophila w1118 male 30 days malpighian tubule


title: w1118 gut 60 days set 1

description: w1118 60 days gut


title: w1118 gut 45 days set 1

description: w1118 45 days gut

source_name: w1118 45 days gut

tag: Drosophila w1118 male 45 days gut


title: w1118 malpighian tubule 15 days set 1

description: w1118 15 days malpighian tubule

source_name: w1118 15 days malpighian tubule

tag: Drosophila w1118 male 15 days malpighian tubule


title: w1118 muscle 20 days set 1

description: w1118 20 days muscle


title: w1118 malpighian tubule 30 days set 2

description: w1118 30 days malpighian tubule


title: w1118 malpighian tubule 60 days set 2

description: w1118 60 days malpighian tubule


title: w1118 gut 30 days set 2

description: w1118 30 days gut

source_name: w1118 30 days gut

tag: Drosophila w1118 male 30 days gut


title: w1118 malpighian tubule 45 days set 2

description: w1118 45 days malpighian tubule


title: w1118 gut 20 days set 2

description: w1118 20 days gut

source_name: w1118 20 days gut

tag: Drosophila w1118 male 20 days gut


title: w1118 malpighian tubule 15 days set 2

description: w1118 15 days malpighian tubule


title: w1118 gut 15 days set 2

description: w1118 15 days gut

source_name: w1118 15 days gut

tag: Drosophila w1118 male 15 days gut


title: w1118 gut 20 days set 1

description: w1118 20 days gut


title: w1118 gut 45 days set 2

description: w1118 45 days gut


title: w1118 brain 45 days set 2

description: w1118 45 days brain

source_name: w1118 3 days brain

tag: Drosophila w1118 male 3 days brain

source_name: w1118 45 days brain

tag: Drosophila w1118 male 45 days brain


title: w1118 brain 30 days set 2

description: w1118 30 days brain

source_name: w1118 30 days brain

tag: Drosophila w1118 male 30 days brain


title: w1118 brain 45 days set 1

description: w1118 45 days brain


title: w1118 brain 60 days set 2

description: w1118 60 days brain

source_name: w1118 60 days brain

tag: Drosophila w1118 male 60 days brain


title: w1118 brain 20 days set 2

description: w1118 20 days brain

source_name: w1118 20 days brain

tag: Drosophila w1118 male 20 days brain


title: w1118 brain 30 days set 1

description: w1118 30 days brain


title: w1118 brain 60 days set 1

description: w1118 60 days brain


title: w1118 accessory gland 60 days set 2

description: w1118 60 days accessory gland

source_name: w1118 3 days accessory gland

tag: Drosophila w1118 male 3 days accessory gland

source_name: w1118 60 days accessory gland

tag: Drosophila w1118 male 60 days accessory gland


title: w1118 accessory gland 30 days set 2

description: w1118 30 days accessory gland

source_name: w1118 30 days accessory gland

tag: Drosophila w1118 male 30 days accessory gland


title: w1118 accessory gland 60 days set 1

description: w1118 60 days accessory gland


title: GMR>RasV12, biological rep1

status: Public on Nov 14 2007

city: Bronx

first: Lucy

middle: Catherine

last: Firth

state: NY

address: 1300 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

description: Gene expression data from eye antennal imaginal discs expressing UAS RasV12 in all cells posterior to the morphogenetic furrow using GMR Gal4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosgenome1 Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Genotype: GMR Gal4/UAS RasV12

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

growth_protocol: Larvae were raised on standard Drosophila medium at 25 degrees C.

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

treatment_protocol: 100 eye antennal imaginal discs were dissected from larvae in PBS. Discs were immediately transferred and collected into Trizol (GibcoBRL).

tag: Genotype

value: GMR Gal4/UAS RasV12

tag: Age

value: Wandering 3rd instar larvae


title: GMR>sSpi, biological rep3

source_name: Genotype: GMR Gal4/+; UAS sSpi/+

value: GMR Gal4/+; UAS sSpi/+


title: GMR>sSpi, biological rep2


title: GMR>RasV12, biological rep2


title: w1118 brain 15 days set 2

description: w1118 15 days brain

source_name: w1118 15 days brain

tag: Drosophila w1118 male 15 days brain


title: w1118 brain 15 days set 1

description: w1118 15 days brain


title: GMR>sSpi, biological rep1


title: GMR>RasV12, biological rep3


title: S.SHR(2)-50379

status: Public on Nov 01 2007

city: Toledo

first: Michael

middle: R

last: Garrett

state: OH

address: 3000 Arlington Ave, MS#1009

department: Physiology and Pharmacology

institute: University of Toledo-Health Science Campus

description: Gene expression from Renal Protective S.SHR(2) Congenic Strain

hyb_protocol: Hybridized chips were automatically washed and stained and at the Medical University of Ohio Bioinformatics & Proteomics/Genomics Program gene array facility using Affymetrix equipment and protocols recommended by manufacturer.

scan_protocol: Genechips®  were scanned at the Medical University of Ohio Bioinformatics & Proteomics/Genomics Program gene array facility using Affymetrix equipment and protocols recommended by manufacturer.

data_processing: Absolute analysis of data were conducted using the default settings of the Affymetrix software (GeneChip Software MAS-5.0)

label: Biotinylated cRNA

organism: Rattus norvegicus

source_name: whole kidney from Renal Protective S.SHR(2) Congenic Strain

label_protocol: Biotinylated cRNA was synthesized from 10 ug of total RNA using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) as directed by the user manual. cRNA quality for each sample was assessed by hybridization of 5ug adjusted kidney cRNA to Affymetrix Genechip® Test3 array. Subsequently, 15ug adjusted kidney cRNA was hybridized to the Genechip® Rat 230 2.0 array.

extract_protocol: Kidney was cut into ~ 0.5cM size cubes, suspended in RNAlater (Ambion, Austin, TX) and stored overnight at 4ºC.  RNA was extracted using Trizol® reagent (Invitrogen, Carlsbad, CA) and purified using Mini RNeasy kit (Qiagen,Valencia, CA ) according to manufacturer’s protocols. RNA quality was assessed by an OD260/280 ratio > 2.0 and visually by ethidium bromide staining on an agarose gel.

tag: Strain

value: Congenic strain derived from SS/Jr and SHR/NHsd


title: S.SHR(2)-50594


title: S.SHR(2)-50957


title: w1118 accessory gland 30 days set 1

description: w1118 30 days accessory gland


title: Dahl S-T1004

description: Gene expression from Dahl salt-sensitive stain

source_name: whole kidney from Dahl Salt-Sensitive

value: SS/Jr


title: w1118 accessory gland 15 days set 2

description: w1118 15 days accessory gland

source_name: w1118 15 days accessory gland

tag: Drosophila w1118 male 15 days accessory gland


title: w1118 accessory gland 45 days set 2

description: w1118 45 days accessory gland

source_name: w1118 45 days accessory gland

tag: Drosophila w1118 male 45 days accessory gland


title: w1118 brain 20 days set 1

description: w1118 20 days brain


title: w1118 accessory gland 20 days set 2

description: w1118 20 days accessory gland

source_name: w1118 20 days accessory gland

tag: Drosophila w1118 male 20 days accessory gland


title: w1118 accessory gland 20 days set 1

description: w1118 20 days accessory gland


title: CGH of E. chaffeensis Liberty

status: Public on Nov 06 2007

type: genomic

city: Columbus

first: Koshiro

last: Miura

address: 1900 Coffey Rd

department: Veterinary Biosciences

institute: The Ohio State University

description: DNA microarray, labeling, hybridization, scan and normalization of data were provided by NimbleGen.

hyb_protocol: Labeled genomic DNA was hybridized to arrays in 1x NimbleGen Hybridization Buffer (NimbleGen).

scan_protocol: The arrays were scanned at 5-micro-m resolution using a Genepix 4000b scanner (Axon Instruments, Union City, CA), and pixel intensities were extracted using NimbleScan software (NimbleGen).

data_processing: VALUE represents normalized ratio of Arkansas/Liberty.

molecule: genomic DNA

organism: Ehrlichia chaffeensis

source_name: Ehrlichia chaffeensis isolate Liberty

label_protocol: Cy3-labeled probes were synthesized from the genomic DNA (1 µg) with a random prime reaction.

extract_protocol:
E. chaffeensis strains were propagated in DH82 cells.  The infected cells were lysed by nitrogen cavitation, and liberated bacteria were purified by Percoll density gradient centrifugation.
Genomic DNA was extracted from the purified organisms with a QIAamp DNA Blood Mini Kit (QIAGEN).

tag: Ehrlichia chaffeensis Liberty genomic DNA

organism: Ehrlichia chaffeensis str. Arkansas

source_name: Arkansas

label_protocol: Cy5-labeled probes were synthesized from the genomic DNA (1 µg) with a random prime reaction.

tag: Ehrlichia chaffeensis Arkansas genomic DNA


title: w1118 accessory gland 45 days set 1

description: w1118 45 days accessory gland

tag: Drosophila w1118 male3 days accessory gland


title: w1118 accessory gland 15 days set 1

description: w1118 15 days accessory gland


title: Dahl S-T1030


title: Right kidney DEX rat 7

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: DEX treated right kidney

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: PLM (probe-level linear model) normalisation in the affylmGUI package of R

source_name: rat kidney

label_protocol: 5 - 8 µg of total RNA was used to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the kidney using Tri-Reagent and further purified using RNeasy spin columns.

tag: Sprague-Dawley, male, right kidney, DEX treated


title: Left kidney rat 5 (Control)

description: Left kidney

tag: Sprague-Dawley, male, left kidney


title: Right kidney Saline rat 6

description: Saline treated right kidney

tag: Sprague-Dawley, male, right kidney, Saline treated


title: w1118 gut 30 days set 1

description: w1118 30 days gut

source_name: w1118 3 days gut

tag: Drosophila w1118 male 3 days gut

source_name: w1118 30 days gut

tag: Drosophila w1118 male 30 days gut


title: Dahl S-T1087


title: Left kidney rat 7 (Control)

description: Left kidney


title: CGH of E. chaffeensis Wakulla

data_processing: VALUE represents normalized ratio of Arkansas/Wakulla.

source_name: Ehrlichia chaffeensis isolate Wakulla

tag: Ehrlichia chaffeensis Wakulla genomic DNA


title: Dahl S-T0996

tag: Gender

value: Male

value: 12 weeks old

tag: Tissue

value: whole kidney

tag: Diet

value: low salt (0.3% NaCl)


title: S.SHR(2)-50386


title: S.SHR(2)-50605


title: Left kidney rat 4 (Control)

description: Left kidney


title: Left kidney rat 3 (Control)

description: Left kidney


title: Right kidney Saline rat 2

description: Saline treated right kidney


title: Right kidney DEX rat 3

description: DEX treated right kidney


title: Right kidney Saline rat 4

description: Saline treated right kidney


title: Right kidney ACTH rat 1

description: ACTH treated right kidney

tag: Sprague-Dawley, male, right kidney, ACTH treated


title: Left kidney rat 8 (Control)

description: Left kidney


title: Right kidney Saline rat 8

description: Saline treated right kidney


title: Left kidney rat 6 (Control)

description: Left kidney


title: Left kidney rat 2 (Control)

description: Left kidney


title: Dahl S-T1051

tag: Strain


title: Right kidney ACTH rat 5

description: ACTH treated right kidney


title: Left kidney rat 1 (Control)

description: Left kidney


title: S.SHR(2)-50376


title: Dahl S-T1010


title: S.SHR(2)-50398

status: Public on Oct 31 2007


title: S.SHR(2)-50380


title: Dahl S-T1059


title: w1118 gut 15 days set 1

description: w1118 15 days gut

source_name: w1118 15 days gut

tag: Drosophila w1118 male 15 days gut


title: S.SHR(2)-50388


title: Dahl S-T0992


title: Old RTSV 1

status: Public on Oct 25 2007

city: Metro Manila

first: IL-RYONG

last: CHOI

address: DAPO Box 7777

country: Philippines

institute: International Rice Research Institute

description: TW16-4 and -69 were sister NIL (BC6) derived from the cross between cultivars TN1 (recurrent parent) and Utri Merah (donor parent). TW16-4 is susceptible to rice tungro spherical virus (RTSV), and TW16-69 is resistant to RTSV.

hyb_protocol: in-situ Hybridization Kit Plus (Agilent Technologies) according to the manufacturer's instrcution.

scan_protocol: DNA microarray scanner (Agilent Technologies) according to the manufacturer's instrcution.

data_processing: Feature Extraction Vert. 8.1 (Agilent Technologies)

organism: Oryza sativa

source_name: TW16-4 RTSV 1

label_protocol: Agilent Low RNA input fluorescent linear amplification kit according to the manufacturer's instrcution.

growth_protocol: Seedlings were grown in greenhouse set at 28C for 14 days.

extract_protocol: Total RNA was extracted with Trizol according to the manufaturer's instruction.

treatment_protocol: Leaves of 7-day old seedlings were inoculated 3 green leafhoppers carrying rice tungro spherical virus for 24 hours. Leaves were harvested 7 days after inoculation.

tag: leaves of 14-day old seedling

source_name: TW16-69 RTSV 1


title: RDA Healthy 1

description: NIL37 and NIL22 were sister NIL (BC4) derived from the cross between varieties Ilpum (recurrent parent) and Shinkwang (donor parent). NIL37 is susceptible to rice stripe virus (RSV), and NIL22 is resistant to RSV.

source_name: NIL37 Healthy 1

growth_protocol: Seedlings were grown in a greenhouse for 14 days.

source_name: NIL22 Healthy 1


title: RDA RSV 2

source_name: NIL37 RSV 2

treatment_protocol: Leaves of 7-day old seedlings were inoculated 3 small brown planthoppers carrying rice stripe virus for 24 hours. Leaves were harvested 7 days after inoculation.

source_name: NIL22 RSV 2


title: Dahl S-T0997

source_name: whole kidney from Dahl Salt-Sensitive

tag: Age

value: 4 weeks old


title: RDA RSV 1

source_name: NIL37 RSV 1

source_name: NIL22 RSV 1


title: New RTSV 2

description: TW16-1263 and -1029 were sister NIL (BC6) derived from the cross between cultivars TN1 (recurrent parent) and Utri Merah (donor parent). TW16-1263 is susceptible to rice tungro spherical virus (RTSV), and TW16-1029 is resistant to RTSV.


title: RSV Healthy 2

source_name: NIL37 Healthy 2

source_name: NIL22 Healthy 2


title: Old RTSV 2

source_name: TW16-4 RTSV 2

source_name: TW16-69 RTSV 2


title: New RTSV 1

tag: leaves of 14-day old leaves


title: New Mock 1

treatment_protocol: 7-day old leaves were inoculated with three green leafhoppers (GLH) for 24 hours. Leaves were harvested 7 days after inoculation.


title: New Healthy 2

source_name: TW16-1263 Healthy 2

source_name: TW16-1029 Healthy 2


status: Public on Jul 07 2007

city: Koganei

first: Tadashi

last: Matsunaga

state: Tokyo

department: Biotechnology

country: Japan

institute: Tokyo University of Agriculture and Technology

description: Five micrograms of purified RNA was reverse transcribed using random 6-mer primers and the fluorochromes Cy3 dUTP and Cy5 dUTP. Cy3–labeled cDNAs (from mRNA of cells grown under several iron condition) and Cy5–labeled cDNAs (from mRNA of cells grown under 0.1 μM iron: reference condition). Deatails of the sample and experiment can be found in the publications Suzuki et al., The Journal of Bacteriology “Global gene expression analysis of iron-inducible genes in Magnetospirillum magneticum AMB-1”.

data_processing: Mean ratios of normalized intensities defined as ch1 divided by ch2.

organism: Paramagnetospirillum magneticum AMB-1

source_name: Grown under 20 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) non-magnetic mutant NMA61 grown under 20 μM initial iron condition.

source_name: Grown under 0.1 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) non-magnetic mutant NMA61 grown under 0.1 μM initial iron condition.


tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) non-magnetic mutant NMA61 grown under 40 μM initial iron condition.

source_name: NMA61 grown under 0.1 μM initial iron condition


title: New Mock 2


tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) non-magnetic mutant NMA61 grown under 80 μM initial iron condition.


source_name: Grown under 100 μM initial iron condition

tag: Magnetospirillum magneticum AMB-1 (ATCC #700264) non-magnetic mutant NMA61 grown under 100 μM initial iron condition.


title: New Healthy 1

source_name: TW16-1263 Healthy 1

source_name: TW16-1029 Healthy 1


title: Old Mock 2

source_name: TW16-4 Mock 2

source_name: TW16-69 Mock 2


title: Macs isolated E-cadherin positive FLSPC isolate 728 vs Adult Liver (pooled) dye reversal

status: Public on Jun 20 2007

type: other

city: New York

first: Leslie

last: Rogler

address: 1300 Morris Park Ave

department: Liver Research Center/ Department of Medicine

description: aRNA was used as target material for all arrays

hyb_protocol: Hybridization was carried out as described at http://microarray1k.aecom.yu.edu. Hybridization was done at 50C for 20 hours.

scan_protocol: After hybridization and washing, the arrays were scanned for Cy3 and Cy5 fluorescence using a GenePix 4000 Microarray Scanner (Axon Instruments, Union City, CA).

data_processing: Images of the red and green fluorescence patterns obtained from the scanner were analyzed using GenePix Pro 3.0 (Axon Instruments, now Molecular Devices, Sunnyvale, CA). Normalization was performed using the implementation of loess found at http://microarray1k.aecom.yu.edu.

molecule: other

organism: Mus musculus

label_protocol: Cy3 and Cy5 labeled hybridization targets were synthesized and arrays were hybridized as previously described [Ader et al, 2006]. The Protocol can be found at http://microarray1k.aecom.yu.edu

growth_protocol: freshly isolated cells

extract_protocol: Total RNAs were prepared from Macs purified FLEC, using Qiagen RNeasy Mini kit (Valencia, CA). Five microgram aliquots of total RNA were used to generate amplified RNA (aRNA) of all probes, using the Ambion Message Amp Kit, following the manufacturer’s instructions (Ambion, Austin, TX).  The quantity of RNA before and after amplification was estimated using a Nanodrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  RNA integrity before and after amplification was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Rockville, MD).

treatment_protocol:
On ED13.5, fetal livers were microdissected from timed pregnant mice and cells isolated as described previously [Nierhoff et al, 2005].  Disaggregated adult liver cells were obtained from 8-week-old C57/Bl6 mice by the two-step collagenase (Liberase Blendzyme, Roche Applied Science, Indianapolis, IN) perfusion method described by Seglen et al. and were centrifuged three times at 50g for 2 minutes to obtain an enriched fraction of hepatocytes [Selgen et al, 1976].
Macs separation.  FLEC were purified from total fetal liver cells using rat anti-mouse E-cadherin (ECCD-2) (TaKaRa, Otsu, Japan) antibody.  E-cadherin was directly targeted with secondary goat anti-rat magnetic bead-conjugated IgG.  The purification over the columns followed the instructions of the manufacturer (MiniMacs, Miltenyi Biotech, Bergisch-Gladbach, Germany).  Purity was assessed by FACS analysis using PE-conjugated secondary donkey anti-rat antibody and confirmed by immunocytochemistry on cytospins for an epithelial-specific pancytokeratin (PanCK) marker

tag: Macs isolated E-cadherin positive fetal liver stem progenitor cells were isolated from C57Bl6 fetuses on day 13.5 of gestation

source_name: Adult mouse liver (pooled)

label_protocol: Cy3 and Cy5 labeled hybridization targets were synthesized and arrays were hybridized as previously described [Ader et al]. The protocol for target labeling can be found at (http://microarray1k.aecom.yu.edu/

growth_protocol: none RNA was isolated from tissues

extract_protocol: Total RNA was isolated from the liver of male 8-week-old C57/Bl6 animals, using a combined Trizol/Li Cl protocol to remove glycogen that interferes with target synthesis.  RNA prepared from the liver of 5 animals was pooled and used as the reference RNA. These RNAs were further purified using the Qiagen RNeasy kit.  Five microgram aliquots of total RNA were used to generate amplified RNA (aRNA) of all probes, using the Ambion Message Amp Kit, following the manufacturer’s instructions (Ambion, Austin, TX).  The quantity of RNA before and after amplification was estimated using a Nanodrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  RNA integrity before and after amplification was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Rockville, MD).

treatment_protocol: Mice were housed according to standard AALAC protocols in the Albert Einstein College of Medicine Institute for Animal Studies.

tag: Liver was isolated from 5, 8-10 week old C57Bl6 adult male mice.


title: Old Healthy 1

description: TW16-4 and -69 were sister NIL (BC6) derived from the cross between a cultivar TN1 (recurrent parent) and Utri Merah (donor parent). TW16-4 is susceptible to rice tungro spherical virus (RTSV), and TW16-69 is resistant to RTSV.

hyb_protocol: in-situ Hybridization Kit Plus (Agilent Technologies) according to the manufacturer's instruction.

scan_protocol: DNA microarray scanner (Agilent Technologies) according to the manufacturer's instruction.

data_processing: Feature Extraction Ver. 8.1 (Agilent Technologies)

source_name: TW16-4 Healthy 1

label_protocol: Agilent Low RNA input fluorescent linear amplification kit according to the manufacturer's instruction.

extract_protocol: Total RNA was extracted with Trizol according to the manufacturer's instruction.

tag: leaves of 14 day-old seedling

source_name: TW16-69 Healthy 1


title: Macs isolated E-cadherin positive FLSPC isolate 515 vs Adult liver (pooled) dye reversal

description: aRNA was used for target preparation for both adult liver and MACS isolated cells.

hyb_protocol: Arrays were hybridized as previously described (Ader et al, 2006) according to the protocol available at(http://microarray1k.aecom.yu.edu/ Arrays were hybridized for 20 hours at 50C.

data_processing: Images of the red and green fluorescence patterns obtained from the scanner were analyzed using GenePix Pro 3.0 (Axon Instruments, now Molecular Devices, Sunnyvale, CA). Loess normalization of the data was performed using the implimentation available at http://microarray1k.aecom.yu.edu.

source_name: Macs isolated E-cadherin positive FLSTPC isolate 515

label_protocol: Cy3 and Cy5 labeled hybridization targets were synthesized and arrays were hybridized as previously described [Ader et al, 2006].

treatment_protocol: FLEC were purified from total fetal liver cells using rat anti-mouse E-cadherin (ECCD-2) (TaKaRa, Otsu, Japan) antibody.  E-cadherin was directly targeted with secondary goat anti-rat magnetic bead-conjugated IgG.  The purification over the columns followed the instructions of the manufacturer (MiniMacs, Miltenyi Biotech, Bergisch-Gladbach, Germany).  Purity was assessed by FACS analysis using PE-conjugated secondary donkey anti-rat antibody and confirmed by immunocytochemistry on cytospins for an epithelial-specific pancytokeratin (PanCK) marker.

tag: Macs isolated E-cadherin positive fetal liver stem progenitor cells were isolated from C57Bl6 fetuses on day 13.5 of gestation.

treatment_protocol: Tissue was snap frozen in 2 methylbutane over dry ice and stored at -80C.


title: Old Healthy 2

source_name: TW16-4 Healthy 2

source_name: TW16-69 Healthy 2


title: Female3, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose

status: Public on May 01 2007

city: Greensboro

first: Elizabeth

middle: Sherman

last: Roberts

state: NC

address: 3200 Northline Ave, Suite 300

institute: Novartis Animal Health US

description: AMM_0_0_Female3_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

data_processing: Affymetrix GCOS 1.0

source_name: Sample Type: Female, Respiratory RNA, Tissue: Nasal respiratory epithelium, Tissue Harvest Methods: Tissue was preserved in RNA Later and collected from nasal passages and from boney turbintates

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen; LPG tube, heavy; DNase Digestion

treatment_protocol: in vivo Treatment: Untreated

tag: Array Type

tag: Amount to Core

tag: Units of Amount

value: microliter

tag: Ratio

tag: Dilution

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: Excellent

tag: Sample Preservation

value: RNA Later

tag: Strain or Line

value: Sprague Dawley

tag: NCBI Taxonomy ID

tag: Individual

value: Female 3

tag: Developmental State

value: Adult

tag: Sacrifice Method

value: Ketamine IP injection overdose

tag: Sex

value: Female

tag: Units of Age

value: Weeks

tag: Genetic Modifications

tag: Disease State


title: Female6, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Female6_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Female, Olfactory RNA, Tissue: Nasal olfactory epithelium, Tissue Harvest Methods: Tissue was preserved in RNA later and collected from nasal passages and from boney turbinates

tag: Array Type

value: Good

value: RNA later

value: Female 6

tag: Age

value: weeks


title: Macs isolated E-cadherin positive FLSPC vs Adult liver (pooled)

description: all RNA samples labeled were aRNA.

hyb_protocol: Cy 3 and Cy5 labeled targets were synthesized using a modified version of the AECOM functional Genomics facility protocol (http://microarray1k.aecom.yu.edu/) as previously described (Plescia, 2001).   Cy3 and Cy5 labeled targets were prepared using 5 ug aRNA, random primers and Superscript reverse transcriptase (Invitrogen).

scan_protocol: Arrays were scanned for Cy3 and Cy5 florescence using a Genepix 4000 scanner (Axon Instruments Inc., Union City, CA).

data_processing: The signal intensity of a spot was considered to be significant if the signal intensity was 200 units greater the background for that spot and if it was not flagged as “not found” by GenePix 3.0 software. These data were normalized using the Loess implementation included at http://microarray1k.aecom.yu.edu/. The value in the data tables is calculated as the log2(normalized chanel 1/ normalized chanel 2 ) for each qualified spot.

label_protocol: Cy3 and Cy5 labeled hybridization targets were synthesized as described in Ader et al, 2006.

growth_protocol: Animals were housed under AALAC approved conditions. No pretreatment was performed.

treatment_protocol: Total RNA was isolated from 5 adult male animals and pooled.  5ug aliqouts were used to synthesize aRNA for labeling.

tag: Total RNA was isolated from the liver of male 8-week-old C57/Bl6 animals, using a combined Trizol/Li Cl protocol to remove glycogen that interferes with target synthesis.  RNA prepared from the liver of 5 animals was pooled and used as the reference RNA.

growth_protocol: Cells are freshly isolated.  There is no invitro culture period.

treatment_protocol:
On ED13.5, fetal livers were microdissected from timed pregnant mice and cells isolated as described previously [8].  Disaggregated adult liver cells were obtained from 8-week-old C57/Bl6 mice by the two-step collagenase (Liberase Blendzyme, Roche Applied Science, Indianapolis, IN) perfusion method described by Seglen et al. and were centrifuged three times at 50g for 2 minutes to obtain an enriched fraction of hepatocytes [16].
Macs separation.  FLEC were purified from total fetal liver cells using rat anti-mouse E-cadherin (ECCD-2) (TaKaRa, Otsu, Japan) antibody.  E-cadherin was directly targeted with secondary goat anti-rat magnetic bead-conjugated IgG.  The purification over the columns followed the instructions of the manufacturer (MiniMacs, Miltenyi Biotech, Bergisch-Gladbach, Germany).  Purity was assessed by FACS analysis using PE-conjugated secondary donkey anti-rat antibody and confirmed by immunocytochemistry on cytospins for an epithelial-specific pancytokeratin (PanCK) marker

tag: Macs isolated E-cadherin positive fetal liver stem progenitor cells from 13.5 day of gestation fetal mouse liver of C57Bl6 fetuses.


title: Male7, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male7_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Male, Respiratory RNA, Tissue: Nasal respiratory epithleium, Tissue Harvest Methods: Tissue was preserved in RNA later and collected from nasal passages and from boney turbinates

tag: Amount to Core

tag: Units of Amount

tag: Ratio

tag: Dilution

value: Male 7

value: Male


title: Macs isolated E-cadherin positive FLSPC cells isolate 728 vs Adult liver (pooled)

growth_protocol: Mice were maintained according to standard AALAC protocol in the Albert Einstein College of Medicine Institute for Animal Research.

treatment_protocol: Livers were isolated from 5, 8-10 week old male C57Bl6 animals. Tissues were snap frozen in 2 methyl butane over dry ice and stored at -80C prior to RNA extraction.

tag: Liver was isolated from 5, 8-10 week old C57Bl6 adult male mice.

tag: Macs isolated E-cadherin positive mouse fetal liver stem progenitor cells isolate 728 were isolated from C57Bl6 fetuses on day 13.5 of gestation.


title: Macs isolated E-cadherin positive FLSPC vs Adult liver (pooled) 412 dye reversal

tag: Macs isolated E-cadherin positive fetal liver stem progenitor cells were isolated from C57Bl6 fetuses on day 13.5 of gestation.


title: Male8, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Male8_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Male, Respiratory RNA, Tissue: Nasal respiratory epithelium, Tissue Harvest Methods: Tissue was preserved in RNA Later and collected from nasal passages and from boney turbintates

tag: RNA Integrity Number

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

value: Male 8

tag: Developmental State


title: Male7, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Male7_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Male, Olfactory RNA, Tissue: Nasal olfactory epithelium, Tissue Harvest Methods: Tissue was preserved in RNA Later and collected from nasal passages and from boney turbintates

tag: Array Type

tag: Sacrifice Method

tag: Sex

tag: Age

tag: Units of Age

tag: Genetic Modifications

tag: Disease State


title: Female4, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Female4_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Amount to Core

tag: Units of Amount

tag: Ratio

tag: Dilution

value: Female 4


title: Macs isolated E-cadherin positive FLSPC isolate 515 vs Adult liver (pooled)

tag: Liver was isolated from 5, 8-10 week old C57Bl6 adult male mice.

source_name: Macs isolated E-cadherin positive fetal liver stem progenitor cells isolate 515

tag: Macs isolated E-cadherin positive fetal liver stem progenitor cells were isolated from C57Bl6 fetuses on day 13.5 of gestation


title: Male4, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male4_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Male, Olfactory RNA, Tissue: Nasal olfactory epithleium, Tissue Harvest Methods: Tissue was preserved in RNA later and collected from nasal passages and from boney turbinates

value: microliter

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line

value: Male 4


title: Male3, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male3_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: RNA Integrity Number

value: Excellent

value: RNA Later

tag: NCBI Taxonomy ID

tag: Individual

value: Male 3

tag: Developmental State


title: Male1, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male1_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Array Type

value: Sprague Dawley

value: Male 1

value: Adult

tag: Sacrifice Method

tag: Sex

tag: Age


title: Male2, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male2_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Amount to Core

value: Male 2

value: Ketamine IP injection overdose

tag: Units of Age

value: Weeks

tag: Genetic Modifications

tag: Disease State


title: Female7, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Female7_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Units of Amount

tag: Ratio

tag: Dilution

value: Good

value: Female 7

value: Female


title: Male4, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male4_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Bioanalyzer Results

tag: Sample Preservation

value: Male


title: Male1, Respiratory RNA_Nasal respiratory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male1_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Strain or Line


title: ykl112w deletion

status: Public on Apr 01 2007

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: ykl112w deletion strain expression profile in mid-log growth

data_processing: raw data and duplicate combining were achieved by using Error Model described in the publication Functional Discovery via a Compendium of Expression Profiles. Cell, Volume 102, Issue 1, Pages 109-126  T. Hughes, M. Marton, A. Jones, C. Roberts, R. Stoughton, C. Armour, H. Bennett, E. Coffey, H. Dai, Y. He

organism: Saccharomyces cerevisiae

source_name: ykl112w deletion mid-log growth

tag: mid-log growth

source_name: WT mid-log growth


title: ymr043w deletion

description: ymr043w deletion strain expression profile in mid-log growth

source_name: ymr043w deletion mid-log growth


title: Female9, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Female9_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

source_name: Sample Type: Female, Respiratory RNA, Tissue: Nasal respiratory epithelium, Tissue Harvest Methods: Tissue was preserved in RNA later and collected from nasal passages and from boney turbinates

tag: RNA Integrity Number

value: RNA later

tag: NCBI Taxonomy ID

tag: Individual

value: Female 9

value: weeks


title: Male3, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male3_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Array Type

value: microliter

tag: Developmental State

tag: Sacrifice Method


title: Male10, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Male10_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Amount to Core

value: Male 10

tag: Sex

tag: Age


title: Male2, Olfactory RNA_Nasal olfactory epithleium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Male2_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

value: RNA Later

tag: Units of Age

tag: Genetic Modifications

tag: Disease State


title: Female8, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Female8_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Units of Amount

tag: Ratio

tag: Dilution

value: Female 8


title: ypl075w deletion

description: ypl075w deletion strain expression profile in mid-log growth

source_name: ypl075w deletion mid-log growth


title: ynl216w deletion

description: ynl216w deletion strain expression profile in mid-log growth

source_name: ynl216w deletion mid-log growth


title: ybr049c deletion

description: ybr049c deletion strain expression profile in mid-log growth

source_name: ybr049c deletion mid-log growth


title: Female6, Respiratory RNA_Nasal respiratory epithelium_Tissue was preserved in RNA Later and collected from nose

description: AMM_0_0_Female6_Resp_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: Bioanalyzer Results

tag: Sample Preservation

tag: Strain or Line

value: Sprague Dawley

value: Female 6


title: ygl073w deletion

description: ygl073w deletion strain expression profile in mid-log growth

source_name: ygl073w deletion mid-log growth

tag: mid-log growth


title: Female8, Olfactory RNA_Nasal olfactory epithelium_Tissue was preserved in RNA later and collected from nose

description: AMM_0_0_Female8_Olfact_Untreated_Rat230_2_McElveen_05-1: Examination of global gene expression of nasal respiratory and olfactory tissues of male and female CD rats

tag: RNA Integrity Number

tag: NCBI Taxonomy ID

tag: Individual

value: Adult


title: Old Mock 1

description: TW16-4 and -69 were sister NIL (BC6) derived from the cross between cultivars TN1 (recurrent parent) and Utri Merah (donor parent). TW16-4 is susceptible to rice tungro spherical virus (RTSV), and TW16-69 is resistant to RTSV.

source_name: TW16-4 Mock 1

tag: leaves of 14-day old seedling

source_name: TW16-69 Mock 1


title: yhr124w deletion

description: yhr124w deletion strain expression profile in mid-log growth

source_name: yhr124w deletion mid-log growth


title: ygr288w deletion

description: ygr288w deletion strain expression profile in mid-log growth

source_name: ygr288w deletion mid-log growth


title: ylr266c deletion

description: ylr266c deletion strain expression profile in mid-log growth

source_name: ylr266c deletion mid-log growth


title: ylr453c deletion

description: ylr453c deletion strain expression profile in mid-log growth

source_name: ylr453c deletion mid-log growth


title: ybr275c deletion

description: ybr275c deletion strain expression profile in mid-log growth

source_name: ybr275c deletion mid-log growth


title: yjl089w deletion

description: yjl089w deletion strain expression profile in mid-log growth

source_name: yjl089w deletion mid-log growth


title: yer045c deletion

description: yer045c deletion strain expression profile in mid-log growth

source_name: yer045c deletion mid-log growth


title: ycr065w deletion

description: ycr065w deletion strain expression profile in mid-log growth

source_name: ycr065w deletion mid-log growth


title: ynl027w deletion

description: ynl027w deletion strain expression profile in mid-log growth

source_name: ynl027w deletion mid-log growth

source_name: WT mid-log growth


title: ypl254w deletion

description: ypl254w deletion strain expression profile in mid-log growth

source_name: ypl254w deletion mid-log growth


title: yil128w deletion

description: yil128w deletion strain expression profile in mid-log growth

source_name: yil128w deletion mid-log growth


title: ylr403w deletion

description: ylr403w deletion strain expression profile in mid-log growth

source_name: ylr403w deletion mid-log growth


title: ygr040w deletion

description: ygr040w deletion strain expression profile in mid-log growth

source_name: ygr040w deletion mid-log growth


title: ykl072w deletion

description: ykl072w deletion strain expression profile in mid-log growth

source_name: ykl072w deletion mid-log growth


title: ygl197w deletion

description: ygl197w deletion strain expression profile in mid-log growth

source_name: ygl197w deletion mid-log growth


title: ymr075w deletion

description: ymr075w deletion strain expression profile in mid-log growth

source_name: ymr075w deletion mid-log growth


title: ygl181w deletion

description: ygl181w deletion strain expression profile in mid-log growth

source_name: ygl181w deletion mid-log growth


title: ydl106c deletion

description: ydl106c deletion strain expression profile in mid-log growth

source_name: ydl106c deletion mid-log growth


title: ygl209w deletion

description: ygl209w deletion strain expression profile in mid-log growth

source_name: ygl209w deletion mid-log growth


title: ylr136c deletion

description: ylr136c deletion strain expression profile in mid-log growth

source_name: ylr136c deletion mid-log growth


title: ypl089c deletion

description: ypl089c deletion strain expression profile in mid-log growth

source_name: ypl089c deletion mid-log growth


title: yml027w deletion

description: yml027w deletion strain expression profile in mid-log growth

source_name: yml027w deletion mid-log growth


title: yer088c deletion

description: yer088c deletion strain expression profile in mid-log growth

source_name: yer088c deletion mid-log growth


title: ynr063w deletion

description: ynr063w deletion strain expression profile in mid-log growth

source_name: ynr063w deletion mid-log growth


title: yor358w deletion

description: yor358w deletion strain expression profile in mid-log growth

source_name: yor358w deletion mid-log growth


title: ykr101w deletion

description: ykr101w deletion strain expression profile in mid-log growth

source_name: ykr101w deletion mid-log growth

source_name: WT mid-log growth


title: yhr041c deletion

description: yhr041c deletion strain expression profile in mid-log growth

source_name: yhr041c deletion mid-log growth


title: yer111c deletion

description: yer111c deletion strain expression profile in mid-log growth

source_name: yer111c deletion mid-log growth


title: yml076c deletion

description: yml076c deletion strain expression profile in mid-log growth

source_name: yml076c deletion mid-log growth


title: ykl222c deletion

description: ykl222c deletion strain expression profile in mid-log growth

source_name: ykl222c deletion mid-log growth


title: yjr140c deletion

description: yjr140c deletion strain expression profile in mid-log growth

source_name: yjr140c deletion mid-log growth


title: ydr520c deletion

description: ydr520c deletion strain expression profile in mid-log growth

source_name: ydr520c deletion mid-log growth


title: yil130w deletion

description: yil130w deletion strain expression profile in mid-log growth

source_name: yil130w deletion mid-log growth


title: ydr009w deletion

description: ydr009w deletion strain expression profile in mid-log growth

source_name: ydr009w deletion mid-log growth


title: ybr150c deletion

description: ybr150c deletion strain expression profile in mid-log growth

source_name: ybr150c deletion mid-log growth


title: yjr094c deletion

description: yjr094c deletion strain expression profile in mid-log growth

source_name: yjr094c deletion mid-log growth


title: ylr131c deletion

description: ylr131c deletion strain expression profile in mid-log growth

source_name: ylr131c deletion mid-log growth


title: ybr033w deletion

description: ybr033w deletion strain expression profile in mid-log growth

source_name: ybr033w deletion mid-log growth


title: ylr278c deletion

description: ylr278c deletion strain expression profile in mid-log growth

source_name: ylr278c deletion mid-log growth


title: ypr018w deletion

description: ypr018w deletion strain expression profile in mid-log growth

source_name: ypr018w deletion mid-log growth


title: yjl206c deletion

description: yjl206c deletion strain expression profile in mid-log growth

source_name: yjl206c deletion mid-log growth


title: ydr266c deletion

description: ydr266c deletion strain expression profile in mid-log growth

source_name: ydr266c deletion mid-log growth


title: ydl048c deletion

description: ydl048c deletion strain expression profile in mid-log growth

source_name: ydl048c deletion mid-log growth

source_name: WT mid-log growth


title: ydr463w deletion

description: ydr463w deletion strain expression profile in mid-log growth

source_name: ydr463w deletion mid-log growth


title: ybr103w deletion

description: ybr103w deletion strain expression profile in mid-log growth

source_name: ybr103w deletion mid-log growth


title: yol067c deletion

description: yol067c deletion strain expression profile in mid-log growth

source_name: yol067c deletion mid-log growth


title: ygl166w deletion

description: ygl166w deletion strain expression profile in mid-log growth

source_name: ygl166w deletion mid-log growth


title: yal051w deletion

description: yal051w deletion strain expression profile in mid-log growth

source_name: yal051w deletion mid-log growth


title: ybr240c deletion

description: ybr240c deletion strain expression profile in mid-log growth

source_name: ybr240c deletion mid-log growth


title: ylr013w deletion

description: ylr013w deletion strain expression profile in mid-log growth

source_name: ylr013w deletion mid-log growth


title: ybr239c deletion

description: ybr239c deletion strain expression profile in mid-log growth

source_name: ybr239c deletion mid-log growth


title: ygr063c deletion

description: ygr063c deletion strain expression profile in mid-log growth

source_name: ygr063c deletion mid-log growth


title: ymr280c deletion

description: ymr280c deletion strain expression profile in mid-log growth

source_name: ymr280c deletion mid-log growth


title: yjl056c deletion

description: yjl056c deletion strain expression profile in mid-log growth

source_name: yjl056c deletion mid-log growth


title: ypr065w deletion

description: ypr065w deletion strain expression profile in mid-log growth

source_name: ypr065w deletion mid-log growth


title: yml007w deletion

description: yml007w deletion strain expression profile in mid-log growth

source_name: yml007w deletion mid-log growth


title: yil084c deletion

description: yil084c deletion strain expression profile in mid-log growth

source_name: yil084c deletion mid-log growth


title: ygl151w deletion

description: ygl151w deletion strain expression profile in mid-log growth

source_name: ygl151w deletion mid-log growth


title: ygr067c deletion

description: ygr067c deletion strain expression profile in mid-log growth

source_name: ygr067c deletion mid-log growth


title: ykl038w deletion

description: ykl038w deletion strain expression profile in mid-log growth

source_name: ykl038w deletion mid-log growth

source_name: WT mid-log growth


title: yor213c deletion

description: yor213c deletion strain expression profile in mid-log growth

source_name: yor213c deletion mid-log growth


title: yil101c deletion

description: yil101c deletion strain expression profile in mid-log growth

source_name: yil101c deletion mid-log growth


title: ynr010w deletion

description: ynr010w deletion strain expression profile in mid-log growth

source_name: ynr010w deletion mid-log growth


title: ygl071w deletion

description: ygl071w deletion strain expression profile in mid-log growth

source_name: ygl071w deletion mid-log growth


title: ydr123c deletion

description: ydr123c deletion strain expression profile in mid-log growth

source_name: ydr123c deletion mid-log growth


title: ygl254w deletion

description: ygl254w deletion strain expression profile in mid-log growth

source_name: ygl254w deletion mid-log growth


title: yhl027w deletion

description: yhl027w deletion strain expression profile in mid-log growth

source_name: yhl027w deletion mid-log growth


title: yil036w deletion

description: yil036w deletion strain expression profile in mid-log growth

source_name: yil036w deletion mid-log growth


title: yer040w deletion

description: yer040w deletion strain expression profile in mid-log growth

source_name: yer040w deletion mid-log growth


title: ydl020c deletion

description: ydl020c deletion strain expression profile in mid-log growth

source_name: ydl020c deletion mid-log growth


title: yol148c deletion

description: yol148c deletion strain expression profile in mid-log growth

source_name: yol148c deletion mid-log growth


title: ydr392w deletion

description: ydr392w deletion strain expression profile in mid-log growth

source_name: ydr392w deletion mid-log growth


title: ynl097c deletion

description: ynl097c deletion strain expression profile in mid-log growth

source_name: ynl097c deletion mid-log growth


title: ynl068c deletion

description: ynl068c deletion strain expression profile in mid-log growth

source_name: ynl068c deletion mid-log growth


title: yml113w deletion

description: yml113w deletion strain expression profile in mid-log growth

source_name: yml113w deletion mid-log growth


title: ydr363w deletion

description: ydr363w deletion strain expression profile in mid-log growth

source_name: ydr363w deletion mid-log growth


title: ydr310c deletion

description: ydr310c deletion strain expression profile in mid-log growth

source_name: ydr310c deletion mid-log growth

source_name: WT mid-log growth


title: yol089c deletion

description: yol089c deletion strain expression profile in mid-log growth

source_name: yol089c deletion mid-log growth


title: ydl042c deletion

description: ydl042c deletion strain expression profile in mid-log growth

source_name: ydl042c deletion mid-log growth


title: yer028c deletion

description: yer028c deletion strain expression profile in mid-log growth

source_name: yer028c deletion mid-log growth


title: yjl103c deletion

description: yjl103c deletion strain expression profile in mid-log growth

source_name: yjl103c deletion mid-log growth


title: ynl021w deletion

description: ynl021w deletion strain expression profile in mid-log growth

source_name: ynl021w deletion mid-log growth


title: ydl070w deletion

description: ydl070w deletion strain expression profile in mid-log growth

source_name: ydl070w deletion mid-log growth


title: ycr084c deletion

description: ycr084c deletion strain expression profile in mid-log growth

source_name: ycr084c deletion mid-log growth


title: ykr036c deletion

description: ykr036c deletion strain expression profile in mid-log growth

source_name: ykr036c deletion mid-log growth


title: ykl043w deletion

description: ykl043w deletion strain expression profile in mid-log growth

source_name: ykl043w deletion mid-log growth


title: ydr207c deletion

description: ydr207c deletion strain expression profile in mid-log growth

source_name: ydr207c deletion mid-log growth


title: ycr106w deletion

description: ycr106w deletion strain expression profile in mid-log growth

source_name: ycr106w deletion mid-log growth


title: ybl008w deletion

description: ybl008w deletion strain expression profile in mid-log growth

source_name: ybl008w deletion mid-log growth


title: yer130c deletion

description: yer130c deletion strain expression profile in mid-log growth

source_name: yer130c deletion mid-log growth


title: ydr451c deletion

description: ydr451c deletion strain expression profile in mid-log growth

source_name: ydr451c deletion mid-log growth


title: yer169w deletion

description: yer169w deletion strain expression profile in mid-log growth

source_name: yer169w deletion mid-log growth


title: ylr228c deletion

description: ylr228c deletion strain expression profile in mid-log growth

source_name: ylr228c deletion mid-log growth


title: ydr073w deletion

description: ydr073w deletion strain expression profile in mid-log growth

source_name: ydr073w deletion mid-log growth

source_name: WT mid-log growth


title: ybr195c deletion

description: ybr195c deletion strain expression profile in mid-log growth

source_name: ybr195c deletion mid-log growth


title: yjr147w deletion

description: yjr147w deletion strain expression profile in mid-log growth

source_name: yjr147w deletion mid-log growth


title: yor304w deletion

description: yor304w deletion strain expression profile in mid-log growth

source_name: yor304w deletion mid-log growth


title: yil010w deletion

description: yil010w deletion strain expression profile in mid-log growth

source_name: yil010w deletion mid-log growth


title: ydr213w deletion

description: ydr213w deletion strain expression profile in mid-log growth

source_name: ydr213w deletion mid-log growth


title: ybl005w deletion

description: ybl005w deletion strain expression profile in mid-log growth

source_name: ybl005w deletion mid-log growth


title: yir017c deletion

description: yir017c deletion strain expression profile in mid-log growth

source_name: yir017c deletion mid-log growth


title: ygl013c deletion

description: ygl013c deletion strain expression profile in mid-log growth

source_name: ygl013c deletion mid-log growth


title: ydr176w deletion

description: ydr176w deletion strain expression profile in mid-log growth

source_name: ydr176w deletion mid-log growth


title: yjl127c deletion

description: yjl127c deletion strain expression profile in mid-log growth

source_name: yjl127c deletion mid-log growth


title: yjl110c deletion

description: yjl110c deletion strain expression profile in mid-log growth

source_name: yjl110c deletion mid-log growth


title: yil038c deletion

description: yil038c deletion strain expression profile in mid-log growth

source_name: yil038c deletion mid-log growth


title: ynl204c deletion

description: ynl204c deletion strain expression profile in mid-log growth

source_name: ynl204c deletion mid-log growth


title: ylr014c deletion

description: ylr014c deletion strain expression profile in mid-log growth

source_name: ylr014c deletion mid-log growth


title: ylr451w deletion

description: ylr451w deletion strain expression profile in mid-log growth

source_name: ylr451w deletion mid-log growth


title: ypl202c deletion

description: ypl202c deletion strain expression profile in mid-log growth

source_name: ypl202c deletion mid-log growth


title: ynl314w deletion

description: ynl314w deletion strain expression profile in mid-log growth

source_name: ynl314w deletion mid-log growth

source_name: WT mid-log growth


title: yjr127c deletion

description: yjr127c deletion strain expression profile in mid-log growth

source_name: yjr127c deletion mid-log growth


title: yor162c deletion

description: yor162c deletion strain expression profile in mid-log growth

source_name: yor162c deletion mid-log growth


title: ygr104c deletion

description: ygr104c deletion strain expression profile in mid-log growth

source_name: ygr104c deletion mid-log growth


title: yhr006w deletion

description: yhr006w deletion strain expression profile in mid-log growth

source_name: yhr006w deletion mid-log growth


title: ypl139c deletion

description: ypl139c deletion strain expression profile in mid-log growth

source_name: ypl139c deletion mid-log growth


title: ymr037c deletion

description: ymr037c deletion strain expression profile in mid-log growth

source_name: ymr037c deletion mid-log growth


title: ynl167c deletion

description: ynl167c deletion strain expression profile in mid-log growth

source_name: ynl167c deletion mid-log growth


title: ypl038w deletion

description: ypl038w deletion strain expression profile in mid-log growth

source_name: ypl038w deletion mid-log growth


title: ygr089w deletion

description: ygr089w deletion strain expression profile in mid-log growth

source_name: ygr089w deletion mid-log growth


title: yol004w deletion

description: yol004w deletion strain expression profile in mid-log growth

source_name: yol004w deletion mid-log growth


title: yhr178w deletion

description: yhr178w deletion strain expression profile in mid-log growth

source_name: yhr178w deletion mid-log growth


title: yor032c deletion

description: yor032c deletion strain expression profile in mid-log growth

source_name: yor032c deletion mid-log growth


title: yfl052w deletion

description: yfl052w deletion strain expression profile in mid-log growth

source_name: yfl052w deletion mid-log growth


title: yor191w deletion

description: yor191w deletion strain expression profile in mid-log growth

source_name: yor191w deletion mid-log growth


title: ybl052c deletion

description: ybl052c deletion strain expression profile in mid-log growth

source_name: ybl052c deletion mid-log growth


title: ydr026c deletion

description: ydr026c deletion strain expression profile in mid-log growth

source_name: ydr026c deletion mid-log growth


title: yor230w deletion

description: yor230w deletion strain expression profile in mid-log growth

source_name: yor230w deletion mid-log growth

source_name: WT mid-log growth


title: ydr043c deletion

description: ydr043c deletion strain expression profile in mid-log growth

source_name: ydr043c deletion mid-log growth


title: ycl055w deletion

description: ycl055w deletion strain expression profile in mid-log growth

source_name: ycl055w deletion mid-log growth


title: ydr448w deletion

description: ydr448w deletion strain expression profile in mid-log growth

source_name: ydr448w deletion mid-log growth


title: ydr259c deletion

description: ydr259c deletion strain expression profile in mid-log growth

source_name: ydr259c deletion mid-log growth


title: ymr016c deletion

description: ymr016c deletion strain expression profile in mid-log growth

source_name: ymr016c deletion mid-log growth


title: ygr044c deletion

description: ygr044c deletion strain expression profile in mid-log growth

source_name: ygr044c deletion mid-log growth


title: ygl131c deletion

description: ygl131c deletion strain expression profile in mid-log growth

source_name: ygl131c deletion mid-log growth


title: yhr154w deletion

description: yhr154w deletion strain expression profile in mid-log growth

source_name: yhr154w deletion mid-log growth


title: ylr418c deletion

description: ylr418c deletion strain expression profile in mid-log growth

source_name: ylr418c deletion mid-log growth


title: ypl133c deletion

description: ypl133c deletion strain expression profile in mid-log growth

source_name: ypl133c deletion mid-log growth


title: yml099c deletion

description: yml099c deletion strain expression profile in mid-log growth

source_name: yml099c deletion mid-log growth


title: ypr009w deletion

description: ypr009w deletion strain expression profile in mid-log growth

source_name: ypr009w deletion mid-log growth


title: yor025w deletion

description: yor025w deletion strain expression profile in mid-log growth

source_name: yor025w deletion mid-log growth


title: ynl199c deletion

description: ynl199c deletion strain expression profile in mid-log growth

source_name: ynl199c deletion mid-log growth


title: ylr113w deletion

description: ylr113w deletion strain expression profile in mid-log growth

source_name: ylr113w deletion mid-log growth


title: ykr064w deletion

description: ykr064w deletion strain expression profile in mid-log growth

source_name: ykr064w deletion mid-log growth


title: yer068w deletion

description: yer068w deletion strain expression profile in mid-log growth

source_name: yer068w deletion mid-log growth

source_name: WT mid-log growth


title: ygl237c deletion

description: ygl237c deletion strain expression profile in mid-log growth

source_name: ygl237c deletion mid-log growth


title: ydl170w deletion

description: ydl170w deletion strain expression profile in mid-log growth

source_name: ydl170w deletion mid-log growth


title: yfl021w deletion

description: yfl021w deletion strain expression profile in mid-log growth

source_name: yfl021w deletion mid-log growth


title: ymr021c deletion

description: ymr021c deletion strain expression profile in mid-log growth

source_name: ymr021c deletion mid-log growth


title: yel009c deletion

description: yel009c deletion strain expression profile in mid-log growth

source_name: yel009c deletion mid-log growth


title: yor298c-a deletion

description: yor298c-a deletion strain expression profile in mid-log growth

source_name: yor298c-a deletion mid-log growth


title: yil131c deletion

description: yil131c deletion strain expression profile in mid-log growth

source_name: yil131c deletion mid-log growth


title: ydr277c deletion

description: ydr277c deletion strain expression profile in mid-log growth

source_name: ydr277c deletion mid-log growth


title: ygl162w deletion

description: ygl162w deletion strain expression profile in mid-log growth

source_name: ygl162w deletion mid-log growth


title: ybr297w deletion

description: ybr297w deletion strain expression profile in mid-log growth

source_name: ybr297w deletion mid-log growth


title: ydl056w deletion

description: ydl056w deletion strain expression profile in mid-log growth

source_name: ydl056w deletion mid-log growth


title: ynl309w deletion

description: ynl309w deletion strain expression profile in mid-log growth

source_name: ynl309w deletion mid-log growth


title: ypr054w deletion

description: ypr054w deletion strain expression profile in mid-log growth

source_name: ypr054w deletion mid-log growth


title: ypr193c deletion

description: ypr193c deletion strain expression profile in mid-log growth

source_name: ypr193c deletion mid-log growth


title: yor380w deletion

description: yor380w deletion strain expression profile in mid-log growth

source_name: yor380w deletion mid-log growth


title: ylr039c deletion

description: ylr039c deletion strain expression profile in mid-log growth

source_name: ylr039c deletion mid-log growth


title: ydr216w deletion

description: ydr216w deletion strain expression profile in mid-log growth

source_name: ydr216w deletion mid-log growth

source_name: WT mid-log growth


title: ynl139c deletion

description: ynl139c deletion strain expression profile in mid-log growth

source_name: ynl139c deletion mid-log growth


title: yfl031w deletion

description: yfl031w deletion strain expression profile in mid-log growth

source_name: yfl031w deletion mid-log growth


title: ydr146c deletion

description: ydr146c deletion strain expression profile in mid-log growth

source_name: ydr146c deletion mid-log growth


title: ymr164c deletion

description: ymr164c deletion strain expression profile in mid-log growth

source_name: ymr164c deletion mid-log growth


title: ykl109w deletion

description: ykl109w deletion strain expression profile in mid-log growth

source_name: ykl109w deletion mid-log growth


title: ypl230w deletion

description: ypl230w deletion strain expression profile in mid-log growth

source_name: ypl230w deletion mid-log growth


title: ybl103c deletion

description: ybl103c deletion strain expression profile in mid-log growth

source_name: ybl103c deletion mid-log growth


title: ypr022c deletion

description: ypr022c deletion strain expression profile in mid-log growth

source_name: ypr022c deletion mid-log growth


title: ygl025c deletion

description: ygl025c deletion strain expression profile in mid-log growth

source_name: ygl025c deletion mid-log growth


title: ydr421w deletion

description: ydr421w deletion strain expression profile in mid-log growth

source_name: ydr421w deletion mid-log growth


title: yol068c deletion

description: yol068c deletion strain expression profile in mid-log growth

source_name: yol068c deletion mid-log growth


title: ymr053c deletion

description: ymr053c deletion strain expression profile in mid-log growth

source_name: ymr053c deletion mid-log growth


title: yfr034c deletion

description: yfr034c deletion strain expression profile in mid-log growth

source_name: yfr034c deletion mid-log growth


title: ylr442c deletion

description: ylr442c deletion strain expression profile in mid-log growth

source_name: ylr442c deletion mid-log growth


title: ydr181c deletion

description: ydr181c deletion strain expression profile in mid-log growth

source_name: ydr181c deletion mid-log growth


title: ygl244w deletion

description: ygl244w deletion strain expression profile in mid-log growth

source_name: ygl244w deletion mid-log growth


title: ydr049w deletion

description: ydr049w deletion strain expression profile in mid-log growth

source_name: ydr049w deletion mid-log growth

source_name: WT mid-log growth


title: yir023w deletion

description: yir023w deletion strain expression profile in mid-log growth

source_name: yir023w deletion mid-log growth


title: yer161c deletion

description: yer161c deletion strain expression profile in mid-log growth

source_name: yer161c deletion mid-log growth


title: yfl044c deletion

description: yfl044c deletion strain expression profile in mid-log growth

source_name: yfl044c deletion mid-log growth


title: yol108c deletion

description: yol108c deletion strain expression profile in mid-log growth

source_name: yol108c deletion mid-log growth


title: ygl096w deletion

description: ygl096w deletion strain expression profile in mid-log growth

source_name: ygl096w deletion mid-log growth


title: ydr191w deletion

description: ydr191w deletion strain expression profile in mid-log growth

source_name: ydr191w deletion mid-log growth


title: ygr249w deletion

description: ygr249w deletion strain expression profile in mid-log growth

source_name: ygr249w deletion mid-log growth


title: ykl005c deletion

description: ykl005c deletion strain expression profile in mid-log growth

source_name: ykl005c deletion mid-log growth


title: ydr253c deletion

description: ydr253c deletion strain expression profile in mid-log growth

source_name: ydr253c deletion mid-log growth


title: ykl015w deletion

description: ykl015w deletion strain expression profile in mid-log growth

source_name: ykl015w deletion mid-log growth


title: ymr019w deletion

description: ymr019w deletion strain expression profile in mid-log growth

source_name: ymr019w deletion mid-log growth


title: ybr245c deletion

description: ybr245c deletion strain expression profile in mid-log growth

source_name: ybr245c deletion mid-log growth


title: yol051w deletion

description: yol051w deletion strain expression profile in mid-log growth

source_name: yol051w deletion mid-log growth


title: yhl025w deletion

description: yhl025w deletion strain expression profile in mid-log growth

source_name: yhl025w deletion mid-log growth


title: ydr423c deletion

description: ydr423c deletion strain expression profile in mid-log growth

source_name: ydr423c deletion mid-log growth


title: ydr443c deletion

description: ydr443c deletion strain expression profile in mid-log growth

source_name: ydr443c deletion mid-log growth


title: yor290c deletion

description: yor290c deletion strain expression profile in mid-log growth

source_name: yor290c deletion mid-log growth

source_name: WT mid-log growth


title: yor363c deletion

description: yor363c deletion strain expression profile in mid-log growth

source_name: yor363c deletion mid-log growth


title: yer184c deletion

description: yer184c deletion strain expression profile in mid-log growth

source_name: yer184c deletion mid-log growth


title: ybr083w deletion

description: ybr083w deletion strain expression profile in mid-log growth

source_name: ybr083w deletion mid-log growth


title: ycr081w deletion

description: ycr081w deletion strain expression profile in mid-log growth

source_name: ycr081w deletion mid-log growth


title: ynl257c deletion

description: ynl257c deletion strain expression profile in mid-log growth

source_name: ynl257c deletion mid-log growth


title: yor229w deletion

description: yor229w deletion strain expression profile in mid-log growth

source_name: yor229w deletion mid-log growth


title: ybl066c deletion

description: ybl066c deletion strain expression profile in mid-log growth

source_name: ybl066c deletion mid-log growth


title: yjl168c deletion

description: yjl168c deletion strain expression profile in mid-log growth

source_name: yjl168c deletion mid-log growth


title: ygl035c deletion

description: ygl035c deletion strain expression profile in mid-log growth

source_name: ygl035c deletion mid-log growth


title: ylr182w deletion

description: ylr182w deletion strain expression profile in mid-log growth

source_name: ylr182w deletion mid-log growth


title: yor113w deletion

description: yor113w deletion strain expression profile in mid-log growth

source_name: yor113w deletion mid-log growth


title: ypr196w deletion

description: ypr196w deletion strain expression profile in mid-log growth

source_name: ypr196w deletion mid-log growth


title: ydr477w deletion

description: ydr477w deletion strain expression profile in mid-log growth

source_name: ydr477w deletion mid-log growth


title: ykr034w deletion

description: ykr034w deletion strain expression profile in mid-log growth

source_name: ykr034w deletion mid-log growth


title: yml081w deletion

description: yml081w deletion strain expression profile in mid-log growth

source_name: yml081w deletion mid-log growth


title: ybr289w deletion

description: ybr289w deletion strain expression profile in mid-log growth

source_name: ybr289w deletion mid-log growth


title: yhl020c deletion

description: yhl020c deletion strain expression profile in mid-log growth

source_name: yhl020c deletion mid-log growth

source_name: WT mid-log growth


title: ynr052c deletion

description: ynr052c deletion strain expression profile in mid-log growth

source_name: ynr052c deletion mid-log growth


title: ydr173c deletion

description: ydr173c deletion strain expression profile in mid-log growth

source_name: ydr173c deletion mid-log growth


title: ykr099w deletion

description: ykr099w deletion strain expression profile in mid-log growth

source_name: ykr099w deletion mid-log growth


title: yor038c deletion

description: yor038c deletion strain expression profile in mid-log growth

source_name: yor038c deletion mid-log growth


title: ygr097w deletion

description: ygr097w deletion strain expression profile in mid-log growth

source_name: ygr097w deletion mid-log growth


title: ylr357w deletion

description: ylr357w deletion strain expression profile in mid-log growth

source_name: ylr357w deletion mid-log growth


title: yir018w deletion

description: yir018w deletion strain expression profile in mid-log growth

source_name: yir018w deletion mid-log growth


title: yil119c deletion

description: yil119c deletion strain expression profile in mid-log growth

source_name: yil119c deletion mid-log growth


title: ygl023c deletion

description: ygl023c deletion strain expression profile in mid-log growth

source_name: ygl023c deletion mid-log growth


title: ygr056w deletion

description: ygr056w deletion strain expression profile in mid-log growth

source_name: ygr056w deletion mid-log growth


title: ymr182c deletion

description: ymr182c deletion strain expression profile in mid-log growth

source_name: ymr182c deletion mid-log growth


title: ynl330c deletion

description: ynl330c deletion strain expression profile in mid-log growth

source_name: ynl330c deletion mid-log growth


title: yol116w deletion

description: yol116w deletion strain expression profile in mid-log growth

source_name: yol116w deletion mid-log growth


title: yhr206w deletion

description: yhr206w deletion strain expression profile in mid-log growth

source_name: yhr206w deletion mid-log growth


title: ykl185w deletion

description: ykl185w deletion strain expression profile in mid-log growth

source_name: ykl185w deletion mid-log growth


title: ybr182c deletion

description: ybr182c deletion strain expression profile in mid-log growth

source_name: ybr182c deletion mid-log growth


title: ymr042w deletion

description: ymr042w deletion strain expression profile in mid-log growth

source_name: ymr042w deletion mid-log growth

source_name: WT mid-log growth


title: ypl248c deletion

description: ypl248c deletion strain expression profile in mid-log growth

source_name: ypl248c deletion mid-log growth


title: ydr169c deletion

description: ydr169c deletion strain expression profile in mid-log growth

source_name: ydr169c deletion mid-log growth


title: yml102w deletion

description: yml102w deletion strain expression profile in mid-log growth

source_name: yml102w deletion mid-log growth


title: ypl042c deletion

description: ypl042c deletion strain expression profile in mid-log growth

source_name: ypl042c deletion mid-log growth


title: yor140w deletion

description: yor140w deletion strain expression profile in mid-log growth

source_name: yor140w deletion mid-log growth


title: yml051w deletion

description: yml051w deletion strain expression profile in mid-log growth

source_name: yml051w deletion mid-log growth


title: yel056w deletion

description: yel056w deletion strain expression profile in mid-log growth

source_name: yel056w deletion mid-log growth


title: ypl177c deletion

description: ypl177c deletion strain expression profile in mid-log growth

source_name: ypl177c deletion mid-log growth


title: yir033w deletion

description: yir033w deletion strain expression profile in mid-log growth

source_name: yir033w deletion mid-log growth


title: ypl129w deletion

description: ypl129w deletion strain expression profile in mid-log growth

source_name: ypl129w deletion mid-log growth


title: ynl236w deletion

description: ynl236w deletion strain expression profile in mid-log growth

source_name: ynl236w deletion mid-log growth


title: ybl021c deletion

description: ybl021c deletion strain expression profile in mid-log growth

source_name: ybl021c deletion mid-log growth


title: ypl049c deletion

description: ypl049c deletion strain expression profile in mid-log growth

source_name: ypl049c deletion mid-log growth


title: yer109c deletion

description: yer109c deletion strain expression profile in mid-log growth

source_name: yer109c deletion mid-log growth


title: yol028c deletion

description: yol028c deletion strain expression profile in mid-log growth

source_name: yol028c deletion mid-log growth


title: ypr199c deletion

description: ypr199c deletion strain expression profile in mid-log growth

source_name: ypr199c deletion mid-log growth


title: ykl020c deletion

description: ykl020c deletion strain expression profile in mid-log growth

source_name: ykl020c deletion mid-log growth

source_name: WT mid-log growth


title: ypl001w deletion

description: ypl001w deletion strain expression profile in mid-log growth

source_name: ypl001w deletion mid-log growth


title: yjl176c deletion

description: yjl176c deletion strain expression profile in mid-log growth

source_name: yjl176c deletion mid-log growth


title: yor344c deletion

description: yor344c deletion strain expression profile in mid-log growth

source_name: yor344c deletion mid-log growth


title: yhl009c deletion

description: yhl009c deletion strain expression profile in mid-log growth

source_name: yhl009c deletion mid-log growth


title: yor028c deletion

description: yor028c deletion strain expression profile in mid-log growth

source_name: yor028c deletion mid-log growth


title: yjr060w deletion

description: yjr060w deletion strain expression profile in mid-log growth

source_name: yjr060w deletion mid-log growth


title: ymr273c deletion

description: ymr273c deletion strain expression profile in mid-log growth

source_name: ymr273c deletion mid-log growth


title: ykl032c deletion

description: ykl032c deletion strain expression profile in mid-log growth

source_name: ykl032c deletion mid-log growth


title: ymr070w deletion

description: ymr070w deletion strain expression profile in mid-log growth

source_name: ymr070w deletion mid-log growth


title: ylr176c deletion

description: ylr176c deletion strain expression profile in mid-log growth

source_name: ylr176c deletion mid-log growth


title: yer051w deletion

description: yer051w deletion strain expression profile in mid-log growth

source_name: yer051w deletion mid-log growth


title: ylr098c deletion

description: ylr098c deletion strain expression profile in mid-log growth

source_name: ylr098c deletion mid-log growth


title: ypr008w deletion

description: ypr008w deletion strain expression profile in mid-log growth

source_name: ypr008w deletion mid-log growth


title: ykl062w deletion

description: ykl062w deletion strain expression profile in mid-log growth

source_name: ykl062w deletion mid-log growth


title: ybl054w deletion

description: ybl054w deletion strain expression profile in mid-log growth

source_name: ybl054w deletion mid-log growth


title: yjr122w deletion

description: yjr122w deletion strain expression profile in mid-log growth

source_name: yjr122w deletion mid-log growth


title: 10 day mating sample

status: Public on Mar 30 2007

city: Riverside

first: Howard

middle: S

last: Judelson

state: CA

address: Boyce Hall

department: Plant Pathology

institute: University of California

description: 10 day mating

data_processing: MAS5.0, per chip normalization

organism: Phytophthora infestans

source_name: Isolates 88069 and 618, mixed

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets using a standard Affymetrix protocol.

growth_protocol: Grown at 18C in the dark.

extract_protocol: Hyphae and oospores were grown to a powder in liquid nitrogen and then total RNA was extracted using the Qiagen Plant Mini RNA kit, using an on-column DNAse treatment protocol.

tag: Isolates 88069 (A1) and 618 (A2) were grown on polycarbonate membranes laid upon rye sucrose agar for 10 days.  By this time, oospores are present at a variety of stages including mature oospores and immature, developing oospores.


title: 3 day mating sample

description: 3 day mating

source_name: Isolates 88069 and 618, mated 3 days

extract_protocol: Hyphae were grown to a powder in liquid nitrogen and then total RNA was extracted using the Qiagen Plant Mini RNA kit, using an on-column DNAse treatment protocol.

tag: Mixture of A1 and A2 mating type strains 88069 and 618, mated for 3 days, hyphae just starting to interact.