title: HCC827CR1

first: Pasi

middle: Antero

last: Jänne

address: 450 Brookline Ave.; M422A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nucleoside triphosphate. The biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucletide (for quality control), and hybridized to a microarray chip overnight at 49 C. The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) followed by biotinylated anti-streptavidin, followed by SAPE.

scan_protocol: Briefly, each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Normalized scan data using D-Chip. CHP files are original from DFCI core.

source_name: HCC827 NSCLC Cell

label_protocol: Labeling was done at Dana-Farber Cancer Institute (DFCI) microarray core. Briefly, the Mapping 250K analysis begins with one aliquot of 250 ng of DNA and is cleaved with StyI. Linkers are ligated to the restriction fragments using T4 DNA ligase. The linkers provide a primer site for the subsequent PCR reaction. The fragments are amplified using Taq polymerase. The PCR products are purified from the primers and free nucleotides by ultrafiltration. They are then quantified spectrophotometrically, and are also assayed using size fractionation on a microfluidics device to determine whether the size distribution of products is as expected. The purified PCR products are fragmented by DNAse I in order to provide 3' hydroxyl groups for subsequent labeling, and to facilitate the subsequent hybridization step.

growth_protocol: Cells were grown in RPMI supplemented with 5% FBS. Cells were growing exponentially before the harvest

extract_protocol: DNA was isolated using DNAeasy Blood-Tissue kit (Qiagen)

tag: cell line

tag: cetuximab resistant clone


title: 57T

status: Public on Nov 23 2011

type: genomic

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: as described for Illumina GoldenGate assay

scan_protocol: Illumina BeadXpress scanner

data_processing: Data was processed with BeadStudio version 3.2 (Illumina).

molecule: genomic DNA

organism: Homo sapiens

source_name: Esophagus

extract_protocol: Genomic DNA was extracted by proteinase-K/SDS digestion. A total of 500 ng of genomic DNA were treated with sodium bisulfite using the EZ DNA Methylation-Gold Kit (Zymo Research). Before bead array analysis, the quality of DNA modification was verified by pyrosequencing.

tag: tissue

value: ESCC tissue


title: HCC827

city: Boston

state: MA

country: USA

label: biotin


title: 70T

label_protocol: as described for Illumina GoldenGate assay


title: HCC827CR3


title: HCC827CR4


title: protoplasted roots_pH 4.6_replicate 3

type: RNA

city: Durham

first: Anjali

middle: S

last: Iyer-Pascuzzi

state: NC

department: Biology

institute: Duke University

hyb_protocol: hybs with fragmented cRNA were preformed by Expression Analysis in Durham, NC

scan_protocol: scans were preformed by Expression Analysis in Durham, NC

data_processing: CHP files contain MAS 5.0 probe set summarizations using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 250.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: protoplasted and sorted whole roots 24 hours after transfer to low pH, rep 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA for whole roots and RNA from approximately 50,000 cells for sorted roots

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media fo the indicated time

extract_protocol: Total RNA was extracted with Qiagen Rneasy Plant mini and micro kits according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to low pH (pH 4.6) media for 24 hours. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH.

tag: ecotype

value: Columbia

tag: developmental stage

value: root cells from whole roots

tag: treatment

value: pH 4.6 for 24H


title: HCC827CR2


title: TAX577747

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) Signal to noise ratio <5 in either Int1 or Int2 channel. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.

value: breast tumor

tag: molecular subtype

tag: genomic subtype

tag: family status

tag: er

value: er neg

tag: pr

value: pr neg

tag: age

tag: size (mm)

tag: lymph node status

tag: histologic grade

tag: s-phase fraction

source_name: promega male reference

tag: sample type

value: promega male reference


title: Hoechst33342 dye sorted side population-10

first: Michael

last: Birrer

address: 70 Blossom Street

department: Medicine

institute: MGH

description: Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.

label: Biotin

source_name: Ovarian Cancer

label_protocol: Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP total RNA using a two-cycle amplification protocol (Affymetrix)

extract_protocol: The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).

treatment_protocol: Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients

tag: cell type

tag: sample

tag: cell population

value: SP


title: 57S

tag: tissue

value: surrounding tissue


title: Hoechst33342 dye sorted main population-10

description: Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells

value: MP


title: Pediatric malignant glioma 08_0188

city: Pittsburgh

first: Aleksandr

last: Lisovich

state: PA

address: 5150 Centre Ave.

department: DBMI

institute: University of Pittsburgh

hyb_protocol: As per manufacturer (Affymetrix)-Gene Chip Human mapping 250K Sty assay

scan_protocol: As per manufacturer (Affymetrix)-Gene Chip Human mapping 250K Sty array

data_processing: CEL files (generated by Affymetrix GTYPE using the DM algorithm) were preprocessed by aroma.affymetrix R package. The preprocessing included: 1) Calibration for crosstalk between allele probe pairs (PMA, PMB). 2)Normalization for 25-mer nucleotide-position probe sequence effects.  3) Robust probe-summarization on replicated PMs with PM=PMA+PMB for SNPs.  4) Normalization for PCR fragment-length effects on summary signals. The VN algorithm was used to generate the reference signal based on 48  Mapping 500k HapMap Trio Dataset template.

source_name: Formalin-fixed Paraffin embedded brain tissue

extract_protocol: Qiagen DNeasy

tag: ID

value: malignant glioma

tag: developmental stage

value: pediatric


title: protoplasted roots_pH 4.6_replicate 2

source_name: protoplasted and sorted whole roots 24 hours after transfer to low pH, rep 2

tag: ecotype

tag: treatment


title: Hoechst33342 dye sorted side population-9

value: high-grade advanced stage ovarian adenocarcinoma


title: Pediatric malignant glioma 08_0191

label_protocol: As per manufacturer (Affymetrix)-Gene Chip Human mapping 250K Sty assay


title: Pediatric malignant glioma 08_0189


title: 4N

value: healthy esophagus


title: 70S


title: protoplasted roots_pH 4.6_replicate 1

source_name: protoplasted and sorted whole roots 24 hours after transfer to low pH, rep 1


title: 1N


title: 3N


title: Hoechst33342 dye sorted side population-8


title: Hoechst33342 dye sorted main population-8


title: Pediatric malignant glioma 08_0185


title: Pediatric malignant glioma 08_0184


title: 2N


title: Hoechst33342 dye sorted side population-6


title: Pediatric malignant glioma 08_0178


title: 105T


title: Leaves-des1.1-REP1

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from leaves (des1-1)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Leaves des1-1 mutant

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the des1-1 mutant (SALK_03855) were grown in soil supplemented with Hoagland media. Plants were grown under a photoperiod of 16 h of white light (120 μE m-2 s-1) at 20ºC and 8 h dark at 18ºC.

extract_protocol: The leaves of 3-week-old plants were collected and RNA extracted from each sample. Total RNA was isolated with Trizol reagent (Invitrogen) followed by cleaning with the RNeasy Plant Mini Kit (Qiagen).

tag: genotype

value: des1-1 mutant


title: Pediatric malignant glioma 08_0181


title: Hoechst33342 dye sorted main population-7


title: Leaves-des1.1-REP2


title: Leaves-des1.1-REP3


title: Leaves-WildType-REP3

description: Gene expression data from leaves (wild type)

source_name: Leaves, Wild Type

value: Wild Type


title: Hoechst33342 dye sorted main population-6


title: Hoechst33342 dye sorted side population-7


title: Pediatric malignant glioma 08_0183


title: Hoechst33342 dye sorted main population-9


title: Pediatric malignant glioma 08_0182


title: Hoechst33342 dye sorted side population-5


title: Pediatric malignant glioma 08_0179


title: Pediatric malignant glioma 08_0175


title: Pediatric malignant glioma 08_0177


title: T84 18 hr IFN-gamma treatment, biological replicate 1

city: Aurora

first: Douglas

last: Kominsky

state: CO

institute: University of Colorado Denver

description:
18.1
Gene expression data following IFN-gamma treatment for 18 hrs.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes, then centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were processed with GeneSpring using the default global scaling normalization method.

source_name: T84, IFN-gamma, 18hr

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: T84 cells were grown in standard conditions with or without IFN-gamma (1000U/ml) for 6 or 18 hours.

extract_protocol: RNA was harvested using Trizol.

treatment_protocol: IFN-gamma (1000U/ml) for 6 or 18 hrs.

tag: cell line

value: intestinal epithelial cells

value: IFN-gamma

tag: treatment duration

value: 18 hr


title: Hoechst33342 dye sorted main population-5


title: Hoechst33342 dye sorted main population-4


title: Pediatric malignant glioma 08_0174


title: Leaves-WildType-REP1


title: Leaves-WildType-REP2


title: Pediatric malignant glioma 08_0173


title: Pediatric malignant glioma 08_0172


title: T84 6 hr IFN-gamma treatment, biological replicate 1

description:
6.1
Gene expression data following IFN-gamma treatment for 6 hrs.

source_name: T84, IFN-gamma, 6hr

value: 6 hr


title: T84 6 hr IFN-gamma treatment, biological replicate 2

description:
6.2
Gene expression data following IFN-gamma treatment for 6 hrs.


title: T84 untreated, biological replicate 1

description:
CTL. Pooled untreated control.
Gene expression data from untreated cells.

source_name: T84, untreated


title: Hoechst33342 dye sorted main population-3


title: Hoechst33342 dye sorted side population-3


title: Hoechst33342 dye sorted side population-4


title: Hoechst33342 dye sorted main population-2


title: Pediatric malignant glioma 08_0015


title: Pediatric malignant glioma 08_0014


title: T84 18 hr IFN-gamma treatment, biological replicate 2

description:
18.2
Gene expression data following IFN-gamma treatment for 18 hrs.


title: Hoechst33342 dye sorted side population-1


title: Hoechst33342 dye sorted main population-1


title: Pediatric malignant glioma 08_0013


title: Sstipitis_RA3

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

description: Scheffersomyces stipitis CBS 6054 on rhamnose. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Scheffersomyces stipitis CBS 6054

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Bioreactor Cultivations: All cultivations for expression arrays were performed in New Brunswick Scientific Bioflo 110 3-L bioreactors with working volumes of 2 l each. The bioreactors were equipped with two impellers rotating at 750 rpm. Bioreactor temperature was controlled at 30 °C and the pH was kept constant at 5.0 by automatic addition of 5 N KOH. A defined minimal medium containing trace metal elements and vitamins in the following was used in all bioreactor cultivations: 2.4 g urea l-1; 3 g KH2 PO4 l-1, 0.5 g MgSO4 7H2O l-1; 1 ml trace element solution l-1; 1 ml vitamin solution l-1; and 0.05 ml antifoam 289 (Sigma A-8436) l-1 (Modified from Verduyn et al. (44)). For L-rhamnose cultivations, a starting concentration of 20 g l-1 sugar was used.  Airflow into the bioreactors for aerobic cultivations was 1 vvm. An aerobic transcriptomics sample taken during the exponential growth phase.  Cultivations and sample collections for each carbon source were performed in triplicate.

extract_protocol: RNA was extracted using the Qiagen RNEasy Maxi kit (Qiagen). Cell breakage was accomplished using glass beads in a BeadBeater (Biospec Products) equipped with a 15 ml chamber. RNA was later further purified and concentrated using the Qiagen RNEasy Mini kit (Qiagen).

tag: strain

tag: carbon source

value: Rhamnose


title: Pediatric malignant glioma 08_0012


title: Sstipitis_RA1

description: Scheffersomyces stipitis CBS 6054 on rhamnose. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Sstipitis_RA2

description: Scheffersomyces stipitis CBS 6054 on rhamnose. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Serum samples of internistic controls (INC) 2

type: protein

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: pool C of 10 serum samples

hyb_protocol: The array consisted of three glass slides (array 6, 7, and 8) that were pretreated according to the manufacturer's instructions and incubated with 2-fold diluted serum pools for 2 hours. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with Cy3-conjugated streptavidin.

scan_protocol: Fluorescence intensities (Cy3) were recorded with an Axon GenePix 4000B scanner.

data_processing: Raw data was analyzed with the Raybiotech analysis tool, a data analysis program based on Microsoft Excel technology specifically designed for the analysis of these microarrays. Signals were normalized using internal, positive and negative controls included on the array. Signals were normalized using positive and negative control features on the microarray, the fold changes are relative expression to positive control features, i.e. a value of 1 is same expression than positive control, 2 a 2 fold higher, 0.5 a 2-fold lower expression.

molecule: protein

source_name: serum

label_protocol: According to manufacturer's protocols. In brief, 70ul of 1,500 fold diluted Fluorescent dye-conjugated streptavidin ws added to each subarray and incubated in a dark room at room temperature for 1-2 hours.

extract_protocol: serum samples

tag: disease state

value: internistic INC

tag: block in gpr file

value: serum


title: RNA control rep5

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

hyb_protocol: Chips hybridized according to Manufacturer's protocol

scan_protocol: standard Affymetrix protocol using GS3000

data_processing: Data corrected to 1500 Baseline

source_name: CD34+ purified control bone marrow

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: CD34+ cells were purified using the autoMACS system (Miltenyi)

extract_protocol: Total RNA isolated using TRI Reagent (Sigma, St. Louis, MO) was purified with an RNeasy mini kit (Qiagen, Valencia, CA).

value: control

value: CD34+ purified control bone marrow

tag: age on study

value: unknown

tag: race

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: Sex

tag: fab

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

tag: cytogenetic risk group

tag: cytogenetics


title: Pediatric malignant glioma 08_0010

tag: ID

tag: tissue

tag: developmental stage


title: Root_SCR-GFP_replicate1_dye-swap

description: SCR:GFP transcription factor ChIP sample v wildtype control (no GFP) ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis

hyb_protocol: Hybridization was performed according to the Agilent ChIP-on-chip protocol with 5µg of each labeled sample.

scan_protocol: Images were obtained with scanner G2565BA with protocol CGH-v4_95_Feb07at a resolution of 5 mm.

data_processing: Signal extraction and initial data processing were done using the Agilent feature extraction software. Additional data processing as described in Tsukagoshi et al. 2010 and Iyer-Pascuzzi et al. 2011

source_name: wild type

label_protocol: Chromatin samples were cleaned using a MinElute kit (Qiagen Sciences, Germantown, MD, USA), amplified, and labeled with either Cy3 or Cy5 dye as in Tsukagoshi et al., 2010.  2µg of linearly amplified DNA was used for labeling.

growth_protocol: scr4/pSCR:SCR:GFP and wild type lines were germinated and grown on 1X MS media for 7 days as described in Iyer-Pascuzzi et al. 2011

extract_protocol: Chromatin Immunoprecipitation as described in Iyer-Pascuzzi et al. 2011

treatment_protocol: Whole root tissue was fixed as described in Iyer-Pascuzzi et al. 2011

tag: genotype

value: wild type

tag: ecotype

value: Columbia

tag: age

value: 7 day old roots

tag: antibody

value: anti-GFP

tag: antibody manufacturer

value: ABCAM

tag: antibody cat#


title: Serum samples of internistic controls (INC) 1

description: pool C of 10 serum samples

tag: disease state

tag: block in gpr file

tag: sample type


title: Hoechst33342 dye sorted side population-2

tag: cell type

value: high-grade advanced stage ovarian adenocarcinoma

tag: sample

tag: cell population

value: SP


title: Serum samples of healthy controls (HC) 4

description: pool B of 10 serum samples

value: healthy HC


title: Pediatric malignant glioma 08_0008

value: malignant glioma

value: pediatric


title: Root_SCR-GFP_replicate2_dye-swap


title: Pediatric malignant glioma 08_0005


title: RNA control rep4

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: Sex

tag: fab

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

tag: cytogenetic risk group


title: RNA control rep6

tag: genotype

tag: disease state

tag: cell type

tag: cytogenetics


title: Pediatric malignant glioma 08_0007

tag: ID

tag: tissue

tag: developmental stage


title: Pediatric malignant glioma 08_0006


title: Serum samples of healthy controls (HC) 3

description: pool B of 10 serum samples

tag: block in gpr file

tag: sample type


title: Pediatric malignant glioma 08_0011


title: RNA control rep3

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: Sex

tag: fab


title: U2AF1 mutation 18 rep

source_name: CD34+ purified MDS bone marrow

tag: upn

value: U2AF1 mutation

value: Myelodysplastic syndrome

value: CD34+ purified MDS bone marrow

value: White

value: male

value: RA

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

tag: cytogenetic risk group

value: Good


title: Pediatric malignant glioma 08_0004

tag: ID

tag: tissue

tag: developmental stage


title: Serum samples of healthy controls (HC) 2

description: pool A of 10 serum samples

tag: disease state

tag: block in gpr file

tag: sample type

value: serum


title: Sstipitis_GA3

description: Scheffersomyces stipitis CBS 6054 on glucose. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

tag: strain

tag: carbon source

value: Glucose


title: U2AF1 mutation 16 rep

tag: genotype

tag: cell type

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: Sex

tag: fab

value: RAEB

value: Poor

tag: cytogenetics


title: Sstipitis_GA2

description: Scheffersomyces stipitis CBS 6054 on glucose. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Sstipitis_GA1

description: Scheffersomyces stipitis CBS 6054 on glucose. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Pediatric malignant glioma 08_0003

tag: ID

tag: tissue


title: Serum samples of patients with Parkinson’s disease (PD) 4

description: pool B of 10 serum samples

tag: disease state

value: Parkinson's disease PD


title: Serum samples of patients with Parkinson’s disease (PD) 3

description: pool B of 10 serum samples

tag: block in gpr file


title: Serum samples of healthy controls (HC) 1

description: pool A of 10 serum samples

tag: sample type


title: Serum samples of patients with Parkinson’s disease (PD) 2

description: pool A of 10 serum samples


title: Serum samples of patients with Parkinson’s disease (PD) 1

description: pool A of 10 serum samples


title: U2AF1 mutation 15 rep

tag: upn

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

tag: cytogenetic risk group


title: Root_SCR-GFP_replicate2

description: Wildtype control (no GFP) ChIP sample v SCR:GFP transcription factor ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis

source_name: pSCR:SCR::GFP 7 day old roots

tag: ecotype

value: Columbia

tag: genotype

value: scr-4 / pSCR:SCR:GFP

tag: age

value: 7 day old roots

tag: antibody

value: anti-GFP

tag: antibody manufacturer

value: ABCAM

tag: antibody cat#

value: wild type


title: DMH-Rep2

city: Shanghai

first: Jing-Yuan

last: Fang

state: Shanghai

address: 145 Middle Shandong Rd

department: Division of Gastroenterology

country: China

institute: Shanghai Jiao-Tong University School of Medicine Ren-Ji Hospital

description:
Gene expression in mice of DMH group
DMH-2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole  Genome Oligo Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization). The positive effect of this median normalization is illustrated in Box-plot, and genes marked present in all samples were chosen for data analysis. Differentially expressed genes were identified through Fold-change and T-test p-value screening.

organism: Mus musculus

source_name: Normal colonic mucosa,DMH group ,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNAs of the normal colonic mucosa are harvested using TRIzol(Invitrogen) and the Rneasy kit(Qiagen) according to manufacturer's instructions.

treatment_protocol: The mice of DMH group were received normal diet(calcium concentration,1.24%) and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks,the mice of high calcium group were received high calcium diet(calcium concentration,3%) and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks.

tag: strain

value: ICR

tag: tissue

value: colonic mucosa

tag: tumor status

value: control

tag: agent

value: DMH


title: Pediatric malignant glioma 08_0001

tag: ID

value: malignant glioma

tag: developmental stage

value: pediatric


title: Serum samples of patients with multisystem atrophy (MSA) 3

description: pool A of 10 serum samples

tag: disease state

value: multisystem atrophy MSA

tag: block in gpr file

tag: sample type

value: serum


title: U2AF1 mutation 3 rep

tag: upn

value: U2AF1 mutation

value: Myelodysplastic syndrome

tag: cell type

value: CD34+ purified MDS bone marrow

tag: age on study

tag: race

value: White

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: Sex

value: male

tag: fab

value: RAEB

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

value: Good

tag: cytogenetics


title: Serum samples of patients with multisystem atrophy (MSA) 2

description: pool A of 10 serum samples

tag: disease state

tag: block in gpr file

tag: sample type


title: DMH-Rep1

description:
Gene expression in mice of DMH group
DMH-1

source_name: Normal colonic mucosa,DMH group ,replicate 1

tag: strain

tag: tissue

tag: tumor status

tag: agent


title: no U2AF1 mutation 20 rep

tag: upn

tag: genotype

value: no U2AF1 mutation

tag: cell type

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

tag: cytogenetic risk group


title: DMH-Rep3

description:
Gene expression in mice of DMH group
DMH-3

source_name: Normal colonic mucosa,DMH group ,replicate 3


title: Root_SCR-GFP_replicate1

tag: ecotype

value: Columbia

value: scr-4 / pSCR:SCR:GFP

tag: age

value: 7 day old roots

tag: antibody

value: anti-GFP

tag: antibody manufacturer

value: ABCAM

tag: antibody cat#

value: wild type


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 2

description: pool A of 10 serum samples

tag: disease state

value: Parkinson's disease, progressive supranuclear palsy PSP/CBS

tag: block in gpr file

tag: sample type


title: no U2AF1 mutation 11 rep

tag: upn

tag: Sex

value: female

tag: fab

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)

tag: iPSs

tag: cytogenetics


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 3

description: pool A of 10 serum samples

value: serum


title: hCA-Tumor-Rep2

description:
Gene expression in mice of high calcium group with tumors
CA2-2

source_name: Normal colonic mucosa,high calcium diet group with tumors,replicate 2

tag: strain

value: ICR

tag: tissue

value: colonic mucosa

tag: tumor status

value: with tumors

tag: agent

value: high calcium


title: Serum samples of patients with progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) 1

description: pool A of 10 serum samples

tag: disease state


title: no U2AF1 mutation 8 rep

tag: genotype

value: Myelodysplastic syndrome

tag: cell type

value: CD34+ purified MDS bone marrow

tag: age on study

tag: race

value: White

tag: banking date

tag: diagnosis date

tag: duration of disease (month)

value: RA

tag: cytogenetic risk group


title: hCA-Tumor-Rep3

description:
Gene expression in mice of high calcium group with tumors
CA2-3

source_name: Normal colonic mucosa,high calcium diet group with tumors,replicate 3


title: no U2AF1 mutation 14 rep

tag: upn

value: no U2AF1 mutation

tag: Sex

value: male

tag: fab

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

value: Intermediate


title: Serum samples of patients with multisystem atrophy (MSA) 1

description: pool A of 10 serum samples

value: multisystem atrophy MSA

tag: block in gpr file

tag: sample type


title: no U2AF1 mutation 5 rep

tag: genotype

tag: disease state

value: RAEB

tag: anc (x10^3/mcl)

tag: iPSs

value: Poor

tag: cytogenetics


title: no U2AF1 mutation 9 rep

tag: cell type

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

value: Good


title: no U2AF1 mutation 10 rep

tag: upn

tag: duration of disease (month)

tag: Sex

tag: fab

tag: cytogenetic risk group


title: hCA-Tumor-Rep1

description:
Gene expression in mice of high calcium group with tumors
CA2-1

source_name: Normal colonic mucosa,high calcium diet group with tumors,replicate 1

tag: strain

tag: tissue

tag: tumor status

tag: agent


title: hCA-Notumor-Rep3

description:
Gene expression in mice of high calcium group without tumors
CA-3

source_name: Normal colonic mucosa,high calcium diet group without tumors,replicate 3

value: without tumors


title: U2AF1 mutation 17 rep

tag: genotype

value: U2AF1 mutation

tag: disease state

value: female

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)


title: no U2AF1 mutation 3 rep

tag: cell type

tag: age on study

tag: race

tag: banking date

tag: diagnosis date

tag: iPSs

tag: cytogenetics


title: hCA-Notumor-Rep2

description:
Gene expression in mice of high calcium group without tumors
CA-2

source_name: Normal colonic mucosa,high calcium diet group without tumors,replicate 2

tag: strain

value: ICR

tag: tissue

value: colonic mucosa


title: U2AF1 mutation 1 rep

tag: upn

tag: duration of disease (month)

tag: Sex

tag: fab

tag: cytogenetic risk group


title: hCA-Notumor-Rep1

description:
Gene expression in mice of high calcium group without tumors
CA-1

source_name: Normal colonic mucosa,high calcium diet group without tumors,replicate 1

tag: tumor status

tag: agent

value: high calcium


title: BMMC-pAPM-miR-221 vs BMMC-pAPM-miR-221m replicate 2

city: Bellinzona

first: Silvia

last: Monticelli

address: Via Vincenzo Vela, 6

country: Switzerland

institute: Institute for Research in Biomedicine

description: Biological replicate 2 of 3. Cells overexpressing miR-221 versus control cells overexpressing miR-221m.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: BMMC transduced with pAPM-miR-221

label_protocol: For the linear T7-based amplification step, 1 μg of each total RNA sample was used as starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies). Control samples miR-221m were labeled with Cy3 and experimental samples miR-221 were labeled with Cy5.

growth_protocol: Bone marrow cells from C57Bl/6 female mice were differentiated and maintained in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-glutamine, 100U/mL penicillin, 100μg/mL streptomycin, 0.1mM non essential amino acids, 50μM β-mercaptoethanol and 50% WEHI-3 conditioned supernatant as a source of IL-3. Three weeks after differentiation the population was homogeneous, with ~95% of the cells in culture being c-Kit+ and FceRI+ at surface staining and testing positive for toluidine blue staining.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. The quality of extracted RNA was analyzed using the Agilent 2100 Bioanalyzer. Samples used for the experiment had RNA integrity numbers (RIN) between 8.5 and 9.3.

treatment_protocol: BMMCs were transduced with pAPM-miR-221 or pAPM-miR-221m lentiviruses, selected with 2mg/mL of puromycin for 48 hours and expanded previous to RNA isolation.

value: Bone marrow-derived mast cells

value: Female

tag: expression

value: wild type miR-221

source_name: BMMC transduced with pAPM-miR-221m

value: mutant miR-221


title: BMMC-pAPM-miR-221 vs BMMC-pAPM-miR-221m replicate 3

description: Biological replicate 3 of 3. Cells overexpressing miR-221 versus control cells overexpressing miR-221m.

tag: cell type


title: HSF-6 (S9)  B+DZNep 3

status: Public on Nov 22 2011

city: Los Angeles

middle: Veronica

last: Diaz-Perez

state: CA

address: 621 Charles Young DR

department: MCDB

institute: UCLA

description: Gene expression of HSF-6 (S9) B+DZNep

hyb_protocol: Hybridization to  Afftmetrix human array U113plus 2.0 chips and was performed as recommended by manufacture, in Affymetrix GeneChip Hybridization Oven 640 for 16 hours

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 30007G using manufacturer's recommended protocol.

data_processing: The data were analyzed with GeneChip Command Console Expression Console with MAS 5 algorithm and TGT setting is 500.

source_name: hESC HSF-6 (S9)

label_protocol: RNA was prepared usng MessageAmp™ Premier RNA Amplification Kit (cat#: 4383452)

growth_protocol: Cells were grown for six days under 37C, 5% CO2  in absent and presence of butyrate and DZNep during 11 passages.

extract_protocol: Cells were collected in RLT Buffer and RNA isolated with the Qiagen Rneasy mini Kit.

treatment_protocol: Cells were dissociated using TrypLE Express.

tag: cell line

value: human embryonic stem cell line HSF6-S9

value: butyrate and DZNep


title: HSF-6 (S9)  B+DZNep 3'

description: Gene expression of HSF-6 (S9) B+DZNep


title: no U2AF1 mutation 12 rep

tag: genotype

value: no U2AF1 mutation

tag: disease state

value: Myelodysplastic syndrome

value: CD34+ purified MDS bone marrow

tag: age on study

tag: race

value: Black

value: male

value: RA

tag: bone marrow myeloblast(%)

tag: wbc (x10^3/mcl)

tag: platelet (x10^3/mcl)

tag: hemoglobin (g/dl)

tag: anc (x10^3/mcl)


title: HSF-6 (8) control 1''

description: Gene expression of HSF-6 (8) control

source_name: hESC HSF-6 (8)

value: human embryonic stem cell line HSF6-8

value: control


title: Mesenchymal stem cell at 24h, biological replicate 2

city: Seoul

first: mingoo

last: kim

address: Seoul

country: South Korea

institute: SNUBI

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip 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.

source_name: Mesenchymal stem cell

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

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

tag: tissue

value: Mesenchymal stem cell


title: HSF-6 (S9)  B+DZNep 3''

description: Gene expression of HSF-6 (S9) B+DZNep


title: Mesenchymal stem cell at 48h, biological replicate 2


title: HSF-6 (8) control 1'

description: Gene expression of HSF-6 (8) control


title: HSF-6 (8)  B+DZNep 2'

description: Gene expression of HSF-6 (8) B+DZNep


title: BMMC-pAPM-miR-221 vs BMMC-pAPM-miR-221m replicate 1

description: Biological replicate 1 of 3. Cells overexpressing miR-221 versus control cells overexpressing miR-221m.

tag: Sex

tag: strain


title: Mesenchymal stem cell at 24h, biological replicate 3


title: Mesenchymal stem cell at 12h, biological replicate 3


title: HSF-6 (8)  B+DZNep 2

description: Gene expression of HSF-6 (8) B+DZNep


title: HSF-6 (8)  B+DZNep 2''

description: Gene expression of HSF-6 (8) B+DZNep


title: Mesenchymal stem cell at 6h, biological replicate 3


title: Mesenchymal stem cell at 24h, biological replicate 1


title: HSF-6 (8) control 1

description: Gene expression of HSF-6 (8)  control


title: Mesenchymal stem cell at 6h, biological replicate 2


title: Mesenchymal stem cell at 48h, biological replicate 1


title: Mesenchymal stem cell at 48h, biological replicate 3


title: Mesenchymal stem cell at 0h, biological replicate 2


title: Mesenchymal stem cell at 12h, biological replicate 1


title: Mesenchymal stem cell at 0h, biological replicate 3


title: Mesenchymal stem cell at 12h, biological replicate 2


title: Mesenchymal stem cell at 0h, biological replicate 1

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


title: Mesenchymal stem cell at 6h, biological replicate 1


title: Human colonic mucosa-EPHB2 neg replicate 2

city: Barcelona

first: Eduard

last: Batlle

state: Barcelona

address: Baldiri i Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine Barcelona

description:
AMSep09--796-2009--96
Gene expression data from EPHB2-negative sorted human mucosa cells

hyb_protocol: 3.75 µg of cDNA was hybridized per Affymetrix GeneChip Human Genome U133 Plus 2.0 Array for 16 hours of hybridization at 45C, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions (http://www.affymetrix.com).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip@ Scanner 3000.

data_processing: RMA background correction, quantile normalization and RMA summarization.

source_name: EPHB2 neg

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: Intestinal epithelial single cell suspensions were obtained from human colonic mucosa after shaking in PBS containing 8mM EDTA followed by enzyme treatment with 0.2mg/mL Dispase, 0.8U/µL DNAse I.

extract_protocol: RNA from sorted cells was extracted using Trizol Reagent and purified using the Qiagen RNeasy MiniKit using the manufacturer's protocols

treatment_protocol: Intestinal single cell suspensions were sorted in a FACS Aria 2.0 (BD) according to high, medium, low, or negative EPHB2 levels (anti-EphB2 Mab 2H9 -Genentech, coupled to APC fluorophor, 2 ug/ml)

value: Normal human mucosa

tag: patient id

tag: ephb2 surface abundance

value: EPHB2 neg


title: Human colonic mucosa-EPHB2 medium replicate 2

description:
AMSep09--794-2009--94
Gene expression data from EPHB2-medium sorted human mucosa cells

source_name: EPHB2 medium

value: EPHB2 medium


title: Human colonic mucosa-EPHB2 high replicate 3

description:
AMSep09--801-2009--105
Gene expression data from EPHB2-high sorted human mucosa cells

source_name: EPHB2 high

value: EPHB2 high


title: Human colonic mucosa-EPHB2 low replicate 3

description:
AMSep09--803-2009--107
Gene expression data from EPHB2-low sorted human mucosa cells

source_name: EPHB2 low

value: EPHB2 low


title: Human colonic mucosa-EPHB2 medium replicate 1

description:
AMSep09--764-2009--90
Gene expression data from EPHB2-medium sorted human mucosa cells


title: Human colonic mucosa-EPHB2 high replicate 2

description:
AMSep09--793-2009--93
Gene expression data from EPHB2-high sorted human mucosa cells


title: Human colonic mucosa-EPHB2 low replicate 2

description:
AMSep09--795-2009--95
Gene expression data from EPHB2-low sorted human mucosa cells


title: Human colonic mucosa-EPHB2 medium replicate 3

description:
AMSep09--802-2009--106
Gene expression data from EPHB2-medium sorted human mucosa cells


title: Human colonic mucosa-EPHB2 neg replicate 1

description:
AMSep09--766-2009--92
Gene expression data from EPHB2-negative sorted human mucosa cells


title: genotype: 88Ab536 - time: 0 days - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: hv cv 88ab536 (germplasm name); po: 0009010 seed, (Organism Part); PO:0001170 seed development stages (Development Stage); not specified (Growth Media).

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: seed (genotype: 88Ab536 - time: 0 days)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

tag: developmental stage

value: out of steeping

value: seed

tag: cultivar


title: Human colonic mucosa-EPHB2 high replicate 1

description:
AMSep09--763-2009--89
Gene expression data from EPHB2-high sorted human mucosa cells


title: genotype: 88Ab536 - time: 3 days - rep1

source_name: seed (genotype: 88Ab536 - time: 3 days)

value: 3 d of germination


title: genotype: 88Ab536 - time: 0 days - rep3


title: genotype: 88Ab536 - time: 3 days - rep3


title: genotype: 88Ab536 - time: 3 days - rep2


title: genotype: 88Ab536 - time: 0 days - rep1


title: genotype: Betzes - rep3 B8

description: gro: 0005000## (Organism Part); mixed cells (Cell type); GRO:0007058 (Development Stage); 3 days after planting (Age); 3MM filter paper (Growth Media).

organism: Triticum aestivum

source_name: 0## (genotype: Betzes)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Seeds were placed in petridishes (100mm x 25mm) containing three layers of Whatman  1 filter paper wetted with 8ml of sterile water. The plates were kept in 4 oC for 96 hours. After cold treatment, the seeds were germinated at 22 oC with 16h/8h long day light (360ueinstein m-1 s-1). 1.5ml of sterile water was added to each plate.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

value: whole organism

value: Betzes


title: genotype: chr6HL - rep2

source_name: 0## (genotype: chr6HL)


title: genotype: chr6HL - rep1


title: genotype: chr7H - rep2

source_name: 0## (genotype: chr7H)


title: genotype: chr6HL - rep3


title: genotype: Chinese Spring - rep2

source_name: 0## (genotype: Chinese Spring)

value: Chinese Spring


title: genotype: Chinese Spring - rep1


title: genotype: chr7H - rep1


title: genotype: Chinese Spring - rep3


title: genotype: chr6H - rep1

source_name: 0## (genotype: chr6H)


title: genotype: Betzes - rep2 B8


title: Human colonic mucosa-EPHB2 low replicate 1

description:
AMSep09--765-2009--91
Gene expression data from EPHB2-low sorted human mucosa cells


title: genotype: chr6HS - rep3

source_name: 0## (genotype: chr6HS)


title: genotype: chr7H - rep3


title: genotype: chr6HS - rep1


title: genotype: chr6HS - rep2


title: genotype: chr6H - rep2


title: genotype: chr5H - rep3

source_name: 0## (genotype: chr5H)


title: genotype: Betzes - rep1 B8


title: genotype: chr6H - rep3


title: genotype: chr5H - rep1


title: genotype: chr5H - rep2


title: genotype: chr3H - rep2

source_name: 0## (genotype: chr3H)


title: genotype: chr4H - rep3

source_name: 0## (genotype: chr4H)


title: genotype: chr4H - rep1


title: genotype: chr2H - rep2

source_name: 0## (genotype: chr2H)


title: genotype: chr3H - rep1


title: genotype: chr2HL - rep2

source_name: 0## (genotype: chr2HL)


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves - rep2

description: ; (organism part); po: 0009012 : plant growth and development stages

source_name: (developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves)

tag: age

value: 21 days past anthesis

value: leaves

value: Karl


title: genotype: chr2H - rep3

tag: genotype


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep1

source_name: (developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels)


title: genotype: chr3H - rep3


title: genotype: chr2HL - rep1


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves - rep1


title: genotype: chr4H - rep2


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels - rep3

source_name: (developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels)


title: genotype: chr2HL - rep3


title: genotype: chr2H - rep1


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep3

source_name: (developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels)

value: 14 days past anthesis


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels - rep2


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels - rep1


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep3


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep2

source_name: (developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves)


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep3


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep3

source_name: (developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves)


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep2


title: dev. stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves - rep3


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep1


title: dev. stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep2


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels - rep1


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep2


title: dev. stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves - rep1


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves - rep1

source_name: (developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves)


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels - rep2

source_name: (developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels)


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels - rep3


title: time: 144 - Treated or untreated: WATER - rep5

description: (organism part); inoculated cells in inflorescence (cell type); 7.03-anthesis completed gro: 0007104 (Development Stage); 8 weeks after effector challenge (Age); Scotts MetroMix 200 (Growth Media).

source_name: (time: 144 - Treated or untreated: WATER)

growth_protocol: Growth Description:  Barley seeds were planted in Scotts MetroMix 200 in 6-inch pots (four seeds/pot) and plants were grown in a growth chamber with 16h day at 20oC, and 8h night at 18oC.  The light intensity at pot level ranged from 160 (edge) to 180 (middle) mmolm-2s-1.  After a week, 5ml Scotts Osmocote 14/14/14 with micronutrients was applied.  Plants were watered every two-three days until 14 days old and then every day until sampling.  After 14 days stakes were placed into the pots. Spikes were spray-inoculated two-three days after emerging from the boot (6.05 emergence of inflorescence completed GRO:0007104) with a freshly prepared spore suspension of 2 x 106 macroconidia per ml in 0.04% (vol/vol) Tween 20 in water or with water plus Tween 20 (mock).  Spray inoculations were performed with an airbrush (Model VL; Paasche Airbrush, Harwood Heights, IL, U.S.A.) adjusted to a pressureof 82.8 kPa.  All inoculations and samplings were carried out at 15:00 h.  After inoculation the spikes were bagged for no more than 72 hours.  Spikes were sampled at 24, 48, 72, 96, and 144 hours after inoculation (hai), flash frozen in liquid nitrogen and stored at 80C.  Spikes were sampled at 15:00 h on each of the sampling days.

value: inflorescence

tag: time

tag: infection

value: Fusarium


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves - rep2


title: time: 144 - Treated or untreated: Fusarium - rep5

source_name: (time: 144 - Treated or untreated: Fusarium)

value: water


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels - rep1

extract_protocol: RNA isolation from starchy endosperm


title: time: 144 - Treated or untreated: Fusarium - rep2


title: time: 96 - Treated or untreated: WATER - rep4

source_name: (time: 96 - Treated or untreated: WATER)


title: time: 144 - Treated or untreated: WATER - rep2


title: time: 96 - Treated or untreated: Fusarium - rep4

source_name: (time: 96 - Treated or untreated: Fusarium)


title: time: 144 - Treated or untreated: Fusarium - rep4


title: time: 144 - Treated or untreated: WATER - rep4


title: dev. stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves - rep3


title: time: 96 - Treated or untreated: Fusarium - rep5

growth_protocol: Growth Description:  Barley seeds were planted in Scotts MetroMix 200 in 6-inch pots (four seeds/pot) and plants were grown in a growth chamber with 16h day at 20oC, and 8h night at 18oC.  The light intensity at pot level ranged from 160 (edge) to 180 (middle) mmolm-2s-1.  After a week, 5ml Scotts Osmocote 14/14/14 with micronutrients was applied.  Plants were watered every two-three days until 14 days old and then every day until sampling.  After 14 days stakes were placed into the pots. Spikes were spray-inoculated two-three days after emerging from the boot (6.05 emergence of inflorescence completed GRO:0007104) with a freshly prepared spore suspension of 2 x 106 macroconidia per ml in 0.04% (vol/vol) Tween 20 in water or with water plus Tween 20 (mock).  Spray inoculations were performed with an airbrush (Model VL; Paasche Airbrush, Harwood Heights, IL, U.S.A.) adjusted to a pressureof 82.8 kPa.  All inoculations and samplings were carried out at 15:00 h.  After inoculation the spikes were bagged for no more than 72 hours.  Spikes were sampled at 24, 48, 72, 96, and 144 hours after inoculation (hai), flash frozen in liquid nitrogen and stored at 80C.  Spikes were sampled at 15:h0 h0 on each of the sampling days.


title: time: 48 - Treated or untreated: Fusarium - rep5

source_name: (time: 48 - Treated or untreated: Fusarium)


title: time: 144 - Treated or untreated: WATER - rep3


title: time: 72 - Treated or untreated: WATER - rep4

source_name: (time: 72 - Treated or untreated: WATER)


title: time: 72 - Treated or untreated: WATER - rep3


title: time: 72 - Treated or untreated: Fusarium - rep2

source_name: (time: 72 - Treated or untreated: Fusarium)


title: time: 96 - Treated or untreated: WATER - rep3


title: time: 96 - Treated or untreated: Fusarium - rep3


title: time: 144 - Treated or untreated: Fusarium - rep3


title: time: 96 - Treated or untreated: Fusarium - rep2


title: time: 72 - Treated or untreated: WATER - rep5


title: time: 72 - Treated or untreated: Fusarium - rep3


title: time: 72 - Treated or untreated: Fusarium - rep4


title: time: 96 - Treated or untreated: WATER - rep2


title: time: 48 - Treated or untreated: WATER - rep4

source_name: (time: 48 - Treated or untreated: WATER)

growth_protocol: Growth Description:  Barley seeds were planted in Scotts MetroMix 200 in 6-inch pots (four seeds/pot) and plants were grown in a growth chamber with 16h day at 20oC, and 8h night at 18oC.  The light intensity at pot level ranged from 160 (edge) to 180 (middle) mmolm-2s-1.  After a week, 5ml Scotts Osmocote 14/14/14 with micronutrients was applied.  Plants were watered every two-three days until 14 days old and then every day until sampling.  After 14 days stakes were placed into the pots. Spikes were spray-inoculated two-three days after emerging from the boot (6.05 emergence of inflorescence completed GRO:0007104) with a freshly prepared spore suspension of 2 x 106 macroconidia per ml in 0.04% (vol/vol) Tween 20 in water or with water plus Tween 20 (mock).  Spray inoculations were performed with an airbrush (Model VL; Paasche Airbrush, Harwood Heights, IL, U.S.A.) adjusted to a pressureof 82.8 kPa.  All inoculations and samplings were carried out at 15h00.  After inoculation the spikes were bagged for no more than 72 hours.  Spikes were sampled at 24, 48, 72, 96, and 144 hours after inoculation (hai), flash frozen in liquid nitrogen and stored at 80C.  Spikes were sampled at 15h00 on each of the sampling days.


title: time: 72 - Treated or untreated: WATER - rep1


title: time: 96 - Treated or untreated: WATER - rep5


title: time: 48 - Treated or untreated: Fusarium - rep4


title: time: 48 - Treated or untreated: WATER - rep3


title: time: 48 - Treated or untreated: Fusarium - rep3


title: time: 48 - Treated or untreated: WATER - rep5


title: time: 72 - Treated or untreated: WATER - rep2


title: time: 48 - Treated or untreated: Fusarium - rep2


title: time: 72 - Treated or untreated: Fusarium - rep1


title: time: 72 - Treated or untreated: Fusarium - rep5

growth_protocol: Growth Description:  Barley seeds were planted in Scotts MetroMix 200 in 6-inch pots (four seeds/pot) and plants were grown in a growth chamber with 16h day at 20oC, and 8h night at 18oC.  The light intensity at pot level ranged from 160 (edge) to 180 (middle) mmolm-2s-1.  After a week, 5ml Scotts Osmocote 14/14/14 with micronutrients was applied.  Plants were watered every two-three days until 14 days old and then every day until sampling.  After 14 days stakes were placed into the pots. Spikes were spray-inoculated two-three days after emerging from the boot (6.05 emergence of inflorescence completed GRO:0007100) with a freshly prepared spore suspension of 2 x 106 macroconidia per ml in 0.04% (vol/vol) Tween 20 in water or with water plus Tween 20 (mock).  Spray inoculations were performed with an airbrush (Model VL; Paasche Airbrush, Harwood Heights, IL, U.S.A.) adjusted to a pressureof 82.8 kPa.  All inoculations and samplings were carried out at 15h00.  After inoculation the spikes were bagged for no more than 72 hours.  Spikes were sampled at 24, 48, 72, 96, and 144 hours after inoculation (hai), flash frozen in liquid nitrogen and stored at 80C.  Spikes were sampled at 15h00 on each of the sampling days.


title: time: 24 - Treated or untreated: WATER - rep2

source_name: (time: 24 - Treated or untreated: WATER)


title: time: 24 - Treated or untreated: Fusarium - rep2

source_name: (time: 24 - Treated or untreated: Fusarium)


title: time: 24 - Treated or untreated: Fusarium - rep5


title: time: 48 - Treated or untreated: WATER - rep2


title: time: 24 - Treated or untreated: Fusarium - rep3


title: time: 24 - Treated or untreated: Fusarium - rep1


title: disease type: Treated (Pathogen Infection) - genotype: mlo5 - rep1

description: gro: 0005679## (Organism Part); GRO:0007061 (Development Stage);

source_name: 9## (disease type: Treated (Pathogen Infection) - genotype: mlo5)

growth_protocol: Growth Description:  Grown in a greenhouse with automatic shading and supplementary light (sodium-halogen lamps) resulting in a light period of 16 h (ca. 06:00 to 22:00 local time). Temperature ranged from 18OC (night) to 21OC (day). Grown in pots (diameter 14 cm) of compost soil (production IPK) without fertilizer.

value: powdery mildew (Bgh)


title: disease type: Treated (Pathogen Infection) - genotype: Mlo - rep1

source_name: 9## (disease type: Treated (Pathogen Infection) - genotype: Mlo)

value: Mlo


title: time: 24 - Treated or untreated: WATER - rep3


title: time: 48 hai - treated or untreated: Water - rep1

description: morex barley (germplasm name); ud: 0000056 inoculated cells in inflorescence, (Organism Part); UD:0000055 7.03-anthesis completed GRO:0007104 (Development Stage); 7 weeks after effector challenge (Age); Scotts MetroMix 200 (Growth Media).

source_name: inoculated cells in inflorescence (time: 48 hai - treated or untreated: Water)

label_protocol: BioArray High-Yield RNA Transcript Labeling Kit Method

growth_protocol: Growth Description:  Barley (cv. Morex) seeds were sterilized in a 5% solution of bleach for 15 minutes and rinsed.  To promote uniform germination, the seeds were cold/dark treated at 4°C for 12 hours. Five seeds were planted in Scotts MetroMix 200 in 6” standard pots and grown in the growth chamber under the following conditions: 20°C for 16h with light and 18°C for 8h under darkness. After one week of planting, 5 ml of Osmocote 14/14/14 was added to each pot. Plants were watered as needed until germination and then watered daily until time of inoculation and sampling. Spikes were inoculated 2 to 3 days after the spikes emerged from the boot (6.05 emergence of inflorescence completed GRO:0007104). Deoxynivalenol was purchased as a white powder and was dissolved into ddH20 before use (Sigma-Aldrich®, St. Louis, MO; CAS: 51481-10-8). The DON concentration for inoculation was 2 µg per floret and was delivered to the floret as a 10 µl dilution (0.2 µg/µl). Six florets on one side and the three florets of the opposite side of the middle portion of each spike were inoculated with either DON or sterile water (mock-control).  The entire spike was then covered in a clear plastic zip bag for up to 72 hours after inoculation (hai). All inoculations were conducted at 11:00 am. Plants were sampled at 1, 12, 24, and 48 hai. Nine florets from a single spike from each of five to seven plants were collected as a sample for each of the six time points and treatments.  Environmental Conditions:  Controlled growth chamber

value: floret

value: 48 hai

tag: treatment

value: untreated


title: time: 24 - Treated or untreated: WATER - rep4


title: time: 24 - Treated or untreated: WATER - rep1


title: disease type: Control - genotype: Mlo - rep1

source_name: 9## (disease type: Control - genotype: Mlo)

value: control


title: disease type: Control - genotype: mlo5 - rep1

source_name: 9## (disease type: Control - genotype: mlo5)


title: time: 48 hai - treated or untreated: Deoxynivalenol - rep2

source_name: inoculated cells in inflorescence (time: 48 hai - treated or untreated: Deoxynivalenol)

value: Deoxynivalenol


title: time: 48 hai - treated or untreated: Water - rep3


title: time: 24 - Treated or untreated: WATER - rep5


title: time: 48 hai - treated or untreated: Deoxynivalenol - rep3


title: time: 48 hai - treated or untreated: Water - rep2


title: time: 48 hai - treated or untreated: Deoxynivalenol - rep1


title: time: 24 - Treated or untreated: Fusarium - rep4


title: time: 24 hai - treated or untreated: Water - rep3

source_name: inoculated cells in inflorescence (time: 24 hai - treated or untreated: Water)

value: 24 hai


title: time: 24 hai - treated or untreated: Deoxynivalenol - rep2

source_name: inoculated cells in inflorescence (time: 24 hai - treated or untreated: Deoxynivalenol)


title: time: 24 hai - treated or untreated: Deoxynivalenol - rep1


title: time: 12 hai - treated or untreated: Deoxynivalenol - rep3

source_name: inoculated cells in inflorescence (time: 12 hai - treated or untreated: Deoxynivalenol)

value: 12 hai


title: time: 24 hai - treated or untreated: Water - rep2


title: time: 12 hai - treated or untreated: Water - rep3

source_name: inoculated cells in inflorescence (time: 12 hai - treated or untreated: Water)


title: time: 1 hai - treated or untreated: Water - rep1

source_name: inoculated cells in inflorescence (time: 1 hai - treated or untreated: Water)

value: 1 hai


title: time: 24 hai - treated or untreated: Deoxynivalenol - rep3


title: time: 24 hai - treated or untreated: Water - rep1


title: time: 12 hai - treated or untreated: Deoxynivalenol - rep2


title: time: 12 hai - treated or untreated: Deoxynivalenol - rep1


title: time: 1 hai - treated or untreated: Deoxynivalenol - rep3

source_name: inoculated cells in inflorescence (time: 1 hai - treated or untreated: Deoxynivalenol)


title: time: 1 hai - treated or untreated: Water - rep3


title: time: 12 hai - treated or untreated: Water - rep1


title: treated or untreated: oil control - time: 48 hrs - rep3

description: hv ssp spontaneum accession shechem 12-32 (germplasm name); po: 0009025 leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); 2 weeks (Age); 50% steamed soil, 50% Metro Mix 200 (Growth Media).

source_name: leaf (treated or untreated: oil control - time: 48 hrs)

growth_protocol: Growth Description:  Growth chamber grown  Environmental Conditions:  Seeds were stored at 4 deg C for one week.  Plants were then moved to a growth chamber set to 20-22 deg C, approx. 70% RH, with 14hr photoperiod provided by 160 W VHO fluorescent and 60 W incandescent lamps.  Plants were watered daily or as needed.

value: leaf

value: 48 hrs

value: oil control


title: time: 1 hai - treated or untreated: Deoxynivalenol - rep2


title: treated or untreated: oil control - time: 48 hrs - rep1


title: treated or untreated: oil control - time: 36 hrs - rep1

source_name: leaf (treated or untreated: oil control - time: 36 hrs)

value: 36 hrs


title: time: 12 hai - treated or untreated: Water - rep2


title: time: 1 hai - treated or untreated: Deoxynivalenol - rep1


title: treated or untreated: oil control - time: 36 hrs - rep2


title: time: 1 hai - treated or untreated: Water - rep2


title: treated or untreated: oil control - time: 24 hrs - rep2

source_name: leaf (treated or untreated: oil control - time: 24 hrs)

value: 24 hrs


title: treated or untreated: oil control - time: 36 hrs - rep3


title: treated or untreated: oil control - time: 48 hrs - rep2


title: treated or untreated: oil control - time: 24 hrs - rep3


title: treated or untreated: oil control - time: 12 hrs - rep1

source_name: leaf (treated or untreated: oil control - time: 12 hrs)

value: 12 hrs


title: treated or untreated: P. hordei (leaf rust) - time: 36 hrs - rep1

source_name: leaf (treated or untreated: P. hordei (leaf rust) - time: 36 hrs)

value: P. hordei (leaf rust)


title: treated or untreated: oil control - time: 12 hrs - rep3


title: treated or untreated: P. hordei (leaf rust) - time: 48 hrs - rep1

source_name: leaf (treated or untreated: P. hordei (leaf rust) - time: 48 hrs)


title: treated or untreated: oil control - time: 24 hrs - rep1


title: treated or untreated: P. hordei (leaf rust) - time: 36 hrs - rep2


title: treated or untreated: P. hordei (leaf rust) - time: 48 hrs - rep2


title: treated or untreated: P. hordei (leaf rust) - time: 12 hrs - rep3

source_name: leaf (treated or untreated: P. hordei (leaf rust) - time: 12 hrs)


title: treated or untreated: P. hordei (leaf rust) - time: 24 hrs - rep2

source_name: leaf (treated or untreated: P. hordei (leaf rust) - time: 24 hrs)


title: treated or untreated: oil control - time: 12 hrs - rep2


title: treated or untreated: water control - time: 48 hrs - rep3

source_name: leaf (treated or untreated: water control - time: 48 hrs)

value: water control


title: treated or untreated: water control - time: 36 hrs - rep1

source_name: leaf (treated or untreated: water control - time: 36 hrs)


title: treated or untreated: P. hordei (leaf rust) - time: 36 hrs - rep3


title: treated or untreated: water control - time: 36 hrs - rep3


title: treated or untreated: P. hordei (leaf rust) - time: 12 hrs - rep2


title: treated or untreated: water control - time: 48 hrs - rep1


title: treated or untreated: P. hordei (leaf rust) - time: 24 hrs - rep3


title: treated or untreated: P. hordei (leaf rust) - time: 12 hrs - rep1


title: treated or untreated: water control - time: 24 hrs - rep2

source_name: leaf (treated or untreated: water control - time: 24 hrs)


title: treated or untreated: water control - time: 36 hrs - rep2


title: treated or untreated: water control - time: 24 hrs - rep1


title: treated or untreated: P. hordei (leaf rust) - time: 24 hrs - rep1


title: treated or untreated: water control - time: 12 hrs - rep3

source_name: leaf (treated or untreated: water control - time: 12 hrs)


title: treated or untreated: water control - time: 48 hrs - rep2


title: treated or untreated: C. sativus (spot blotch) - time: 48 hrs - rep2

source_name: leaf (treated or untreated: C. sativus (spot blotch) - time: 48 hrs)

value: C. sativus (spot blotch)


title: treated or untreated: water control - time: 24 hrs - rep3


title: treated or untreated: water control - time: 12 hrs - rep1


title: treated or untreated: water control - time: 12 hrs - rep2


title: treated or untreated: C. sativus (spot blotch) - time: 36 hrs - rep2

source_name: leaf (treated or untreated: C. sativus (spot blotch) - time: 36 hrs)


title: treated or untreated: C. sativus (spot blotch) - time: 12 hrs - rep3

source_name: leaf (treated or untreated: C. sativus (spot blotch) - time: 12 hrs)


title: treated or untreated: C. sativus (spot blotch) - time: 48 hrs - rep1


title: treated or untreated: C. sativus (spot blotch) - time: 36 hrs - rep3


title: treated or untreated: C. sativus (spot blotch) - time: 24 hrs - rep1

source_name: leaf (treated or untreated: C. sativus (spot blotch) - time: 24 hrs)


title: genotype: 7HL - rep2

description: po: 0000003## (Organism Part); whole plant  PO:0000003 (Cell type); one leaf visiblePO:0007094 (Development Stage); 3 days after planting (Age); 3MM filter paper (Growth Media).

source_name: ## (genotype: 7HL)

growth_protocol: Growth Description:  Seeds of both parents, and ditelosomic addition lines were cold-treated at 4oC in the dark for 96 h in sterile petri dishes on three layers of filter paper wetted with 8.0 mL of distilled water.  Following the cold treatment, the petri dishes were placed in a growth chamber in a randomized complete block design with three replications, where they were kept at 22oC with a 16h light/8h dark regime at a light intensity of 360 µ einstein m-1 s-1.  After both 24 and 48 hours, 1.0 mL of sterile water was added to each petri dish to maintain moisture levels. After 72 hours, 11 to 13 seedlings per replication were sampled for each genotype by detaching the seedling from the seed.  The seedling tissue was immediately frozen in liquid nitrogen.

value: whole organism

tag: line


title: treated or untreated: C. sativus (spot blotch) - time: 48 hrs - rep3


title: genotype: 7HS - rep1

source_name: ## (genotype: 7HS)


title: genotype: 7HL - rep3


title: genotype: 7HS - rep2


title: treated or untreated: C. sativus (spot blotch) - time: 36 hrs - rep1


title: treated or untreated: C. sativus (spot blotch) - time: 12 hrs - rep2


title: treated or untreated: C. sativus (spot blotch) - time: 24 hrs - rep2


title: genotype: 5HL - rep1

source_name: ## (genotype: 5HL)


title: genotype: 7HL - rep1


title: treated or untreated: C. sativus (spot blotch) - time: 24 hrs - rep3


title: treated or untreated: C. sativus (spot blotch) - time: 12 hrs - rep1


title: genotype: 5HL - rep3


title: genotype: 5HS - rep2

source_name: ## (genotype: 5HS)


title: genotype: 7HS - rep3


title: genotype: 4HL - rep2

source_name: ## (genotype: 4HL)


title: genotype: 5HS - rep3


title: genotype: 4HL - rep3


title: genotype: 3HL - rep1

source_name: ## (genotype: 3HL)


title: genotype: 4HS - rep3

source_name: ## (genotype: 4HS)


title: genotype: 3HL - rep3


title: genotype: 3HS - rep2

source_name: ## (genotype: 3HS)


title: genotype: 5HS - rep1


title: genotype: 5HL - rep2


title: genotype: 1HS - rep2

source_name: ## (genotype: 1HS)


title: genotype: 1HS - rep3


title: genotype: 4HS - rep2


title: genotype: 2HS - rep3

source_name: ## (genotype: 2HS)


title: genotype: 3HS - rep1


title: genotype: 3HL - rep2


title: genotype: 4HS - rep1

description: po: 0000003## (Organism Part); whole plant  PO:0000003 (Cell type); LP.01 one leaf visible PO:0007094 (Development Stage); 3 days after planting (Age); 3MM filter paper (Growth Media).


title: genotype: 2HS - rep2


title: genotype: 3HS - rep3


title: genotype: 4HL - rep1


title: genotype: 2HS - rep1


title: treated or untreated: P. hordei (leaf rust) - time: 48 hrs - rep3

source_name: leaf (treated or untreated: P. hordei (leaf rust) - time: 48 hrs)


title: genotype: CS (Chinese Spring) - rep3

source_name: ## (genotype: CS (Chinese Spring))

value: CS (Chinese Spring)


title: genotype: 1HS - rep1


title: genotype: Betzes - rep2

source_name: ## (genotype: Betzes)

value: Betzes


title: genotype: Betzes - rep3


title: line: Steptoe - rep1

description: po: 0009007## (Organism Part); PO:0009007 (Development Stage);

hyb_protocol: Affymetrix GeneChip Hyb

source_name: ## (line: Steptoe)

extract_protocol: Trizol RNA extraction followed by RNeasy purification

value: Steptoe


title: line: Steptoe - rep2


title: genotype: CS (Chinese Spring) - rep2

description: po: 0000003## (Organism Part); whole plant  PO:0000003 (Cell type); LP.01 one leaf visiblePO:0007094 (Development Stage); 3 days after planting (Age); 3MM filter paper (Growth Media).


title: line: nad1-1 - rep1


title: line: nad1-3 - rep3


title: line: nad1-2 - rep2


title: time: 96 hai. - Treated or untreated: MUTANT - rep1

source_name: (time: 96 hai. - Treated or untreated: MUTANT)

growth_protocol: Growth Description:  Barley seeds were planted in Scotts MetroMix 200 in 6-inch pots (four seeds/pot) and plants were grown in a growth chamber with 16h day at 20oC, and 8h night at 18oC.  The light intensity at pot level ranged from 160 (edge) to 180 (middle) mmolm-2s-1.  After a week, 5ml Scotts Osmocote 14/14/14 with micronutrients was applied.  Plants were watered every two-three days until 14 days old and then every day until sampling.  After 14 days stakes were placed into the pots. Spikes were spray-inoculated two-three days after emerging from the boot (7.03 emergence of inflorescence completed GRO:0007104) with a freshly prepared spore suspension of 2 x 106 macroconidia of mutant or wild type strains of F. graminearum per ml in 0.04% (vol/vol) Tween 20 in water or with water plus Tween 20 (mock).  Dip inoculation was performed. All inoculations and samplings were carried out at 15:00h.  After inoculation the spikes were bagged for no more than 72 hours.  Spikes were sampled at 48 and 96 hours after inoculation (hai), flash frozen in liquid nitrogen and stored at 80C.  Spikes were sampled at 15:00h on each of the sampling days.

value: inflorescence


title: time: 96 hai. - Treated or untreated: WILD TYPE - rep2

source_name: (time: 96 hai. - Treated or untreated: WILD TYPE)


title: time: 96 hai. - Treated or untreated: WILD TYPE - rep1


title: line: nad1-1 - rep3


title: line: nad1-3 - rep1


title: line: Steptoe - rep3


title: line: nad1-1 - rep2


title: line: nad1-4 (FN242) - rep1


title: genotype: CS (Chinese Spring) - rep1


title: line: nad1-2 - rep3


title: line: nad1-2 - rep1


title: time: 96 hai. - Treated or untreated: MUTANT - rep2


title: time: 96 hai. - Treated or untreated: WILD TYPE - rep3


title: time: 96 hai. - Treated or untreated: MUTANT - rep3


title: line: nad1-3 - rep2


title: line: nad1-4 (FN242) - rep3


title: line: nad1-4 (FN242) - rep2


title: time: 48 hai. - Treated or untreated: WILD TYPE - rep2

source_name: (time: 48 hai. - Treated or untreated: WILD TYPE)


title: time: 96 hai. - Treated or untreated: WATER - rep3

source_name: (time: 96 hai. - Treated or untreated: WATER)

value: control


title: time: 96 hai. - Treated or untreated: WATER - rep1


title: time: 48 hai. - Treated or untreated: WATER - rep1

source_name: (time: 48 hai. - Treated or untreated: WATER)


title: time: 48 hai. - Treated or untreated: WILD TYPE - rep3


title: genotype: Sultan 5 (wild type) - rep1

description: gro: 0005118## (Organism Part); N/A (Cell type); GRO:0007062 (Development Stage); 10 days after beginning of stage (Age); Cereal mix (Growth Media).

source_name: 8## (genotype: Sultan 5 (wild type))

value: Sultan 5


title: time: 48 hai. - Treated or untreated: WILD TYPE - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai - rep1

description: gro: 0005118##GRO:0005306##GRO:0005106## (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai)

growth_protocol: Growth Description:  Seedlings were grown in the greenhouse for 7 days. Seven-day old seedlings were inoculated with powdery mildew isolates and then transferred to the growth chamber.

value: seedling

value: 32 hai

value: Bgh K1


title: time: 96 hai. - Treated or untreated: WATER - rep2


title: genotype: rar1-2 (mutant) - rep1

source_name: 8## (genotype: rar1-2 (mutant))


title: time: 48 hai. - Treated or untreated: MUTANT - rep3

source_name: (time: 48 hai. - Treated or untreated: MUTANT)


title: time: 48 hai. - Treated or untreated: MUTANT - rep2


title: genotype: rar1-2 (mutant) - rep2


title: time: 48 hai. - Treated or untreated: WATER - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai - rep2

description: gro: 0005118##GRO:0005306##GRO:0005304##GRO:0005016##GRO:0005300## (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).

value: 24 hai


title: genotype: Sultan 5 (wild type) - rep2


title: time: 48 hai. - Treated or untreated: MUTANT - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai - rep1

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai)


title: time: 48 hai. - Treated or untreated: WATER - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai - rep3


title: genotype: Betzes - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai - rep3

value: 20 hai


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 16 hai - rep1

value: 16 hai


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai - rep2

description: gro: 0005306##GRO:0005304##GRO:0005016##GRO:0005300## (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai - rep1

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai)


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai - rep2

value: 8 hai


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai)

value: 0 hai


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 24 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai)


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 16 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 24 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai)


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 16 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 20 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai)


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 20 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 8 hai - rep3


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 8 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 8 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 0 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 24 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 32 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 24 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 24 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 24 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 32 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 32 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 0 hai - rep1


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 0 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 20 hai - rep2


title: genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 20 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 20 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 20 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 16 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 16 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 8 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 16 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 8 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 8 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 0 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 0 hai - rep2


title: Western European 157

city: Evry

first: Cyril

last: Dalmasso

address: 23 bd de France

department: Mathématiques

institute: Université d'Evry Val d'Essonne

hyb_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.

data_processing: DNA copy-number changes, we considered the log-ratio between the signal and a reference signal estimated from a pool of hybridized samples corresponding to HapMap data, that were matched for ethnicity. Systematic sources of variation (GC content, fragment length) were removed by subtracting for each log-ratio its estimated predicted values inferred from the least squares estimates of the parameters. Data from the sex chromosomes were not considered. To reduce measurement variability while keeping a sufficient level of resolution, we averaged the intensities over fifty consecutive probes leading to a total of 17,769 genomic segments (average size of 150kb) providing tiling coverage of the human genome.

source_name: Lung adenocarcinoma, Western European

growth_protocol: Tumor samples were immediately frozen at –80°C until retrieved.

extract_protocol: DNA was extracted from frozen samples using the Nucleon DNA extraction kit (BACC2, Amersham Biosciences, Buckinghamshire, UK).

treatment_protocol: Only tissue samples with tumor cells >50% were selected.

tag: origin

value: Western European

tag: cell type

value: Lung adenocarcinoma


title: Western European 152

scan_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.


title: Western European 158

label_protocol: Samples were processed and hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 0 hai - rep1


title: Western European 163


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai - rep3


title: Western European 151


title: Western European 161


title: Western European 154


title: Western European 148


title: Western European 149


title: Western European 153


title: Western European 144


title: Western European 159


title: Western European 143


title: Western European 142


title: Western European 145


title: Western European 155


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai - rep1

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai)


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai - rep2


title: Western European 160


title: Western European 156


title: Western European 138


title: Western European 136


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai)


title: Western European 139


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 20 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 20 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai)


title: Western European 150


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai - rep1


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai)


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai - rep1


title: Western European 130


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai - rep1


title: Western European 131


title: Western European 134


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 0 hai - rep2


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 0 hai - rep3


title: Western European 129


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 20 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 32 hai - rep2


title: Western European 132


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 32 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai - rep2


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 32 hai - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 24 hai - rep3


title: genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 0 hai - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 24 hai - rep2


title: Western European 125


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 24 hai - rep1


title: Western European 128


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 20 hai - rep2


title: Western European 127


title: Western European 124


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 16 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 20 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 20 hai - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 16 hai - rep2


title: Western European 123


title: Western European 126


title: Western European 118


title: Western European 135


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 16 hai - rep1


title: Western European 122


title: Western European 117


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 8 hai - rep1


title: Western European 119


title: Western European 116


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 0 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 8 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 8 hai - rep2


title: Western European 115


title: Western European 133


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 0 hai - rep2


title: Western European 112


title: Western European 113


title: Western European 104


title: Western European 108


title: Western European 103


title: Western European 110


title: Western European 102


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai - rep2


title: Western European 97


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 0 hai - rep1


title: Western European 101


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai - rep1

description: gro: 0005118##GRO:0005306##GRO:0005106## (Organism Part); GRO:0007060 (Development Stage); 7 days after planting (Age); garden soil (Growth Media).

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai)


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai)


title: Western European 91


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai)


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai - rep2


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai)


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai - rep1

description: gro: 0005306##GRO:0005304##GRO:0005016##GRO:0005300## (Organism Part); GRO:0007060 (Development Stage); 7 days after planting (Age); garden soil (Growth Media).


title: Western European 88


title: Western European 84


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai - rep2

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai)


title: Western European 107


title: Western European 83


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai - rep1


title: Western European 105


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai - rep3


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai - rep3

source_name: 8##GRO:0005306##GRO:0005106## (genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai)


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai - rep2


title: Western European 79


title: Western European 77


title: Western European 74


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai - rep3


title: genotype: M955 WT sib-selection - year: 2004 - rep2

description: (organism part); 7. developing seed stagepo: 0004506 (Development Stage); 0 after other::days after anthesis (Age);

source_name: (genotype: M955 WT sib-selection - year: 2004)

value: WT


title: genotype: M955 WT sib-selection - year: 2004 - rep1


title: genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai - rep1


title: Western European 82


title: Western European 87


title: genotype: M955 WT sib-selection - year: 2003 - rep3

source_name: (genotype: M955 WT sib-selection - year: 2003)


title: Western European 73


title: Western European 71


title: Western European 85


title: Western European 70


title: Western European 68


title: genotype: M955 WT sib-selection - year: 2003 - rep1


title: genotype: M955 LPA sib-selection - year: 2004 - rep2

source_name: (genotype: M955 LPA sib-selection - year: 2004)

value: LPA


title: Western European 69


title: genotype: M955 WT sib-selection - year: 2003 - rep2


title: Western European 66


title: Western European 67


title: Western European 90


title: Western European 64


title: genotype: M955 LPA sib-selection - year: 2003 - rep2

source_name: (genotype: M955 LPA sib-selection - year: 2003)


title: genotype: M955 LPA sib-selection - year: 2004 - rep1


title: Western European 72


title: genotype: M955 LPA sib-selection - year: 2003 - rep1