title: Sharpin.cpdm_GroupII_Bioreplicate.IT_Unstim_000min

status: Public on Aug 31 2011

type: RNA

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

country: USA

institute: Seattle Biomedical Research Institute

hyb_protocol: 600ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 C and 10rpm.  The arrays were washed for 1 minute in Agilent GE Wash Buffer 1 and then for another minute in Agilent GE Wash Buffer 2.

scan_protocol: Scanning was performed using an Agilent High-Resolution DNA Microarray Scanner, with 3 micron resolution and 20-bit dynamic range. The resulting images were processed with Agilent Feature Extraction version 10.7.3.1 to generate raw probe intensity data.

data_processing: Arrays were normalized using the normalize.quantiles function in the Bioconductor package preprocessCore.  Repeated measurements for a given gene were averaged in the following manner:

molecule: total RNA

organism: Mus musculus

source_name: Total RNA derived from unstimulated murine bone marrow derived macrophages

label_protocol: Labeling was performed with the One-Color Microarray-Based Gene Expression Analysis protocol version 6.5 (Agilent).  Briefly, double-stranded cDNA was synthesized from 200ng of total RNA using a T7-oligo(dT) primer, followed by in vitro transcription by T7 RNA polymerase with incorporation of Cy3-labeled CTP.

growth_protocol: Bone marrow derived macrophage cultures: Bone marrow was collected from femurs and cultured for 7-10 days in complete RPMI containing 10% heat-inactivated FCS (Hyclone Laboratories), 100U/ml penicillin, 100µg/ml streptomycin, 2mM l-glutamine and 50ng/ml rmM-CSF (Chiron).

extract_protocol: Total RNA was isolated from bone marrow-derived macrophages using TRIzol (Invitrogen) according to the manufacturer's instructions.  Prior to labeling, the integrity of samples was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Bone marrow derived macrophages were left unstimulated or stimulated for 12hrs prior to harvest with 300ng/mL Pam3CSK4 (EMC microcollections GmbH)

tag: mouse genotype

tag: strain

value: Sharpin

tag: bioreplicate comparison groups (which mutant replicate goes with which wt replicate)

value: GroupII

tag: bioreplicate id

tag: stimulation condition

value: Unstim

tag: time post-stimulation

tag: in vivo or in vitro

value: in vitro


title: Sharpin.cpdm_GroupI_Bioreplicate.HH_Pam3CSK4_720min

source_name: Total RNA derived from murine bone marrow derived macrophages stimulated for 12hrs with PAM3CSK4 (300ng/mL)

value: GroupI


title: Il10.KO_GroupIV_Bioreplicate.LL_Pam3CSK4_720min

value: GroupIV


title: Il10.KO_GroupIII_Bioreplicate.EK_Unstim_000min

value: GroupIII


title: Ikbkg.panr2_GroupV_Bioreplicate.GK_Unstim_000min

value: Ikbkg

value: GroupV


title: Ikbkg.panr2_GroupV_Bioreplicate.GK_Pam3CSK4_720min


title: Sharpin.cpdm_GroupI_Bioreplicate.HH_Unstim_000min


title: Nfkb1.KO_GroupIV_Bioreplicate.LI_Unstim_000min


title: Bl6.WT_GroupIV_Bioreplicate.LR_Pam3CSK4_720min


title: Nfkb1.KO_GroupIII_Bioreplicate.EI_Unstim_000min


title: Ikbkg.panr2_GroupVI_Bioreplicate.GM_Pam3CSK4_720min

value: GroupVI


title: Nfkb1.KO_GroupIV_Bioreplicate.LI_Pam3CSK4_720min


title: Il10.KO_GroupIII_Bioreplicate.EK_Pam3CSK4_720min


title: Sharpin.WT_GroupII_Bioreplicate.IS_Unstim_000min


title: Sharpin.WT_GroupII_Bioreplicate.IS_Pam3CSK4_720min


title: Ikbkg.panr2_GroupVI_Bioreplicate.GM_Unstim_000min


title: Sharpin.cpdm_GroupII_Bioreplicate.IT_Pam3CSK4_720min


title: Nfkb1.KO_GroupIII_Bioreplicate.EI_Pam3CSK4_720min


title: Ikbkg.WT_GroupVI_Bioreplicate.GL_Pam3CSK4_720min


title: Sharpin.WT_GroupI_Bioreplicate.HG_Unstim_000min


title: Ikbkg.WT_GroupV_Bioreplicate.GJ_Pam3CSK4_720min


title: Ikbkg.WT_GroupVI_Bioreplicate.GL_Unstim_000min


title: Bl6.WT_GroupIII_Bioreplicate.LE_Pam3CSK4_720min


title: Il10.KO_GroupIV_Bioreplicate.LL_Unstim_000min


title: Bl6.WT_GroupIV_Bioreplicate.LR_Unstim_000min


title: Ikbkg.WT_GroupV_Bioreplicate.GJ_Unstim_000min


title: Sharpin.WT_GroupI_Bioreplicate.HG_Pam3CSK4_720min


title: Bl6.WT_GroupIX_Bioreplicate.KK1_Pam3CSK4_0720min

description:
probe_group_file: BrainArray version 14: MoEx10stv1_Mm_ENTREZG
meta-probeset_file: BrainArray version 14: MoEx10stv1_Mm_ENTREZG

hyb_protocol: Samples were hybridized according to the Whole Transcript Sense Target Labeling protocol: *Heat cocktails at 99° for 5 minutes, 42° for 5 minutes, and then centrifuged at 13,200g for 1 minute. *Transfer 200uL of hyb solution to each array. *Hybridize 16 hours at 45° at 60rpm. *Wash and stain using fluidics protocol FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization.

label: biotin

label_protocol: Total RNA samples were labeled as described in the Whole Transcript Sense Target Labeling protocol (Affymetrix)

value: GroupIX


title: Atf3.KO_GroupIV_Bioreplicate.LS_Pam3CSK4_720min


title: Map3k8.sluggish_GroupVII_Bioreplicate.CZ_Unstim_0000min

value: GroupVII


title: Bl6.WT_GroupIX_Bioreplicate.KK2_Unstim_0000min


title: Bl6.WT_GroupIII_Bioreplicate.LE_Unstim_000min


title: Map3k8.sluggish_GroupVII_Bioreplicate.CZ_Pam3CSK4_0720min


title: Map3k8.sluggish_GroupVIII_Bioreplicate.DL_Pam3CSK4_0720min

value: GroupVIII


title: Tnf.KO_GroupIX_Bioreplicate.EK_Pam3CSK4_0720min

value: Tnf


title: Tnf.KO_GroupIX_Bioreplicate.EK_Unstim_0000min


title: Map3k8.WT_GroupVIII_Bioreplicate.DJ_Unstim_0000min


title: Map3k8.WT_GroupVII_Bioreplicate.CX_Unstim_0000min


title: Atf3.KO_GroupIV_Bioreplicate.LS_Unstim_000min


title: Atf3.KO_GroupIII_Bioreplicate.LF_Pam3CSK4_720min


title: Map3k8.WT_GroupVII_Bioreplicate.CX_Pam3CSK4_0720min


title: Atf3.KO_GroupIII_Bioreplicate.LF_Unstim_000min


title: Map3k8.WT_GroupVIII_Bioreplicate.DJ_Pam3CSK4_0720min


title: Bl6.WT_GroupIX_Bioreplicate.KK1_Unstim_0000min


title: Map3k8.sluggish_GroupVIII_Bioreplicate.DL_Unstim_0000min


title: Bl6.WT_GroupIX_Bioreplicate.KK2_Pam3CSK4_0720min


title: genotype, Drought susceptible (S) A24-39 , terminal drought - rep1

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:
Triticum turgidum subsp. dicoccoides (Germplasm Name); Drought susceptible (S) A24-39 (Ecotype); PO:0006001 phyllome, (Organism Part); PO:0007130 B reproductive growth (Development Stage); 10 weeks (Age); pure quartz sand and peat (4:1 v/v) (Growth Media).
Drought resistant genotype (R) Y12-3 under well watered conditions

hyb_protocol: Affymetrix GeneChip method

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: Triticum dicoccoides

source_name: phyllome (genotype: Drought susceptible (S) A24-39 - treated or untreated: terminal drought)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: genotype

value: Drought susceptible (S) A24-39

tag: treatment

value: terminal drought

tag: tissue

value: phyllome


title: genotype, Drought susceptible (S) A24-39 , terminal drought - rep2


title: genotype, Drought susceptible (S) A24-39 , terminal drought - rep3


title: genotype, Drought susceptible (S) A24-39 , Well-watered - rep2

source_name: phyllome (genotype: Drought susceptible (S) A24-39 - treated or untreated: Well-watered)

value: Well-watered


title: genotype, Drought susceptible (S) A24-39 , Well-watered - rep1


title: genotype, Drought susceptible (S) A24-39 , Well-watered - rep3


title: genotype, Drought resistant (R) Y12-3 , terminal drought - rep3

description:
Triticum turgidum subsp. dicoccoides (Germplasm Name); Drought resistan (R) Y-12-3 (Ecotype); PO:0006001 phyllome, (Organism Part); PO:0007130 B reproductive growth (Development Stage); 10 weeks (Age); pure quartz sand and peat (4:1 v/v) (Growth Media).
Drought resistant genotype (R) Y12-3 under well watered conditions

source_name: phyllome (genotype: Drought resistant (R) Y12-3 - treated or untreated: terminal drought)

value: Drought resistant (R) Y12-3


title: genotype, Drought resistant (R) Y12-3 , terminal drought - rep2


title: genotype, Drought resistant (R) Y12-3 , Well-watered - rep1

source_name: phyllome (genotype: Drought resistant (R) Y12-3 - treated or untreated: Well-watered)


title: genotype, Drought resistant (R) Y12-3 , Well-watered - rep3


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR37 - rep2

description:
Wheat cv. Renan (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); other (Growth Media).
14 day old wheat leaf tissue 24 hpi, inoculated with wheat adapted Magnaporthe isolate BR37

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

organism: Triticum aestivum

source_name: juvenile leaf (pathogen isolates: Wheat adapted Magnaporthe isolate BR37)

label_protocol: Standard Affymetrix protocol

value: Wheat adapted Magnaporthe isolate BR37

value: leaf

tag: cultivar

value: Renan


title: genotype, Drought resistant (R) Y12-3 , terminal drought - rep1


title: pathogen isolates: Yr1-virulent wheat yellow rust isolate 169E136 - rep2

description:
Avocet*6/Yr1 (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); peat/perlite/soil (Growth Media).
Fourteen day old Avocet*6/Yr1 inoculated with wheat yellow rust isolate 169E136 (virulent).  Sample prepared from pooled RNA (16 μg RNA per time point) extracted from leaf material collected 6, 12, 24, 48 and 72 hpi

hyb_protocol: Affy- Eukaryotic Target Hybridization

source_name: juvenile leaf (pathogen isolates: Yr1-virulent wheat yellow rust isolate 169E136)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Trizol RNA extraction followed by RNeasy purification


title: genotype, Drought resistant (R) Y12-3 , Well-watered - rep2


title: pathogen isolates: Mock inoculated (Control) - rep1

description:
Avocet*6/Yr1 (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); peat/perlite/soil (Growth Media).
Fourteen day old Avocet*6/Yr1 inoculated with talcum powder (control).  Sample prepared from pooled RNA (16 μg RNA per time point) extracted from leaf material collected 6, 12, 24, 48 and 72 hpi

source_name: juvenile leaf (pathogen isolates: Mock inoculated (Control))

value: Mock inoculated (Control)


title: pathogen isolates: Yr1-virulent wheat yellow rust isolate 169E136 - rep1


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR32 - rep1

description:
Wheat cv. Renan (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); other (Growth Media).
14 day old wheat leaf tissue 24 hpi, inoculated with wheat adapted Magnaporthe isolate BR32

source_name: juvenile leaf (pathogen isolates: Wheat adapted Magnaporthe isolate BR32)

value: Wheat adapted Magnaporthe isolate BR32


title: pathogen isolates: Yr1-avirulent wheat yellow rust isolate 232E137 - rep3

description:
Avocet*6/Yr1 (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); peat/perlite/soil (Growth Media).
Fourteen day old Avocet*6/Yr1 inoculated with wheat yellow rust isolate 232E137 (avirulent).  Sample prepared from pooled RNA (16 μg RNA per time point) extracted from leaf material collected 6, 12, 24, 48 and 72 hpi

source_name: juvenile leaf (pathogen isolates: Yr1-avirulent wheat yellow rust isolate 232E137)


title: pathogen isolates: Mock inoculated (Control) - rep3


title: pathogen isolates: Yr1-avirulent wheat yellow rust isolate 232E137 - rep2


title: pathogen isolates: Yr1-avirulent wheat yellow rust isolate 232E137 - rep1


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR32 - rep3


title: pathogen isolates: Yr1-virulent wheat yellow rust isolate 169E136 - rep3


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR37 - rep3


title: pathogen isolates: Mock inoculated (Control) - rep2


title: genotype: CS-5AL - stress condition: Severe stress - rep3

description:
Chinese Spring deletion line (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring 5A long arm deletion line (CS-5AL10)
Severe stress

hyb_protocol: Affymetrix Basic Protocol

source_name: glume (genotype: CS-5AL - stress condition: Severe stress)

label_protocol: Affy-Eukaryotic Target Preparation for mRNA

growth_protocol: Growth Description:  Soil water content was maintained close to field capacity (28%) until plants reached the stage of 3 days post anthesis (3DPA), when watering was stopped. The water status of the plants was monitored by measuring the water potential with a pressure chamber (PMS Instrument Co., Corvallis, OR, USA). The soil of water stressed plants was allowed to dry until 12.5% of SWC. These stress conditions resulted in flag leaf water potentials of -3.3 / -3.9 MPa  Environmental Conditions:  The plants were grown at 10°C day/7°C night, 60% relative humidity,12h light:12h darkness, 500µmol m-2 s-1photon flux density until the third leaf stage. Then 22°C day/18°C night, 55% relative humidity,16h light:8h darkness 500µmol m-2 s-1photon flux density until harvesting of the samples.

extract_protocol: RNA Isolation Using Trizol And Qiagen RNAeasy Columns

value: CS

value: Severe drought stress

value: glume


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR37 - rep1


title: pathogen isolates: Wheat adapted Magnaporthe isolate BR32 - rep2


title: pathogen isolates: Mock-inoculated (Control) - rep2

description:
Wheat cv. Renan (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); other (Growth Media).
14 day old wheat leaf tissue 24 hpi, mock inoculated control

source_name: juvenile leaf (pathogen isolates: Mock-inoculated (Control))

value: Mock-inoculated (Control)


title: pathogen isolates: Wheat non-adapted Magnaporthe isolate BR29 - rep3

description:
Wheat cv. Renan (Germplasm Name); PO:0006339 juvenile leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); other (Growth Media).
14 day old wheat leaf tissue 24 hpi, inoculated with wheat non-adapted Magnaporthe isolate BR29

source_name: juvenile leaf (pathogen isolates: Wheat non-adapted Magnaporthe isolate BR29)


title: pathogen isolates: Mock-inoculated (Control) - rep1


title: pathogen isolates: Mock-inoculated (Control) - rep3


title: genotype: CS-5AL - stress condition: Control - rep1

description:
Chinese Spring deletion line (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring 5A long arm deletion line (-5AL10)
Control

source_name: glume (genotype: CS-5AL - stress condition: Control)

growth_protocol: Growth Description:  Soil water content was maintained close to field capacity (28%) until plants reached the stage of 3 days post anthesis (3DPA), when watering was stopped. The water status of the plants was monitored by measuring the water potential with a pressure chamber (PMS Instrument Co., Corvallis, OR, USA). The soil of control plants continued to be watered.  Environmental Conditions:  The plants were grown at 10°C day/7°C night, 60% relative humidity,12h light:12h darkness, 500µmol m-2 s-1photon flux density until the third leaf stage. Then 22°C day/18°C night, 55% relative humidity,16h light:8h darkness 500µmol m-2 s-1photon flux density until harvesting of the samples.

value: Control


title: genotype: CS-5AL - stress condition: Mild stress - rep2

description:
Chinese Spring deletion line (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring 5A long arm deletion line (CS-5AL10)
Moderate stress

source_name: glume (genotype: CS-5AL - stress condition: Mild stress)

growth_protocol: Growth Description:  Soil water content was maintained close to field capacity (28%) until plants reached the stage of 3 days post anthesis (3DPA), when watering was stopped. The water status of the plants was monitored by measuring the water potential with a pressure chamber (PMS Instrument Co., Corvallis, OR, USA). The soil of water stressed plants was allowed to dry until 18% of SWC. These stress conditions resulted in flag leaf water potentials of -2.1 / -2.6 MPa  Environmental Conditions:  The plants were grown at 10°C day/7°C night, 60% relative humidity,12h light:12h darkness, 500µmol m-2 s-1photon flux density until the third leaf stage. Then 22°C day/18°C night, 55% relative humidity,16h light:8h darkness 500µmol m-2 s-1photon flux density until harvesting of the samples.

value: Mild drought stress


title: pathogen isolates: Wheat non-adapted Magnaporthe isolate BR29 - rep1


title: genotype: CS - stress condition: Control - rep2

description:
Chinese Spring cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring (Bread wheat)
Control

source_name: glume (genotype: CS - stress condition: Control)


title: genotype: CS-5AL - stress condition: Severe stress - rep2


title: genotype: CS - stress condition: Severe stress - rep3

description:
Chinese Spring cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring (Bread wheat)
Severe stress

source_name: glume (genotype: CS - stress condition: Severe stress)


title: genotype: CS - stress condition: Severe stress - rep1


title: genotype: CS-5AL - stress condition: Control - rep2


title: genotype: CS-5AL - stress condition: Severe stress - rep1


title: genotype: Creso - stress condition: Severe stress - rep3

description:
Creso cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000052 7 post anthesis (Development Stage); 3 months old plants, 7 days after anthesis (Age); garden soil (Growth Media).
Genotype: Creso (Durum wheat)
Severe stress

organism: Triticum turgidum subsp. durum

source_name: glume (genotype: Creso - stress condition: Severe stress)

value: Creso


title: genotype: CS - stress condition: Control - rep1


title: genotype: CS-5AL - stress condition: Control - rep3


title: pathogen isolates: Wheat non-adapted Magnaporthe isolate BR29 - rep2


title: genotype: CS-5AL - stress condition: Mild stress - rep3


title: genotype: CS-5AL - stress condition: Mild stress - rep1


title: genotype: Creso - stress condition: Severe stress - rep2


title: genotype: Creso - stress condition: Severe stress - rep1


title: genotype: CS - stress condition: Mild stress - rep1

description:
Chinese Spring cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000054 10 post anthesis (Development Stage); 3 months old plants, 10 days after anthesis (Age); garden soil (Growth Media).
Genotype: Chinese Spring (Bread wheat)
Moderate stress

source_name: glume (genotype: CS - stress condition: Mild stress)


title: genotype: Creso - stress condition: Control - rep3

description:
Creso cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000052 7 post anthesis (Development Stage); 3 months old plants, 7 days after anthesis (Age); garden soil (Growth Media).
Genotype: Creso (Durum wheat)
Control

source_name: glume (genotype: Creso - stress condition: Control)


title: genotype: CS - stress condition: Severe stress - rep2


title: genotype: Creso - stress condition: Mild stress - rep2

description:
Creso cultivar (Germplasm Name); PO:0009039 glume, (Organism Part); UD:0000052 7 post anthesis (Development Stage); 3 months old plants, 7 days after anthesis (Age); garden soil (Growth Media).
Genotype: Creso (Durum wheat)
Moderate stress

source_name: glume (genotype: Creso - stress condition: Mild stress)


title: genotype: Creso - stress condition: Mild stress - rep1


title: genotype: CS - stress condition: Mild stress - rep3


title: genotype: Creso - stress condition: Mild stress - rep3


title: genotype: CS - stress condition: Mild stress - rep2


title: genotype: Creso - stress condition: Control - rep2


title: genotype susceptible, water, time 48 hai, rep1

description:
A wheat NIL pair 260-1-1-2 (Fhb1+) and 260-1-1-4 (Fhb1-) carrying resistant and susceptible alleles, respectively for Fhb1 was used in this study. (Germplasm Name); PO:0009007 tissue, (Organism Part); PO:0007021 plant structure development stages (Development Stage); Scotts MetroMix 200 (Growth Media).
Ten sampled spikes from each replication were pooled and used for RNA isolation.

hyb_protocol: Affymetrix GeneChip Hyb

source_name: genotype: susceptible - treated or untreated: water - time: 48 hai

growth_protocol: Environmental Conditions:  The seeds were planted in Scotts MetroMix 200 in 6-inch pots (five seeds per pot) and grown in growth chamber at 20°C for 16h with light and at 18°C for 8h under darkness.  The light intensity at pot level was approximately 170 ± 20 µE m-2s-1.  Five ml of Osmocote 14/14/14 (Marysville, OH) was applied to each pot at one week after planting.  Plants were watered everyday until sampling.

value: FHB susceptible allele

value: water

tag: time

value: 48 hai

value: root


title: genotype susceptible, water, time 96 hai, rep3

source_name: genotype: susceptible - treated or untreated: water - time: 96 hai

value: 96 hai


title: genotype susceptible, water, time 96 hai, rep2


title: genotype: CS - stress condition: Control - rep3


title: genotype susceptible, water, time 96 hai, rep1


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 96 hai, rep2

source_name: genotype: susceptible - treated or untreated: Fusarium graminearum strain Butte 86 - time: 96 hai

value: Fusarium graminearum strain Butte 86


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 96 hai, rep3


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 96 hai, rep1


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 48 hai, rep3

source_name: genotype: susceptible - treated or untreated: Fusarium graminearum strain Butte 86 - time: 48 hai


title: genotype susceptible, water, time 48 hai, rep3


title: genotype: Creso - stress condition: Control - rep1


title: genotype resistant, water, time 48 hai, rep2

source_name: genotype: resistant - treated or untreated: water - time: 48 hai

value: FHB resistant allele


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 48 hai, rep1


title: genotype susceptible, water, time 48 hai, rep2


title: genotype resistant, water, time 96 hai, rep2

source_name: genotype: resistant - treated or untreated: water - time: 96 hai


title: genotype resistant, water, time 96 hai, rep1


title: genotype resistant, water, time 96 hai, rep3


title: genotype susceptible, Fusarium graminearum strain Butte 86, time 48 hai, rep2


title: genotype resistant, Fusarium graminearum strain Butte 86, time 48 hai, rep1

source_name: genotype: resistant - treated or untreated: Fusarium graminearum strain Butte 86 - time: 48 hai


title: genotype resistant, Fusarium graminearum strain Butte 86, time 96 hai, rep3

source_name: genotype: resistant - treated or untreated: Fusarium graminearum strain Butte 86 - time: 96 hai


title: genotype resistant, Fusarium graminearum strain Butte 86, time 96 hai, rep2


title: genotype resistant, water, time 48 hai, rep1


title: genotype resistant, Fusarium graminearum strain Butte 86, time 48 hai, rep3


title: genotype yr39, time 48 hpi, P. s. tritici-inoculated, rep2

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 48 hours after pathogen challenge (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [pathogen infection].

source_name: genotype: yr39 - time: 48 hpi - Treated or untreated: P. s. tritici-inoculated

growth_protocol: Growth Description:  For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.

extract_protocol: Trizol Plus RNA Purification (Invitrogen)

value: 48 hpi

value: leaf


title: genotype yr39, time 48 hpi, P. s. tritici-inoculated, rep1


title: genotype yr39, time 24 hpi, Mock-inoculated, rep3

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 24 hours after mock-inoculation (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [water and talc].

source_name: genotype: yr39 - time: 24 hpi - Treated or untreated: Mock-inoculated

value: 24 hpi


title: genotype yr39, time 48 hpi, Mock-inoculated, rep3

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 48 hours after mock-inoculation (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [water and talc].

source_name: genotype: yr39 - time: 48 hpi - Treated or untreated: Mock-inoculated


title: genotype yr39, time 24 hpi, Mock-inoculated, rep1


title: genotype yr39, time 48 hpi, Mock-inoculated, rep1


title: genotype resistant, water, time 48 hai, rep3


title: genotype yr39, time 48 hpi, Mock-inoculated, rep2


title: genotype resistant, Fusarium graminearum strain Butte 86, time 48 hai, rep2


title: genotype yr39, time 24 hpi, P. s. tritici-inoculated, rep3

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 24 hours after pathogen challenge (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [pathogen infection].

source_name: genotype: yr39 - time: 24 hpi - Treated or untreated: P. s. tritici-inoculated


title: genotype yr39, time 24 hpi, Mock-inoculated, rep2


title: genotype resistant, Fusarium graminearum strain Butte 86, time 96 hai, rep1


title: genotype yr39, time 12 hpi, P. s. tritici-inoculated, rep2

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 12 hours after pathogen challenge (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [pathogen infection].

source_name: genotype: yr39 - time: 12 hpi - Treated or untreated: P. s. tritici-inoculated

value: 12 hpi


title: genotype yr39, time 12 hpi, P. s. tritici-inoculated, rep3


title: genotype yr39, time 48 hpi, P. s. tritici-inoculated, rep3


title: genotype yr39, time 12 hpi, Mock-inoculated, rep1

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 12 hours after mock-inoculation (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [yr39 recombinant inbred line (F6)].  Treatment application type: [water and talc].

source_name: genotype: yr39 - time: 12 hpi - Treated or untreated: Mock-inoculated


title: genotype yr39, time 12 hpi, Mock-inoculated, rep2


title: genotype Yr39, time 48 hpi, Mock-inoculated, rep3

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 48 hours after mock-inoculation (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [Yr39 recombinant inbred line (F6)].  Treatment application type: [water and talc].

source_name: genotype: Yr39 - time: 48 hpi - Treated or untreated: Mock-inoculated


title: genotype yr39, time 24 hpi, P. s. tritici-inoculated, rep1


title: genotype yr39, time 12 hpi, Mock-inoculated, rep3


title: genotype yr39, time 24 hpi, P. s. tritici-inoculated, rep2


title: genotype Yr39, time 24 hpi, Mock-inoculated, rep3

description:
PO:0000003## (Organism Part); leaf fully expandedPO:0001053, flag leaf visiblePO:0007099 (Development Stage); 24 hours after mock-inoculation (Age); other::potting mix (6 peat moss 4 vermiculite with lime 3 sand (Growth Media).
For each of three biological replications, Yr39 and yr39 seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  For each genotype in each biological replication, 8 pots were planted with 3 seedlings in each, where groups of 2 pots were randomly assigned one of 3 harvest times (12, 24 and 48 h post-inoculation).  Seedlings from the remaining group of pots were used to monitor the expected disease responses to inoculation.  .  Genetic Variation: [genotype].  Development stage: [Seedlings were grown to the flag leaf stage with ligule emerged (Feekes stage 9.0, ~35 days) in a greenhouse with a diurnal temperature cycle of 10ºC (2:00 am) to 25ºC (2:00 pm) and a 16 h light/8 h dark cycle].  Part of organism: [Flag leaves only].  Sample type: [other::Flag leaf].  Individual genetic trait genotype: [Yr39 recombinant inbred line (F6)].  Treatment application type: [water and talc].

source_name: genotype: Yr39 - time: 24 hpi - Treated or untreated: Mock-inoculated


title: genotype Yr39, time 48 hpi, P. s. tritici-inoculated, rep3

source_name: genotype: Yr39 - time: 48 hpi - Treated or untreated: P. s. tritici-inoculated


title: genotype Yr39, time 48 hpi, Mock-inoculated, rep2


title: genotype Yr39, time 48 hpi, P. s. tritici-inoculated, rep2


title: genotype Yr39, time 48 hpi, Mock-inoculated, rep1


title: genotype Yr39, time 48 hpi, P. s. tritici-inoculated, rep1


title: genotype Yr39, time 24 hpi, Mock-inoculated, rep2


title: genotype yr39, time 12 hpi, P. s. tritici-inoculated, rep1


title: genotype Yr39, time 12 hpi, P. s. tritici-inoculated, rep3

source_name: genotype: Yr39 - time: 12 hpi - Treated or untreated: P. s. tritici-inoculated


title: genotype Yr39, time 12 hpi, Mock-inoculated, rep1

source_name: genotype: Yr39 - time: 12 hpi - Treated or untreated: Mock-inoculated


title: genotype Yr39, time 12 hpi, Mock-inoculated, rep2


title: genotype yr5 isoline, time 48h, Mock-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 48 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [other::water and talc].

source_name: genotype: yr5 isoline - time: 48h - Treated or untreated: Mock-inoculated

growth_protocol: Growth Description:  For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.

value: yr5 isoline

value: Mock-inoculated


title: genotype Yr39, time 24 hpi, P. s. tritici-inoculated, rep1

source_name: genotype: Yr39 - time: 24 hpi - Treated or untreated: P. s. tritici-inoculated


title: genotype yr5 isoline, time 48h, P. s. tritici-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 48 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [pathogen infection].

source_name: genotype: yr5 isoline - time: 48h - Treated or untreated: P. s. tritici-inoculated

value: P. s. tritici-inoculated


title: genetic line: Pavon Dt1BL - rep1

description:
(Organism Part); PO:0000003 (Development Stage);
Sample type: [whole plant].  Individual genetic trait genotype: [wheat_ditelosmic_line (missing 1B short arm)].

source_name: genetic line: Pavon Dt1BL

tag: genetic line

value: Pavon Dt1BL - rep1

value: seedling without starchy endosperm


title: genotype Yr39, time 24 hpi, P. s. tritici-inoculated, rep2


title: genotype Yr39, time 24 hpi, Mock-inoculated, rep1


title: genetic line: Pavon - rep2

description:
(Organism Part); PO:0000003 (Development Stage);
Sample type: [whole plant].  Individual genetic trait genotype: [normal wheat_line].

source_name: genetic line: Pavon

value: Pavon - rep2


title: genetic line: T-1 - rep1

description:
(Organism Part); PO:0000003 (Development Stage);
Sample type: [whole plant].  Individual genetic trait genotype: [wheat_translocation_line (terminal wheat and proximal rye segments on wheat 1BS)].

source_name: genetic line: T-1

value: T-1 - rep1


title: genotype Yr39, time 12 hpi, P. s. tritici-inoculated, rep1


title: genotype Yr39, time 12 hpi, Mock-inoculated, rep3


title: genotype Yr39, time 12 hpi, P. s. tritici-inoculated, rep2


title: genetic line: 1B+5 - rep1

description:
(Organism Part); PO:0000003 (Development Stage);
Sample type: [whole plant].  Individual genetic trait genotype: [wheat_translocation_line (terminal rye and proximal wheat segments on wheat 1BS)].

source_name: genetic line: 1B+5


title: genetic line: T-1 - rep2

value: T-1 - rep2


title: genotype yr5 isoline, time 48h, P. s. tritici-inoculated, rep1


title: genetic line: Pavon Dt1BL - rep2

value: Pavon Dt1BL - rep2


title: genotype Yr39, time 24 hpi, P. s. tritici-inoculated, rep3


title: genetic line: 1B+5 - rep2


title: genetic line: 1RS.1BL - rep1

description:
(Organism Part); PO:0000003 (Development Stage);
Sample type: [whole plant].  Individual genetic trait genotype: [wheat_translocation_line (rye 1R Short arm replaced wheat 1B Short arm)].

source_name: genetic line: 1RS.1BL

value: 1RS.1BL - rep1


title: genetic line: 1RS.1BL - rep2

value: 1RS.1BL - rep2


title: genotype yr5 isoline, time 48h, P. s. tritici-inoculated, rep2


title: genotype yr5 isoline, time 48h, Mock-inoculated, rep1


title: genotype yr5 isoline, time 48h, Mock-inoculated, rep2


title: genotype yr5 isoline, time 24h, Mock-inoculated, rep2

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 24 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [other::water and talc].

source_name: genotype: yr5 isoline - time: 24h - Treated or untreated: Mock-inoculated


title: genotype yr5 isoline, time 24h, Mock-inoculated, rep3


title: genotype yr5 isoline, time 24h, P. s. tritici-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 24 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [pathogen infection].

source_name: genotype: yr5 isoline - time: 24h - Treated or untreated: P. s. tritici-inoculated


title: genotype yr5 isoline, time 12h, Mock-inoculated, rep2

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 12 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [other::water and talc].

source_name: genotype: yr5 isoline - time: 12h - Treated or untreated: Mock-inoculated


title: genotype yr5 isoline, time 12h, Mock-inoculated, rep1


title: genetic line: Pavon - rep1

value: Pavon - rep1


title: genotype yr5 isoline, time 06h, P. s. tritici-inoculated, rep2

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 6 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [pathogen infection].

source_name: genotype: yr5 isoline - time: 06h - Treated or untreated: P. s. tritici-inoculated


title: genotype yr5 isoline, time 24h, Mock-inoculated, rep1


title: genotype yr5 isoline, time 12h, P. s. tritici-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 12 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [pathogen infection].

source_name: genotype: yr5 isoline - time: 12h - Treated or untreated: P. s. tritici-inoculated


title: genotype yr5 isoline, time 06h, Mock-inoculated, rep2

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 6 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5- isoline].  Treatment application type: [other::water and talc].

source_name: genotype: yr5 isoline - time: 06h - Treated or untreated: Mock-inoculated


title: genotype yr5 isoline, time 12h, P. s. tritici-inoculated, rep2


title: genotype Yr5 isoline, time 48h, Mock-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 48 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [other::water and talc].

source_name: genotype: Yr5 isoline - time: 48h - Treated or untreated: Mock-inoculated

value: Yr5 isoline


title: genotype yr5 isoline, time 06h, P. s. tritici-inoculated, rep3


title: genotype yr5 isoline, time 24h, P. s. tritici-inoculated, rep2


title: genotype yr5 isoline, time 12h, Mock-inoculated, rep3


title: genotype yr5 isoline, time 06h, Mock-inoculated, rep1


title: genotype yr5 isoline, time 24h, P. s. tritici-inoculated, rep1


title: genotype Yr5 isoline, time 48h, P. s. tritici-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 48 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [pathogen infection].

source_name: genotype: Yr5 isoline - time: 48h - Treated or untreated: P. s. tritici-inoculated


title: genotype Yr5 isoline, time 24h, Mock-inoculated, rep2

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 24 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [other::water and talc].

source_name: genotype: Yr5 isoline - time: 24h - Treated or untreated: Mock-inoculated


title: genotype yr5 isoline, time 12h, P. s. tritici-inoculated, rep3


title: genotype yr5 isoline, time 06h, Mock-inoculated, rep3


title: genotype yr5 isoline, time 06h, P. s. tritici-inoculated, rep1


title: genotype Yr5 isoline, time 48h, P. s. tritici-inoculated, rep2


title: genotype Yr5 isoline, time 24h, Mock-inoculated, rep3


title: genotype Yr5 isoline, time 48h, Mock-inoculated, rep2


title: genotype Yr5 isoline, time 48h, Mock-inoculated, rep3


title: genotype Yr5 isoline, time 48h, P. s. tritici-inoculated, rep3


title: genotype Yr5 isoline, time 24h, P. s. tritici-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 24 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [pathogen infection].

source_name: genotype: Yr5 isoline - time: 24h - Treated or untreated: P. s. tritici-inoculated


title: genotype Yr5 isoline, time 24h, Mock-inoculated, rep1


title: genotype Yr5 isoline, time 24h, P. s. tritici-inoculated, rep1


title: genotype Yr5 isoline, time 24h, P. s. tritici-inoculated, rep2


title: genotype Yr5 isoline, time 12h, Mock-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 12 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [other::water and talc].

source_name: genotype: Yr5 isoline - time: 12h - Treated or untreated: Mock-inoculated


title: Control, rep4

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description:
Array7-Ctrl_cy3

HFKs were isolated at the University of Washington.

hyb_protocol: Labeled cDNA were hybridized to the Agilent Human GE 4x44K microarray using Agilent Hi-RPM hybridization solution in an Agilent Hybridization chamber.

scan_protocol: Microarray images were captured using a Genepix 4000B laser scanner and images processed using GenePix 6.0 software.

data_processing:
The signal intensity of each gene was globally normalized using LOWESS and median centered within the R statistics package. The normalized data was analyzed using the commercial SAS 9.1.3 program. An approximate F test on least-square means was used to estimate the significance of difference for each gene in each comparison.

Each channel of the dual-channel array was analyzed independently.

organism: Homo sapiens

source_name: Human foreskin keratinocytes maintained in growth medium

label_protocol: 5 ug of HFK total RNA was converted to cDNA and labeled with either CyDye3-dCTP or CyDye5-dCTP in a crossover dye-swap design using the LabelStar kit and random nonomers.

growth_protocol: Primary human foreskin kerotinocytes were grown to 90% confluency in six-well plates.

extract_protocol: After treatment, the biofilm/medium was removed, and RNA was isolated using an RNeasy mini kit following the manufacturer’s instructions for adherent cells.  Extracted RNA was then ethanol precipitated.

treatment_protocol: S. aureus biofilms were placed with confluent keratinocytes for 24 hours. Control cells were placed in fresh EpiLife growth medium for 24 hours.

tag: cell type

value: primary human foreskin keratinocytes

value: planktonic culture

tag: treatment time

value: 24 hours


title: Treated, rep3

description:
Array5-Tx'd_cy5

HFKs were isolated at the University of Washington.

source_name: Human foreskin keratinocytes in co-culture with S. aureus biofilm

value: Staphylococcus aureus biofilm


title: genotype Yr5 isoline, time 12h, P. s. tritici-inoculated, rep3

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 12 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [pathogen infection].

source_name: genotype: Yr5 isoline - time: 12h - Treated or untreated: P. s. tritici-inoculated

value: leaf


title: genotype Yr5 isoline, time 12h, Mock-inoculated, rep1

value: Mock-inoculated


title: genotype Yr5 isoline, time 12h, P. s. tritici-inoculated, rep2

value: P. s. tritici-inoculated


title: genotype Yr5 isoline, time 06h, Mock-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 6 hours after other::mock-inoculation (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [other::water and talc].

source_name: genotype: Yr5 isoline - time: 06h - Treated or untreated: Mock-inoculated


title: genotype Yr5 isoline, time 06h, Mock-inoculated, rep2


title: Control, rep3, dye-swap

description:
Array6-Ctrl_cy5

HFKs were isolated at the University of Washington.


title: Control, rep4, dye-swap

description:
Array8-Ctrl_cy5

HFKs were isolated at the University of Washington.


title: Control, rep1, dye-swap

description:
Array2-Ctrl_cy5

HFKs were isolated at the University of Washington.


title: genotype Yr5 isoline, time 06h, P. s. tritici-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 6 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [pathogen infection].

source_name: genotype: Yr5 isoline - time: 06h - Treated or untreated: P. s. tritici-inoculated


title: genotype Yr5 isoline, time 12h, Mock-inoculated, rep2


title: genotype Yr5 isoline, time 06h, Mock-inoculated, rep3


title: Treated, rep2

description:
Array3-Tx'd_cy5

HFKs were isolated at the University of Washington.


title: Treated, rep4, dye-swap

description:
Array8-Tx'd_cy3

HFKs were isolated at the University of Washington.


title: genotype Yr5 isoline, time 06h, P. s. tritici-inoculated, rep2


title: Control, rep2

description:
Array3-Ctrl_cy3

HFKs were isolated at the University of Washington.


title: Treated, rep4

description:
Array7-Tx'd_cy5

HFKs were isolated at the University of Washington.


title: Control, rep1

description:
Array1-Ctrl_cy3

HFKs were isolated at the University of Washington.


title: Treated, rep3, dye-swap

description:
Array6-Tx'd_cy3

HFKs were isolated at the University of Washington.


title: Epi_200_0Gy rep3

city: New York

first: Alexandre

last: Mezentsev

state: NY

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

description: Gene expression in 0 Gy-proton irradiated tissue model, 4h postirradiation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 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 4x44k array slides (Scan setting with eXtended dynamic range, 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 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91_1 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded

source_name: human foreskin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and 4 h prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

extract_protocol: Total RNA was isolated with RNaqueous Kit (Applied Biosystems), tested for spectral characteristics (NanoDrop, Thermo Scientific) and electrophoretically (Bioanalyser 2100, Agilent).

treatment_protocol: Tissues were irradiated with 0 and 0.5Gy of alpha particles

tag: sample type

value: epidermis model


title: Epi_200_0.5Gy rep3

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 4h postirradiation


title: Treated, rep1

description:
Array1-Tx'd_cy5

HFKs were isolated at the University of Washington.


title: Tissue_model_Epi_200_24h_2.5Gy_rep_3

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 16h postirradiation

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91_1 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and Significant were excluded

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and indicated time prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

treatment_protocol: Tissues were irradiated with 0 and 2.5Gy of X-rays


title: Control, rep3

description:
Array5-Ctrl_cy3

HFKs were isolated at the University of Washington.


title: Epi_200_0Gy rep1


title: genotype Yr5 isoline, time 12h, P. s. tritici-inoculated, rep1

description:
(Organism Part); 10. rapid elongation of leaf bladePO:0001023, 18. LP.02 two leaves visiblePO:0007098 (Development Stage); 12 hours after other::pathogen challenge (Age);
For each of three biological replications, individual genotypes were planted in separate 25 X 42.5-cm flats using a custom prepared potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate).  Each flat consisted of 10 rows of 6 seedlings, with rows randomly assigned one of 4 harvest times (6, 12, 24 and 48 hours post-inoculation).  Seedlings from the 10th row were used to monitor the expected disease responses to inoculation.  Seedlings were grown to the second leaf stage (~10 days after planting) in a glasshouse with a diurnal temperature cycle of 10 degrees C (2:00 am) to 25 degrees C (2:00 pm) and a 16 h light/8 h dark cycle.  .  Development stage: [2-leaf stage approximately 10 days after germination].  Part of organism: [Whole leaf tissue].  Sample type: [leaf].  Individual genetic trait genotype: [Yr5+ isoline].  Treatment application type: [pathogen infection].


title: Tissue_model_Epi_200_24h_0Gy_rep_3

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 16h postirradiation

value: 24h 0Gy


title: Epi_200_0.5Gy rep2


title: genotype Yr5 isoline, time 06h, P. s. tritici-inoculated, rep3


title: Tissue_model_Epi_200_24h_2.5Gy_rep_1


title: Tissue_model_Epi_200_24h_2.5Gy_rep_2


title: Epi_200_0.5Gy rep1


title: Tissue_model_Epi_200_16h_2.5Gy_rep_2

description: Gene expression in 0 Gy-proton irradiated tissue model, 16h postirradiation


title: Tissue_model_Epi_200_24h_0Gy_rep_2


title: Treated, rep1, dye-swap

description:
Array2-Tx'd_cy3

HFKs were isolated at the University of Washington.


title: Epi_200_0Gy rep2


title: Tissue_model_Epi_200_16h_2.5Gy_rep_3


title: Tissue_model_Epi_200_16h_0Gy_rep_2

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 4h postirradiation

value: 16h 0Gy


title: Tissue_model_Epi_200_24h_0Gy_rep_1


title: Tissue_model_Epi_200_16h_2.5Gy_rep_1


title: Tissue_model_Epi_200_16h_0Gy_rep_3


title: Tissue_model_Epi_200_4h_0.1Gy_rep_2


title: Tissue_model_Epi_200_4h_0Gy_rep_2

value: 4h 0Gy


title: Tissue_model_Epi_200_4h_0Gy_rep_1


title: Tissue_model_Epi_200_0.5Gy_250_500_um_rep3


title: Tissue_model_Epi_200_16h_0Gy_rep_1


title: Tissue_model_Epi_200_0.5Gy_750_1000_um_rep2


title: Tissue_model_Epi_200_4h_0.1Gy_rep_3


title: Tissue_model_Epi_200_0.5Gy_500_750_um_rep2


title: Tissue_model_Epi_200_0Gy_750_1000_um_rep3


title: Tissue_model_Epi_200_0Gy_500_750_um_rep2


title: Tissue_model_Epi_200_0.5Gy_250_500_um_rep2


title: Tissue_model_Epi_200_4h_2.5Gy_rep_1


title: Tissue_model_Epi_200_0.5Gy_500_750_um_rep3


title: Tissue_model_Epi_200_0.5Gy_750_1000_um_rep3


title: Tissue_model_Epi_200_0Gy_250_500_um_rep3


title: Tissue_model_Epi_200_0Gy_250_500_um_rep2


title: Tissue_model_Epi_200_4h_0Gy_rep_3


title: Tissue_model_Epi_200_0Gy_500_750_um_rep3


title: Tissue_model_Epi_200_2.5Gy_whole_tissue_rep1

description: Source of irradiation: protons

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with extended dynamic range, 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%).

source_name: human foreskin, male, epidermis, keratinocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and 16 h prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

treatment_protocol: Tissues were irradiated with 0 and 2.5Gy of protons

value: 2.5Gy whole-tissue


title: Tissue_model_Epi_200_2.5Gy_whole_tissue_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_whole_tissue_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0.5Gy_625_875_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_500_750_um_rep1


title: Tissue_model_Epi_200_0Gy_750_1000_um_rep1


title: Tissue_model_Epi_200_0.5Gy_250_500_um_rep1


title: Tissue_model_Epi_200_0Gy_whole_tissue_rep2

description: Source of irradiation: protons

value: 0Gy whole-tissue


title: Tissue_model_Epi_200_0.5Gy_500_750_um_rep1


title: Tissue_model_Epi_200_0Gy_whole_tissue_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_whole_tissue_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_125_375_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_375_625_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_625_875_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_125_375_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_250_500_um_rep1


title: Tissue_model_Epi_200_0Gy_375_625_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0.5Gy_625_875_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_125_375_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0.5Gy_625_875_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_625_875_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_125_375_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_125_375_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_375_625_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_375_625_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_625_875_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_375_625_um_rep4

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_375_625_um_rep3

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_125_375_um_rep2

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_375_625_um_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_125_375_um_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0.5Gy_625_875_um_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_375_625_um_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_0Gy_625_875_um_rep1

description: Source of irradiation: protons


title: Tissue_model_Epi_200_2.5Gy_125_375_um_rep1

description: Source of irradiation: protons


title: Lung_epithelium_smoke_donor_4

city: Loughborough

first: Iain

last: Dougall

address: Bakewell Road

country: United Kingdom

institute: AstraZeneca R&D Charnwood

hyb_protocol: Following fragmentation, cRNA was hybridized for on HGU133 plus2 human Affymetrix GeneChips according to standard protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were normalised using the Robust Multichip Average (RMA) algorithm in Bioconductor run in R v2.4.0. Statistical analyses were carried out in SAS v 9.2.

source_name: Air-liquid interface lung epithelial culture, cigarette smoke

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

growth_protocol: ALI cultures were maintained in proprietary MatTek media

extract_protocol: RNA was isolated using an RNAqueous-4PCR kit(Ambion AM1914).

treatment_protocol: Cultures were placed in smoking chambers with basal surface in contact with media. Cutures were subsequently exposed to smoke at a constant smoke/air dilution of 1:10 or 1:20. The cells were continually exposed to smoke (from filtered Kentucky reference (3R4F) cigarettes) for 30mins on days 1, 2, 5 and 6.

tag: age

tag: gender

value: Male

tag: ethnicity

value: Caucasian

tag: smoker status

value: Smoker


title: Lung_epithelium_smoke_donor_3

value: Female


title: Lung_epithelium_control_donor_4

source_name: Air-liquid interface lung epithelial culture, control


title: Lung_epithelium_smoke_donor_2

value: Non-smoker


title: Lung_epithelium_control_donor_1


title: 2427 tumor cell line

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description: Gene expression data from human primary cell line of SCC 2427

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® U133 Plus 2.0 in the Affymetrix GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1996] were used for pre-processing of the 6 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

source_name: human lung squamous cell carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix ROC technical manual 701021 Rev.5).

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturers’ instructions.

treatment_protocol: tumor tissue and lymph node metastasis were obtained from volunteer donors undergoing lung surgery for newly diagnosed NSCLC. Tissues were divided, snap frozen and stored at -80°C, and for cell isolation and culturing immediately placed on ice and prepared as described by Sugaya et al. with minor modifications

value: primary cell line

tag: cell line

value: 2427 tumor cell line


title: Lung_epithelium_control_donor_2


title: 2427 tumor tissue

description: Gene expression data from human lung squamous cell carcinoma 2427

value: primary lung cancer

value: 2427 lung squamous cell carcinoma tumor tissue


title: Lung_epithelium_smoke_donor_1


title: Lung_epithelium_control_donor_3


title: Tissue_model_Epi_200_0Gy_750_1000_um_rep2


title: Tissue_model_Epi_200_0.5Gy_750_1000_um_rep1


title: Continuous Light: ZT44 - rep1

description:
B73 (Germplasm Name); PO:0009006 shoot, PO:0009025 leaf, (Organism Part); PO:0007131 seedling growth (Development Stage); garden soil (Growth Media).
Maize inbred B73
Circadian entrainment continuous light LL treatment

organism: Zea mays

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT44)

value: Continuous Light

value: leaf and shoot of seedling

tag: inbred line


title: 2hr_mated_rep5, GeneSpring GC-RMA

city: College Station

first: Ginger

last: Carney

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description:
I3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol using an Affymetrix GCS 3000 7G scanner.

data_processing: All 15 chips were analyzed simultaneously by 4 platforms (5 algorithms): dCHIP, GCOS, Bioconductor, GeneSpring GX 7.3.1. dChip uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM and PM procedures under default parameters. Expression values were also computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0). We also utilized the GC-RMA model-based algorithm in the R-language platform. Bioconductor provided the open source GCRMA and associated packages. In addition, we used the GCRMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies). Default normalization was the raw intensity value for each probe set on a chip divided by the overall median intensity value for that chip. This “pre-normalized” value was then divided by the median “pre-normalized” value for that specific probe set across all 15 chips in the experiment.

organism: Drosophila melanogaster

source_name: 2hr_male head_mated

label_protocol: Standard Affymetrix protocol.

growth_protocol: Stocks were maintained on cornmeal/sugar media at 25oC.

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

treatment_protocol: Virgin males were raised in groups of 20 or fewer flies at 25oC. On day 4, they were transferred to individual vials. On day 5, they were exposed to a virgin female, a cauterized virgin female fly, or no female. 2 hrs after the mated male finished copulating with the female, a male from each group was collected for RNA isolation.

tag: strain

value: isogenized Canton-S

value: male

value: head

value: 5 days

value: exposure to a virgin female fly

value: 2 hours


title: Continuous Light: ZT40 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT40)


title: 2106 lymph node tissue cell line

description: Gene expression data from human primary cell line of pulmonary lymph node 2106

value: 2106 lymph node tissue cell line


title: 2hr_mated_rep4, GeneSpring GC-RMA

description:
G3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Continuous Light: ZT32 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT32)


title: 2106 lymph node tissue

description: Gene expression data from human pulmonary lymph node 2106

value: pulmonary lymph node

value: 2106 lymph node tissue


title: Continuous Light: ZT36 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT36)


title: 2106 tumor cell line

description: Gene expression data from human primary cell line of SCC 2106

value: 2106 tumor cell line


title: 2hr_mated_rep3, GeneSpring GC-RMA

description:
C3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2106 tumor tissue

description: Gene expression data from human lung squamous cell carcinoma 2106

value: 2106  lung squamous cell carcinoma  tumor tissue


title: Continuous Light: ZT28 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT28)


title: 240min EGF treated MCF10A cells 240C

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

data_processing: Plier + lowess. For the PLIER I use the Affymetrix expression console 1.1. the lowess procedure used is a script i developed for multi-array correction, which is similar to a method published in: Ann L. Oberg Karla V. Ballman, Diane E. Grill and Terry M. Therneau. Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics, 20(16):2778â??2786, 2004.!Sample_data_row_count = 1384231

source_name: 240min EGF treated MCF10A cells

label_protocol: According to Affymetrix manual

growth_protocol: biological triplicates of low passage MCF10A cells (from ATCC) were cultured as described in (Katz M et al., Nat Cell Biol 2007), plated for 24h in cell culture medium without EGF, starved for 24h in DMEM/F12 with 1% horse serum and Pen/Strep, and then stimulated with EGF (20ng/ml) for 0,20,40,60,120,240,480 minutes.

extract_protocol: 5 Prime Perfect Pure RNA Extraction kit including DNAse digestion, followed by rRNA removal

treatment_protocol: EGF 20ng/ml

value: EGF treated

tag: treatment time(minutes)


title: 2hr_mated_rep2, GeneSpring GC-RMA

description:
B3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_mated_rep1, GeneSpring GC-RMA

description:
A3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Continuous Light: ZT24 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT24)


title: Continuous Light: ZT20 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT20)


title: 2hr_courtship_rep5, GeneSpring GC-RMA

description:
I2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

source_name: 2hr_male head_courtship

value: exposure to a cauterized virgin female fly


title: 2hr_courtship_rep4, GeneSpring GC-RMA

description:
G2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Continuous Light: ZT16 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT16)


title: 480min EGF treated MCF10A cells 480C

source_name: 480min EGF treated MCF10A cells


title: 2hr_courtship_rep1, GeneSpring GC-RMA

description:
A2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Continuous Light: ZT0 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT0)


title: 240min EGF treated MCF10A cells 240A


title: Continuous Light: ZT4 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT4)


title: 2hr_control_rep5, GeneSpring GC-RMA

description:
I1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

source_name: 2hr_male head_control

value: exposure to no female fly


title: 60min EGF treated MCF10A cells 60B

source_name: 60min EGF treated MCF10A cells


title: Mig-6 d/d liver-3

city: Grand Rapids

first: TaeHoon

last: Kim

state: Michigan

address: 333 Bostwick Avenue NE

department: Department of Obstetrics, Gynecology & Reproductive Biology

institute: Michigan State University College of Human Medicine

description: Gene expression data from Mig-6 d/d liver

hyb_protocol: Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

scan_protocol: Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

data_processing: All samples were defined using normalized dChIP values. We selected differentially expressed genes within each time exposure using two sample comparisons according to the following criteria lower bound of 90% confidence interval of fold change greater than 1.2 and an absolute value of difference between groups means greater than 50. After excluding expressed sequence tags with no functional annotation, differentially expressed genes were classified according to Gene Ontology function using Affymetrix annotation, literature search in PubMed, and Ingenuity Pathways Analysis (Ingenuity Systems Inc., Redwood City, CA).

source_name: Liver

label_protocol: Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)

growth_protocol: Animals were maintained on a 12-h light/12-h dark cycle (0600 h/1800 h) and fed standard chow diet.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA) manufactures instructions as described.

treatment_protocol: Eight week old Mig-6f/f and Mig-6d/d male mice were assessed after undergoing a 24 hour fast.

tag: genotype

value: Mig-6 d/d

value: Male

value: 8 weeks old

value: mixed background


title: Continuous Light: ZT12 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT12)

tag: treatment

value: Continuous Light

value: leaf and shoot of seedling


title: Continuous Light: ZT8 - rep1

source_name: shoot, PO:0009025 leaf (Continuous Light: ZT8)

tag: tissue


title: 40min EGF treated MCF10A cells 40C

source_name: 40min EGF treated MCF10A cells


title: 2hr_courtship_rep2, GeneSpring GC-RMA

description:
B2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: male

value: head

value: 5 days


title: 2hr_control_rep3, GeneSpring GC-RMA

description:
C1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: 2 hours


title: 120min EGF treated MCF10A cells 120A

source_name: 120min EGF treated MCF10A cells


title: Mig-6 d/d liver-1


title: 120min EGF treated MCF10A cells 120C


title: 2hr_control_rep4, GeneSpring GC-RMA

description:
G1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 40min EGF treated MCF10A cells 40B


title: 60min EGF treated MCF10A cells 60C


title: 480min EGF treated MCF10A cells 480B


title: 2hr_control_rep2, GeneSpring GC-RMA

description:
B1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_control_rep1, GeneSpring GC-RMA

description:
A1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 60min EGF treated MCF10A cells 60A


title: Mig-6 f/f liver-3

description: Gene expression data from Mig-6 f/f liver

value: Mig-6 f/f


title: Mig-6 f/f liver-2


title: 240min EGF treated MCF10A cells 240B


title: Mig-6 f/f liver-1


title: 2hr_mated_rep3, R/Bioconductor GC-RMA

source_name: 2hr_male head_mated

value: exposure to a virgin female fly


title: 40min EGF treated MCF10A cells 40A


title: 2hr_mated_rep4, R/Bioconductor GC-RMA

description:
G3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_mated_rep5, R/Bioconductor GC-RMA

description:
I3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_mated_rep2, R/Bioconductor GC-RMA


title: 2hr_mated_rep1, R/Bioconductor GC-RMA


title: 2hr_courtship_rep4, R/Bioconductor GC-RMA


title: 2hr_courtship_rep5, R/Bioconductor GC-RMA


title: HetFlk-1PRa+(DP)rep2

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

department: Stem Cell Biology

country: Japan

institute: RIKEN CDB

description: Day5 HetFlk-1PRa+(DP)ES

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm using the R/Bioconductor package (R version 2.8.0, Bioconductor version 2.3).

label_protocol: The 3'IVT Express Kit was used for biotin labeling according to manufacturer's instructions (Affymetrix)

growth_protocol: Etv2+/- and -/- ES cells differentiated to Flk-1+ cells. Flk-1+/PDGFRa+ (DP)cells were sorted to compare gene expression in Etv2+/- or -/- DP cells.

extract_protocol: Extract RNA from sorted cells using Micro-elute RNA extraction Kit (Qiagen)

treatment_protocol: ES cells( Etv2+/- vs. -/- ) differentiated to Flk-1+/PDGFRa+ (DP)cells.

tag: cell-line


title: 2hr_courtship_rep3, GeneSpring GC-RMA

description:
C2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 20min EGF treated MCF10A cells 20B

source_name: 20min EGF treated MCF10A cells


title: Flk-1+/Etv2-rep2

source_name: Etv2-Venus ES Day5OP9

growth_protocol: Etv2-Venus knock-in Het ES cells differentiated to Flk-1+ cells.

treatment_protocol: Diffrerntiated Flk-1+ cells were separately sorted into  Flk-1+/Etv2- (P3) and  Flk-1+/Etv2+ (P4) populations


title: HetFlk-1PRa+(DP)rep1


title: 20min EGF treated MCF10A cells 20A


title: 480min EGF treated MCF10A cells 480A


title: 20min EGF treated MCF10A cells 20C


title: 2hr_courtship_rep3, R/Bioconductor GC-RMA


title: 120min EGF treated MCF10A cells 120B


title: Flk-1+/Etv2+rep2


title: Flk-1+/Etv2+rep1


title: Mig-6 d/d liver-2


title: KO Flk-1PRa+(DP)rep1

description: Day5KO Flk-1PRa+(DP)ES

source_name: KO Flk-1PRa+(DP)ES


title: untreated MCF10A cells 0C

source_name: untreated MCF10A cells

value: untreated


title: KO Flk-1PRa+(DP)rep2

description: Day5KO Flk-1PRa+(DP)ES


title: untreated MCF10A cells 0A

data_processing: Plier + lowess. For the PLIER I use the Affymetrix expression console 1.1. the lowess procedure used is a script i developed for multi-array correction, which is similar to a method published in: Ann L. Oberg Karla V. Ballman, Diane E. Grill and Terry M. Therneau. Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics, 20(16):2778â??2786, 2004.


title: 2hr_mated_rep5, MAS5.0


title: 2hr_mated_rep4, MAS5.0


title: 2hr_courtship_rep2, R/Bioconductor GC-RMA

source_name: 2hr_male head_courtship


title: 2hr_courtship_rep1, R/Bioconductor GC-RMA


title: 2hr_control_rep1, R/Bioconductor GC-RMA


title: 2hr_control_rep4, R/Bioconductor GC-RMA


title: untreated MCF10A cells 0B


title: 2hr_mated_rep1, MAS5.0


title: 2hr_courtship_rep5, MAS5.0


title: 2hr_mated_rep2, MAS5.0