title: E_coli_AL151_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 151 cultured in vitro.


title: 1,500(1) CFU, t=3h, replicate 3

status: Public on Nov 16 2010

type: genomic

city: Nijmegen

first: Peter

last: Burghout

address: Kapittelweg 29

department: Laboratory of Pediatric Infectious Diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: n.a.

hyb_protocol: Fluorescently labeled DNA probes were combined and hybridized in Slidehyb buffer 1 (Ambion) to pneumococcal microarrays, which are super-amine glass slides spotted with duplicates of amplicons representing 2,087 S. pneumoniae TIGR4 ORFs and 184 ORFs unique to R6 (PMID: 16787930 ).The microarrays were incubated for 16 hours at 45°C, and then washed with 2xSSC (Invitrogen) containing 0.25% SDS for 5 min, followed by 2 washes in 1xSSC and 0.5xSSC for 5 min each. Finally, slides were dipped into H2O and dried by centrifugation.

scan_protocol: Dual channel array images were acquired on a GenePix 4200AL microarray scanner and analyzed with GenePix Pro software (Axon Instruments, Union City, CA, USA). Spots were screened visually to identify those of low quality.

data_processing: Microarray scan files were analyzed with GenePix Pro software (Axon Instruments, Union City, CA). Spots were screened visually to identify those of low quality and removed from the data set prior to analysis. A net mean intensity filter based on hybridization signals obtained with oligomer-spots representing open reading frames unique for S. pneumoniae strain R6 that were present on the pneumococcal microarray as well, was applied in all experiments. Slide data were processed and normalized using MicroPreP Slide data were processed and normalized using MicroPreP as described (PMID: 15130795). Further analysis was performed using a Cyber-T implementation of the Student’s t test (cybert.microarray.ics.uci.edu). This web-based program lists the ratios of all intra-replicates (duplicate spots) and inter-replicates (different slides), the mean ratios per gene, and standard deviations and (Bayesian) p values assigned to the mean ratios. For identification of conditionally essential genes, only genes with a minimum of 6/8 reliable measurements and a Bayesian p-value < 0.001 were included.

molecule: genomic DNA

organism: Streptococcus pneumoniae

source_name: GAF control 1,500(1) CFU mutant library

label_protocol: Chromosomal DNA extracts was digested with AluI (New England Biolabs). The resulting DNA fragments were used as a template for an in vitro T7 RNA polymerase reaction (T7 MegaScript, Ambion). After removal of template DNA by DNAseI treatment, fluorescent Cy3/Cy5-labeled dUTP nucleotides (GE Healthcare) were incorporated by reverse transcription using Superscript III (Invitrogen).

growth_protocol: Control and CSF samples obtained during the experimental rabbit meningitis experiments were defrosted, diluted in GM17 medium supplemented with spectinomycin, and grown to mid-log phase.

extract_protocol: Chromosomal DNA was isolated from pneumococcal cultures by cetyl-trimethylammonium bromide (CTAB) extraction as described previously (PMID: 8057895).

tag: strain

value: TIGR4 marinerT7 mutant library

tag: mutant library size

tag: sample type

value: control

source_name: GAF 1,500(1) CFU mutant library t=3h replicate 3

value: CSF


title: 1,000 CFU, t=15h, replicate 3

description: n.a.

source_name: GAF control 1,000 CFU mutant library

treatment_protocol: Chromosomal DNA extracts was digested with AluI (New England Biolabs). The resulting DNA fragments were used as a template for an in vitro T7 RNA polymerase reaction (T7 MegaScript, Ambion). After removal of template DNA by DNAseI treatment, fluorescent Cy3/Cy5-labeled dUTP nucleotides (GE Healthcare) were incorporated by reverse transcription using Superscript III (Invitrogen).

source_name: GAF 1,000 CFU mutant library t=15h replicate 3


title: 1,500(1) CFU, t=3h, replicate 1

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=3h replicate 1


title: E_coli_AL151_vitro_rep1

type: RNA

city: Ann Arbor

first: Harry

last: Mobley

state: MI

address: 5641 Medical Sciences II  1150 W. Medical Center Dr.

country: USA

institute: University of Michigan

description: First of three biological replicates of E. coli patient isolate 151 cultured in vitro.

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

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

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

molecule: total RNA

organism: Escherichia coli

source_name: Escherichia coli, 151, vitro

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

extract_protocol: Total RNA was extracted using the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the RNeasy Mini kit (Qiagen) and DNA was removed by TURBO DNase digestion (Ambion Inc., Austin, TX, USA). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer at the University of Michigan Affymetrix and Microarray Core Facility (University of Michigan Medical School, Ann Arbor, MI USA) and RNA concentration determined with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Rockford, IL, USA).

tag: isolate

tag: condition

value: urine in vitro culture


title: 1,000 CFU, t=15h, replicate 4

description: n.a.

source_name: GAF 1,000 CFU mutant library t=15h replicate 4


title: E_coli_AL051_vitro_rep2

description: Second of three biological replicates of E. coli patient isolate 051 cultured in vitro.

source_name: Escherichia coli, 051, vitro


title: E_coli_AL051_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 051 cultured in vitro.


title: 1,000 CFU, t=9h, replicate 2

description: n.a.

source_name: GAF 1,000 CFU mutant library t=9h replicate 2


title: 1,500(1) CFU, t=3h, replicate 2

description: n.a.

source_name: GAF 1,500(1) CFU mutant library t=3h replicate 2


title: 1,000 CFU, t=9h, replicate 3

description: n.a.

source_name: GAF 1,000 CFU mutant library t=9h replicate 3


title: E_coli_AL051_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 051 cultured in vitro.


title: 1,000 CFU, t=3h, replicate 4

description: n.a.

source_name: GAF 1,000 CFU mutant library t=3h replicate 4


title: E_coli_AL121_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 121 cultured in vitro.

source_name: Escherichia coli, 121, vitro


title: E_coli_AL291_vitro_rep3

description: Third of three biological replicates of E. coli patient isolate 291 cultured in vitro.

source_name: Escherichia coli, 291, vitro


title: 1,000 CFU, t=15h, replicate 2

description: n.a.

source_name: GAF 1,000 CFU mutant library t=15h replicate 2


title: skin_1Gy_24h_rep2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Tecnical replicate 2 of 2; 1 Gy 24h

hyb_protocol: The labeled aRNAs (Cy3 sample and Cy5 sample mixed) were added to 50 µl of hybridization buffer containing 50% formamide, 10X SSC, 0.2% SDS. After hybridization, slides were washed sequential

scan_protocol: Scanned on an PerkinElmer ScanArray Lite scanner. Images were quantified using ScanArray Express and GenePix Pro 6.1 software

data_processing: LOWESS normalized, median background intensity subtraction, with Goulphar script running on R software. We filtered the data to exclude artifacts, saturated spots, and low signal spots

organism: Mus musculus

source_name: mouse irradiated skin, 1 Gy, 24h

label_protocol: 1 µg of total RNA was amplified and labeled with Cy3 or Cy5 using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification Kit (AM1753, Applied Biosystems/Ambion, Austin, TX)

extract_protocol: Total RNA extracted using TriPure Isolation Reagent (Roche, Indianapolis, IN) following manufacturer's instructions

tag: gender

value: Male

tag: age

value: three months old

tag: tissue

value: skin

source_name: mouse skin sham-irradiated


title: 1,000 CFU, t=3h, replicate 2

description: n.a.

source_name: GAF 1,000 CFU mutant library t=3h replicate 2


title: 1,000 CFU, t=3h, replicate 3

description: n.a.

source_name: GAF 1,000 CFU mutant library t=3h replicate 3


title: E_coli_AL121_vitro_rep1

description: First of three biological replicates of E. coli patient isolate 121 cultured in vitro.


title: E_coli_AL121_vitro_rep2

description: Second of three biological replicates of  E. coli patient isolate 121 cultured in vitro.


title: 1,000 CFU, t=9h, replicate 1

description: n.a.

source_name: GAF control 1,000 CFU mutant library

source_name: GAF 1,000 CFU mutant library t=9h replicate 1


title: 1,000 CFU, t=9h, replicate 4

description: n.a.

source_name: GAF 1,000 CFU mutant library t=9h replicate 4


title: 1,000 CFU, t=15h, replicate 1

description: n.a.

source_name: GAF 1,000 CFU mutant library t=15h replicate 1


title: skin_0.2Gy_24h_rep2

description: Tecnical replicate 2 of 2; 0.2 Gy 24h

source_name: mouse irradiated skin, 0.2 Gy, 24h


title: Sarda, 1st animal

city: Bologna

first: Pier Luigi

last: Martelli

address: via Irnerio 42

institute: University of Bologna

hyb_protocol: NimbleGen Hybridization Kit

scan_protocol: NimbleGen MS 200 Microarray Scanner with default parameters

data_processing: Data normalization was conducted using the normalize.qsline method from the Bioconductor package in R. Then data were analysed for each hybridization using normalized log2 ratios using the CGHweb server.

organism: Ovis aries

source_name: Reference Sheep (Sarda)

label_protocol: NimbleGen Dual-Color DNA Labeling Kit

extract_protocol: Wizard® Genomic DNA Purification kit (Promega Corporation, Madison, WI) extraction protocol

tag: breed

value: Sarda

value: female

source_name: Test Sheep (Sarda, animal 1)


title: skin_0.2Gy_6h_rep2

description: Tecnical replicate 2 of 2; 0.2 Gy 6h

source_name: mouse irradiated skin, 0.2 Gy, 6h


title: skin_0.2Gy_6h_rep1

description: Tecnical replicate 1 of 2; 0.2 Gy 6h


title: Valle del Belice

source_name: Test Sheep (Valle del Belice)

value: Valle del Belice


title: human tumor A06

city: Paris

first: Laure

last: Gibault

address: 26 rue d'Ulm

country: France

institute: Curie Institute

description: Gene expression data from human tumor samples

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm using dChip 2008 (5/8/08)

label: biotin

organism: Homo sapiens

source_name: Human soft tissue sarcoma

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies)

value: frozen tumor

value: Female


title: Massese, 2nd animal

source_name: Test Sheep (Massese, animal 2)

value: Massese


title: 1,000 CFU, t=3h, replicate 1

description: n.a.

source_name: GAF 1,000 CFU mutant library t=3h replicate 1


title: 110

city: New York

first: Edgar

middle: D.

last: Charles

state: NY

address: 1230 York Avenue, Box 64

department: Virology and Infectious Disease

institute: Rockefeller University

hyb_protocol: Illumina Hybridization protocol performed at 48 C

scan_protocol: Illumina BeadChip Protocol

data_processing:
The GeneSpring normalization procedure was as follows:
Threshold raw signals were set to 1.0.
Raw signals were scaled to the 50th percentile.
Baseline transformation was not applied.

source_name: peripheral IgM+CD27+ B Cell

label_protocol: UNG biotinylation

extract_protocol: Rneasy Plus Micro Kit (QIAgen); NUGEN WT-Ovation Amplification

tag: hcvab+

value: Y

tag: hcv rna+

tag: igm mc+


title: skin_1Gy_6h_rep1

description: Tecnical replicate 1 of 2; 1 Gy 6h

source_name: mouse irradiated skin, 1 Gy, 6h


title: Sarda, 2nd animal

source_name: Test Sheep (Sarda, animal 2)


title: Brain of day 5 of the pupa

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

country: China

institute: Southwest University

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for reference samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: Scanned on an confocal LuxScan 10 KA scanner (CapitalBio Corp.). The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from imagines using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing.
The one with signal intensity lower than 800 after subtracting the background was considered as an unexpressed gene since signal at that detection level was not reliable.

organism: Bombyx mori

source_name: Brain of day 5 of the pupa

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the Institute of Sericulture and System Biology (Southwest University, China) were reared on mulberry leaves at 25°C-26°C

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

value: Mix-sex

value: Brain

tag: developmental stage

value: day 5 of the pupa

source_name: Whole body of day 6 of the fifth instar larva

value: Whole body

value: the fifth instar larva


title: Massese (1st animal)

source_name: Test Sheep (Massese, animal 1)


title: skin_1Gy_6h_rep2

description: Tecnical replicate 2 of 2; 1 Gy 6h

source_name: mouse skin sham-irradiated


title: skin_0.2Gy_24h_rep1

description: Tecnical replicate 1 of 2; 0.2 Gy 24h


title: LDU 125


title: 1931


title: ECH 537

value: N


title: cell line LMS148L

description: Gene expression data from cell line

source_name: cell line dirived from human soft tissue sarcomas

tag: cell line


title: AEPC, rep2

city: Sendai

first: Hiroshi

last: Kubo

address: 2-1 Seiryoumachi, Aobaku

department: Advanced Preventive Medicine for Infectious Disease

country: Japan

institute: Tohoku University Graduate School of Medicine

description: AEPC-2 at passage 4, H-13A

hyb_protocol: The purified and fragmented cRNA (12.5 μg) was hybridized to GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). The array was incubated for 16 hours at 45°C, then automatically washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The probe array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console (Affymetrix).

source_name: AEPC-2 at passage4

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA according to the manufacturer's protocol using GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: AEPCs were isolated on feeders of mitotically inactivated mouse embryonic fibroblasts in DMEM/10%FCS/1% amino acids. AEPCs were maintained with feeder-conditioned medium on a plastic dish.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) and cleaned up using miRNeasy mini kit (Qiagen, Tokyo, Japan)

value: human distal lung

value: 78 years old

value: male

tag: number


title: skin_1Gy_24h_rep1

description: Tecnical replicate 1 of 2; 1 Gy 24h

source_name: mouse irradiated skin, 1 Gy, 24h

value: Male

value: three months old

value: skin


title: cell line S19L

description: Gene expression data from cell line


title: Laticauda, 2nd animal

source_name: Reference Sheep (Sarda)

value: Sarda

value: female

source_name: Test Sheep (Laticauda, animal 2)

value: Laticauda


title: AEPC, rep1

description: AEPC-1 at passage 4, H-2

source_name: AEPC-1 at passage4

value: 69 years old


title: human tumor A02

value: frozen tumor

value: Female


title: Comisana, 1st animal

source_name: Test Sheep (Comisana, animal 1)

value: Comisana


title: Brain of day 1 of the pupa

source_name: Brain of day 1 of the pupa

value: Mix-sex

value: Brain

value: day 1 of the pupa


title: ECH 542

value: Y

value: N


title: Laticauda, 1st animal

source_name: Test Sheep (Laticauda, animal 1)


title: genetic line: QxSM097 - treatment: Mock - rep1

status: Public on Nov 15 2010

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:
qxsm097 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

hyb_protocol: Affymetrix standard protocol:  Eukaryotic Target Hybridization

scan_protocol: Affymetrix standard protocol:  Array Scanning

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

organism: Hordeum vulgare

source_name: (genetic line: QxSM097 - treated or untreated: Mock)

label_protocol: Affymetrix standard protocol: Eukaryotic Target Preparation

growth_protocol: Growth Description:  Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated with stem rust isolate TTKS (Ug99), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.  Environmental Conditions:  St. Paul 2007, Cereal Disease Lab GH#1 & #10

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: genetic line

value: seedling


title: donor 3_TX527 sample

city: Leuven

first: Femke

last: Baeke

address: O&N1, Herestraat 49 box 902

department: Experimental Medicine

country: Belgium

institute: Katholieke Universiteit Leuven

hyb_protocol: Fragmented biotinylated cRNA (10 µg) was hybridized overnight to the Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained with Streptavidin-phycoerytrin on an automated Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 GeneScanner.

data_processing: The image files (.dat) were analyzed using Affymetrix GCOS Software and the RMA-algorithm (Expression console software) was used to calculate the signal intensities for each probe cell (.cel file).

source_name: Human activated T cells, treated with TX527 (10-8M)

label_protocol: Total RNA (500 ng) was reverse-transcribed into cDNA using the IVT express kit (Affymetrix, Santa Clara, CA, USA) with oligo-dT primers containing a T7 RNA polymerase  promoter site. cDNA was further in vitro transcribed to cRNA and biotin labeled, according to Affymetrix user manual 702646Rev.8. Biotinylated cRNA was purified and fragmented. The quality of labeled and fragmented cRNA, respectively, was assessed with the Agilent 2100 Bioanalyzer.

growth_protocol: Human CD3+ T lymphocytes were activated in culture plates coated with anti-CD3/anti-CD28. Every second day, cells were split and supplemented with IL-2 (12.5 ng/ml).

extract_protocol: Total RNA was extracted using the High Pure RNA Isolation kit (Roche, Mannheim, Germany), according to the manual.

treatment_protocol: From day 2 on, cells were treated with TX527 (10-8M) or vehicle (ethanol) every other day until day 10.

tag: donor

value: peripheral blood

tag: cell type

value: CD3+ T lymphocytes

tag: agent

tag: dose


title: donor 2_TX527 sample


title: donor 1_TX527 sample


title: Comisana, 2nd animal

source_name: Test Sheep (Comisana, 2nd animal)


title: donor 2_control sample

source_name: Human activated T cells, treated with vehicle

value: control (ethanol vehicle)


title: AEPC, rep3

description: AEPC-3 at passage 4, H-14

source_name: AEPC-3 at passage4

value: human distal lung

value: 59 years old

value: male


title: donor 4_control sample


title: genetic line: QxSM095 - treatment: Mock - rep1

description:
qxsm095 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM095 - treated or untreated: Mock)


title: Brain of day 3 of the pupa

source_name: Brain of day 3 of the pupa

tag: strain

value: day 3 of the pupa

source_name: Whole body of day 6 of the fifth instar larva

value: Whole body

value: the fifth instar larva


title: LDU 128

source_name: peripheral IgM+CD27+ B Cell


title: NaCl Stress (0.1 M) vs. Control Slide 5

city: San Antonio

first: Wenbo

last: Zhang

state: TX

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

institute: The University of Texas Health Science Center at San Antonio

description: In vitro transcriptome of M. genitalium in the presence of 0.1 M NaCl

hyb_protocol: We exactly followed the protocol "Microbial Hybridization of Labeled Probes" from http://pfgrc.jcvi.org/index.php/microarray/protocols.html.

scan_protocol: The slides were scanned with a GenePix 4000B microarray scanner at 10-µm resolution. PMT voltages were adjusted using GenePix Pro 6.0 to obtain maximal signal intensities of each feature with a saturation of <0.005% and count ratio close to 1.0.

data_processing: The images was gridded and processed using GenePix Pro 6.0 to obtain signal intensity for each spot. The data were further imported into and analyzed by Acuity 4.0 software. VALUE is log2 ratio median pixel intensity (local - background) between test and reference. No further processing.

organism: Mycoplasmoides genitalium

source_name: Mycoplasma genitalium stressed with 0.1 M NaCl

label_protocol: We followed the protocol "Microbial RNA Aminoallyl Labeling" from http://pfgrc.jcvi.org/index.php/microarray/protocols.html. Briefly, 4 µg of total RNA were reverse transcribed into cDNA using a set of gene-specific primers in the presence of aminoallyl-labeled dUTP (2:1 ratio of aa-dUTP to dTTP). The cDNA obtained was cleaned with Qiagen MinElute column and labeled with Cy3 dye

growth_protocol: M. genitalium was grown to log phase in SP-4 medium. A stock of 5 M NaCl was added to the medium to the final concentratioin of 0.1 M. Continue to grow at 37 C for 1 hour

extract_protocol: Total RNA was extracted using the Tri Reagent per the manufacturer's instructions. RNA was further cleaned up with RNeasy Mini Column. RNA samples were then quantified using OD260.

tag: stress

value: 0.1 M NaCl

source_name: Mycoplasma genitalium control

label_protocol: We followed the protocol "Microbial RNA Aminoallyl Labeling" from http://pfgrc.jcvi.org/index.php/microarray/protocols.html. Briefly, 4 µg of total RNA were reverse transcribed into cDNA using a set of gene-specific primers in the presence of aminoallyl-labeled dUTP (2:1 ratio of aa-dUTP to dTTP). The cDNA obtained was cleaned with Qiagen MinElute column and labeled with Cy5 dye

growth_protocol: M. genitalium was grown to log phase in SP-4 medium. Without NaCl treatment. Continue to grow at 37 C for 1 hour

value: control


title: genetic line: QxSM095 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM095 - treated or untreated: Inoculated - Pgt TTKS)


title: Bagnolese, 1st animal

source_name: Reference Sheep (Sarda)

value: Sarda

tag: gender

value: female

source_name: Test Sheep (Bagnolese, animal 1)

value: Bagnolese


title: Brain of day 7 of the fifth instar larva

value: Mix-sex

value: Brain

value: day 7 of the fifth instar larva


title: genetic line: QxSM091 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm091 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM091 - treated or untreated: Inoculated - Pgt TTKS)

value: seedling


title: genetic line: QxSM091 - treatment: Mock - rep1

source_name: (genetic line: QxSM091 - treated or untreated: Mock)


title: genetic line: QxSM090 - treatment: Mock - rep1

description:
qxsm090 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM090 - treated or untreated: Mock)


title: donor 5_TX527 sample

value: peripheral blood

value: CD3+ T lymphocytes


title: donor 4_TX527 sample


title: Bagnolese, 2nd animal

source_name: Test Sheep (Bagnolese, animal 2)


title: NaCl Stress (0.1 M) vs. Control Slide 1

growth_protocol: M. genitalium was grown to log phase in SP-4 medium. A stock of 5 M NaCl was added to the medium to the final concentratioin of 0.2 M. Continue to grow at 37 C for 1 hour


title: NaCl Stress (0.1 M) vs. Control Slide 3


title: donor 5_control sample

source_name: Human activated T cells, treated with TX527 (10-8M)

value: control (ethanol vehicle)


title: donor 3_control sample


title: genetic line: QxSM097 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM097 - treated or untreated: Inoculated - Pgt TTKS)


title: donor 1_control sample

source_name: Human activated T cells, treated with vehicle


title: NaCl Stress (0.2 M) vs. Control Slide 6

description: In vitro transcriptome of M. genitalium in the presence of 0.2 M NaCl

source_name: Mycoplasma genitalium stressed with 0.2 M NaCl

value: 0.2 M NaCl


title: genetic line: QxSM088 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm088 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM088 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM094 - treatment: Mock - rep1

description:
qxsm094 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM094 - treated or untreated: Mock)


title: genetic line: QxSM094 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM094 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM093 - treatment: Mock - rep1

description:
qxsm093 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM093 - treated or untreated: Mock)


title: genetic line: QxSM087 - treatment: Mock - rep1

description:
qxsm087 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM087 - treated or untreated: Mock)


title: NaCl Stress (0.2 M) vs. Control Slide 4

source_name: Mycoplasma genitalium control


title: NaCl Stress (0.3 M) vs. Control Slide 6

description: In vitro transcriptome of M. genitalium in the presence of 0.3 M NaCl

source_name: Mycoplasma genitalium stressed with 0.3 M NaCl

growth_protocol: M. genitalium was grown to log phase in SP-4 medium. A stock of 5 M NaCl was added to the medium to the final concentratioin of 0.3 M. Continue to grow at 37 C for 1 hour

value: 0.3 M NaCl


title: genetic line: QxSM087 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM087 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM085 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm085 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM085 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM086 - treatment: Mock - rep1

description:
qxsm086 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM086 - treated or untreated: Mock)


title: genetic line: QxSM086 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM086 - treated or untreated: Inoculated - Pgt TTKS)


title: NaCl Stress (0.3 M) vs. Control Slide 5


title: NaCl Stress (0.3 M) vs. Control Slide 4


title: genetic line: QxSM093 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM093 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM083 - treatment: Mock - rep1

description:
qxsm083 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM083 - treated or untreated: Mock)


title: genetic line: QxSM082 - treatment: Mock - rep1

description:
qxsm082 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM082 - treated or untreated: Mock)


title: genetic line: QxSM082 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM082 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM084 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm084 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM084 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM078 - treatment: Mock - rep1

description:
qxsm078 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM078 - treated or untreated: Mock)


title: genetic line: QxSM080 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm080 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM080 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM077 - treatment: Mock - rep1

description:
qxsm077 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM077 - treated or untreated: Mock)


title: genetic line: QxSM078 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM078 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM080 - treatment: Mock - rep1

source_name: (genetic line: QxSM080 - treated or untreated: Mock)


title: NaCl Stress (0.1 M) vs. Control Slide 4

description: In vitro transcriptome of M. genitalium in the presence of 0.1 M NaCl

source_name: Mycoplasma genitalium stressed with 0.1 M NaCl


title: genetic line: QxSM076 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm076 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM076 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM070 - treatment: Mock - rep1

description:
qxsm070 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM070 - treated or untreated: Mock)


title: genetic line: QxSM073 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm073 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM073 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM070 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM070 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM089 - treatment: Mock - rep1

description:
qxsm089 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM089 - treated or untreated: Mock)


title: NaCl Stress (0.1 M) vs. Control Slide 2

source_name: Mycoplasma genitalium control


title: genetic line: QxSM089 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM089 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM088 - treatment: Mock - rep1

description:
qxsm088 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM088 - treated or untreated: Mock)


title: genetic line: QxSM090 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm090 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM090 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM068 - treatment: Mock - rep1

description:
qxsm068 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM068 - treated or untreated: Mock)


title: NaCl Stress (0.2 M) vs. Control Slide 5

description: In vitro transcriptome of M. genitalium in the presence of 0.2 M NaCl

source_name: Mycoplasma genitalium stressed with 0.2 M NaCl


title: genetic line: QxSM066 - treatment: Mock - rep1

description:
qxsm066 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM066 - treated or untreated: Mock)


title: genetic line: QxSM067 - treatment: Mock - rep1

description:
qxsm067 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM067 - treated or untreated: Mock)


title: genetic line: QxSM066 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM066 - treated or untreated: Inoculated - Pgt TTKS)


title: NaCl Stress (0.2 M) vs. Control Slide 3


title: genetic line: QxSM065 - treatment: Mock - rep1

description:
qxsm065 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM065 - treated or untreated: Mock)


title: NaCl Stress (0.2 M) vs. Control Slide 2


title: genetic line: QxSM065 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM065 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM063 - treatment: Mock - rep1

description:
qxsm063 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM063 - treated or untreated: Mock)


title: NaCl Stress (0.2 M) vs. Control Slide 1


title: genetic line: QxSM063 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM063 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM085 - treatment: Mock - rep1

description:
qxsm085 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM085 - treated or untreated: Mock)


title: genetic line: QxSM084 - treatment: Mock - rep1

description:
qxsm084 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM084 - treated or untreated: Mock)


title: genetic line: QxSM062 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm062 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM062 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM060 - treatment: Mock - rep1

description:
qxsm060 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM060 - treated or untreated: Mock)


title: genetic line: QxSM059 - treatment: Mock - rep1

description:
qxsm059 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM059 - treated or untreated: Mock)


title: NaCl Stress (0.3 M) vs. Control Slide 2

description: In vitro transcriptome of M. genitalium in the presence of 0.3 M NaCl

source_name: Mycoplasma genitalium control

source_name: Mycoplasma genitalium stressed with 0.3 M NaCl


title: NaCl Stress (0.3 M) vs. Control Slide 1


title: genetic line: QxSM059 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM059 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM061 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm061 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM061 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM057 - treatment: Mock - rep1

description:
qxsm057 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM057 - treated or untreated: Mock)


title: NaCl Stress (0.3 M) vs. Control Slide 3


title: genetic line: QxSM058 - treatment: Mock - rep1

description:
qxsm058 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM058 - treated or untreated: Mock)


title: genetic line: QxSM083 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm083 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM083 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM079 - treatment: Mock - rep1

description:
qxsm079 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM079 - treated or untreated: Mock)


title: genetic line: QxSM058 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM058 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM057 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM057 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM056 - treatment: Mock - rep1

description:
qxsm056 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM056 - treated or untreated: Mock)


title: genetic line: QxSM052 - treatment: Mock - rep1

description:
qxsm052 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM052 - treated or untreated: Mock)


title: genetic line: QxSM054 - treatment: Mock - rep1

description:
qxsm054 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM054 - treated or untreated: Mock)


title: genetic line: QxSM079 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM079 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM077 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm077 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM077 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM050 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm050 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM050 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM075 - treatment: Mock - rep1

description:
qxsm075 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM075 - treated or untreated: Mock)


title: genetic line: QxSM075 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM075 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM049 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm049 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM049 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM076 - treatment: Mock - rep1

description:
qxsm076 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM076 - treated or untreated: Mock)


title: genetic line: QxSM054 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM054 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM049 - treatment: Mock - rep1

source_name: (genetic line: QxSM049 - treated or untreated: Mock)


title: genetic line: QxSM069 - treatment: Mock - rep1

description:
qxsm069 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM069 - treated or untreated: Mock)


title: genetic line: QxSM047 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm047 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM047 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM074 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm074 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM074 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM073 - treatment: Mock - rep1

description:
qxsm073 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM073 - treated or untreated: Mock)


title: genetic line: QxSM069 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM069 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM050 - treatment: Mock - rep1

source_name: (genetic line: QxSM050 - treated or untreated: Mock)


title: genetic line: QxSM052 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM052 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM047 - treatment: Mock - rep1

source_name: (genetic line: QxSM047 - treated or untreated: Mock)


title: genetic line: QxSM048 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm048 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM048 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM045 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm045 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM045 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM046 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm046 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM046 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM067 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm067 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM067 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM074 - treatment: Mock - rep1

source_name: (genetic line: QxSM074 - treated or untreated: Mock)


title: genetic line: QxSM068 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm068 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM068 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM043 - treatment: Mock - rep1

description:
qxsm043 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM043 - treated or untreated: Mock)


title: genetic line: QxSM042 - treatment: Mock - rep1

description:
qxsm042 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM042 - treated or untreated: Mock)


title: genetic line: QxSM042 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM042 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM062 - treatment: Mock - rep1

description:
qxsm062 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM062 - treated or untreated: Mock)


title: Pt#36

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: patient's CD34+ cells DNA hybridized against its own T cells DNA

hyb_protocol: According to the manufactuer's recommendations.

scan_protocol: Human 105K arrays were scanned with Agilent G2505B Micro-Array Scanner System. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. All arrays were then treated by the WACA algorithm [Lepretre et al., NAR 2010]. This algorithm was used to remove all false aberrations, without modifying real aberrations, allowing efficient further analysis. CGH analytics software V3.4, the Human Genome built 17 and the database of Genomic Variants built 36 (March 2006) were at last used for copy number detection and analysis.

source_name: Pt#36, CD34+ cells

label_protocol: manufacturer's instructions

extract_protocol: For each patient, CD34+ and T-lymphocytes (CD3+) cell separation from bone marrow and peripheral blood samples respectively were performed by positive-selection magnetic beads sorting using a MiniMACS device (Miltenyi Biotec Auburn, CA) according to the manufacturer’s instructions. DNAs were obtained using the QIAmp mini kit system (QIAGEN, Hilden, Germany) and whole genome amplification (GenomePlex Complete Whole Genome Amplification Kit, Sigma-Aldrich, Saint Louis) was performed according to the manufactuer’s recommendations. WGA DNAs from T-cells were used as references for the CGH array experiment, which was achieved using Agilent Human Genome 105K CGH oligonucleotide arrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s recommendations.

tag: group

value: Imatinib responder

value: CD34+ cells

source_name: Pt#36, T cells

value: T cells


title: Pt#34

source_name: Pt#34, CD34+ cells

source_name: Pt#34, T cells


title: genetic line: QxSM060 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm060 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM060 - treated or untreated: Inoculated - Pgt TTKS)

tag: tissue


title: genetic line: QxSM061 - treatment: Mock - rep1

description:
qxsm061 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM061 - treated or untreated: Mock)


title: genetic line: QxSM055 - treatment: Mock - rep1

description:
qxsm055 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM055 - treated or untreated: Mock)


title: genetic line: QxSM056 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm056 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM056 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM055 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM055 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM037 - treatment: Mock - rep1

description:
qxsm037 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM037 - treated or untreated: Mock)


title: Pt#35

source_name: Pt#35, CD34+ cells

source_name: Pt#35, T cells


title: Pt#33

source_name: Pt#33, CD34+ cells

source_name: Pt#33, T cells


title: Pt#32

source_name: Pt#32, CD34+ cells

source_name: Pt#32, T cells


title: genetic line: QxSM037 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM037 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM036 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm036 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM036 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM048 - treatment: Mock - rep1

source_name: (genetic line: QxSM048 - treated or untreated: Mock)


title: genetic line: QxSM046 - treatment: Mock - rep1

source_name: (genetic line: QxSM046 - treated or untreated: Mock)


title: genetic line: QxSM039 - treatment: Mock - rep1

description:
qxsm039 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM039 - treated or untreated: Mock)


title: genetic line: QxSM045 - treatment: Mock - rep1

source_name: (genetic line: QxSM045 - treated or untreated: Mock)


title: genetic line: QxSM041 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm041 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM041 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM036 - treatment: Mock - rep1

source_name: (genetic line: QxSM036 - treated or untreated: Mock)


title: genetic line: QxSM038 - treatment: Mock - rep1

description:
qxsm038 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM038 - treated or untreated: Mock)


title: genetic line: QxSM043 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM043 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM035 - treatment: Mock - rep1

description:
qxsm035 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM035 - treated or untreated: Mock)


title: genetic line: QxSM038 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM038 - treated or untreated: Inoculated - Pgt TTKS)


title: Pt#30

source_name: Pt#30, CD34+ cells

source_name: Pt#30, T cells


title: Pt#29

source_name: Pt#29, CD34+ cells

source_name: Pt#29, T cells


title: genetic line: QxSM033 - treatment: Mock - rep1

description:
qxsm033 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM033 - treated or untreated: Mock)


title: genetic line: QxSM034 - treatment: Mock - rep1

description:
qxsm034 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM034 - treated or untreated: Mock)


title: Pt#31

source_name: Pt#31, CD34+ cells

source_name: Pt#31, T cells


title: genetic line: QxSM033 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM033 - treated or untreated: Inoculated - Pgt TTKS)


title: Pt#27

source_name: Pt#27, CD34+ cells

source_name: Pt#27, T cells


title: genetic line: QxSM031 - treatment: Mock - rep1

description:
qxsm031 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM031 - treated or untreated: Mock)


title: genetic line: QxSM034 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM034 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_UPC2_rep6

city: Dublin

first: Alessandro

last: Guida

address: belfield

country: Ireland

institute: University College Dublin

hyb_protocol: Purified cDNA was denatured at 95 degree Celsius  for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software. The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

organism: Candida albicans

source_name: Total RNA from Candida albicans UPC2 delete TW14920, grown in YPD medium at 30 degree celsius at 1% Oxygen.

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg/μl with RNase free water. A mixture of 24 μg  RNA, 2 μl Candida albicans specific RT primers mix (0.1 pmol μl (Eurogentec)) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-3 (Cy3) dye. A mixture of 8 μll 5X  First Strand buffer, 4 μll 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1 μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy3 (Cy3-dCTP from Amersham Biosciences, 25 nmol) or Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg ml-1) and 1 μl NRase H (0.05 units ml-1) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures of C. albicans TW14920  (at 21% oxygen) were diluted to an A600 of 0.2 in 50 ml of YPD medium pre-conditioned with 1% oxygen, and culture was incubated at 200 rpm at 30 degrees and 1% oxygen for 3.5 hours.

extract_protocol: RNA was isolated using a RiboPure Yeast kit (Ambion)

tag: age

value: 3 h

tag: growth condition

value: 30 degree Celsius and 1% Oxygen.

tag: medium

tag: genotype

value: UPC2 deletion

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius at 1% Oxygen.

growth_protocol: Overnight cultures of C. albicans DAY286  (at 21% oxygen) were diluted to an A600 of 0.2 in 50 ml of YPD medium pre-conditioned with 1% oxygen, and culture was incubated at 200 rpm at 30 degrees and 1% oxygen for 3.5 hours.

value: 30 degree Celsius and 1% oxygen

value: YPD medium preconditioned overnight at 1% Oxygen.

value: wild type


title: Pt#28

source_name: Pt#28, CD34+ cells

source_name: Pt#28, T cells


title: genetic line: QxSM035 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM035 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_UPC2_rep5

value: YPD medium preconditioned overnight at 1% Oxygen


title: genetic line: QxSM041 - treatment: Mock - rep1

source_name: (genetic line: QxSM041 - treated or untreated: Mock)


title: Candida_albicans_UPC2_rep9


title: genetic line: QxSM039 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM039 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM031 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM031 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_UPC2_rep4


title: Pt#26

source_name: Pt#26, CD34+ cells

source_name: Pt#26, T cells


title: Candida_albicans_UPC2_rep8


title: Pt#25

source_name: Pt#25, CD34+ cells

value: Imatinib resistant

source_name: Pt#25, T cells


title: genetic line: QxSM030 - treatment: Mock - rep1

description:
qxsm030 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM030 - treated or untreated: Mock)

value: seedling


title: Candida_albicans_UPC2_rep3


title: Candida_albicans_UPC2_rep2


title: Candida_albicans_ketoconazole_rep4

source_name: Total RNA from Candida albicans DAY286, grown in YPD medium at 30 degree celsius supplemented with 10 μl 100% ethanol.

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg/μl with RNase free water. A mixture of 24 μg  RNA, 2 μl Candida albicans specific RT primers mix (0.1 pmol μl-1 (Eurogentec)) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-5 (Cy5) dye. A mixture of 8 μl 5X  First Strand buffer, 4 μl 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1 μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) or Cy3 (Cy3-dCTP from Amersham Biosciences, 25 nmol)was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg ml-1) and 1 μl NRase H (0.05 units/ml) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium supplemented  with 10 μl 100% ethanol, and culture was incubated at 200 rpm at 30 degree for 3.5 hours.

value: 30 degree Celsius supplemented with 10 μl 100% ethanol.

value: YPD medium

tag: treatment

value: ethanol

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius supplemented with 0.04 μg/ml ketoconazole.

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium supplemented  with 0.04 μg/ml ketoconazole, and culture was incubated at 200 rpm at 30 degree for 3.5 hours.

value: 30 degree Celsius supplemented with 0.04 μg/ml ketoconazole.

value: ketoconazole


title: Pt#23

source_name: Pt#23, CD34+ cells

source_name: Pt#23, T cells


title: genetic line: QxSM028 - treatment: Mock - rep1

description:
qxsm028 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM028 - treated or untreated: Mock)


title: Candida_albicans_UPC2_rep1

source_name: Total RNA from Candida albicans UPC2 delete TW14920, grown in YPD medium at 30 degree celsius at 1% Oxygen.

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius at 1% Oxygen.


title: genetic line: QxSM029 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm029 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM029 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_UPC2_rep7


title: Pt#19

description: patient's CD34+ cells DNA hybridized against its own T cells DNA

source_name: Pt#19, CD34+ cells

source_name: Pt#19, T cells


title: genetic line: QxSM026 - treatment: Mock - rep1

description:
qxsm026 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM026 - treated or untreated: Mock)


title: Pt#20

source_name: Pt#20, CD34+ cells

source_name: Pt#20, T cells


title: Pt#17

source_name: Pt#17, CD34+ cells

source_name: Pt#17, T cells


title: Pt#24

source_name: Pt#24, CD34+ cells

source_name: Pt#24, T cells


title: Pt#21

source_name: Pt#21, CD34+ cells

source_name: Pt#21, T cells


title: Pt#18

source_name: Pt#18, CD34+ cells

source_name: Pt#18, T cells


title: Pt#22

source_name: Pt#22, CD34+ cells

source_name: Pt#22, T cells


title: genetic line: QxSM030 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM030 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM028 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM028 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM029 - treatment: Mock - rep1

source_name: (genetic line: QxSM029 - treated or untreated: Mock)


title: Candida_albicans_ketoconazole_rep2

source_name: Total RNA from Candida albicans DAY286, grown in YPD medium at 30 degree celsius supplemented with 10 μl 100% ethanol.

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius supplemented with 0.04 μg/ml ketoconazole.


title: genetic line: QxSM026 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM026 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_ketoconazole_rep1


title: genetic line: QxSM023 - treatment: Mock - rep1

description:
qxsm023 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM023 - treated or untreated: Mock)


title: genetic line: QxSM023 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM023 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM019 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm019 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM019 - treated or untreated: Inoculated - Pgt TTKS)


title: Candida_albicans_ketoconazole_rep3


title: Candida_albicans_normoxia_vs_hypoxia_rep7

hyb_protocol: Purified cDNA was denatured at 95 degree celsius for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software.

source_name: Total RNA from Candida albicans DAY286, grown in YPD medium at 30 degree celsius and 21% oxygen (normoxia).

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg /μl with RNase free water. A mixture of 24 μg  RNA, 2 μl Candida albicans specific RT primers mix (0.1 pmol μl-1 (Eurogentec)) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-5 (Cy5) dye. A mixture of 8 μl 5X  First Strand buffer, 4 μl 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1  μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg/ml) and 1 μl NRase H (0.05 units /ml) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium at 21% oxygen (normoxia), and culture was incubated at 200 rpm at 30 degrees celsius for 3.5 hours.

value: normoxia

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius and 1% oxygen (hypoxia)

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium at 1% oxygen (hypoxia), and culture was incubated at 200 rpm at 30 degree for 3.5 hours.

value: 30 degree Celsius and 1% oxygen (hypoxia).

value: hypoxia


title: Pt#15

source_name: Pt#15, CD34+ cells

value: CD34+ cells

source_name: Pt#15, T cells

value: T cells


title: Candida_albicans_normoxia_vs_hypoxia_rep8

value: 30 degree celsius and 21% oxygen (normoxia).


title: Candida_albicans_normoxia_vs_hypoxia_rep4


title: genetic line: QxSM019 - treatment: Mock - rep1

source_name: (genetic line: QxSM019 - treated or untreated: Mock)


title: Candida_albicans_normoxia_vs_hypoxia_rep3


title: Candida_albicans_normoxia_vs_hypoxia_rep5


title: Pt#16

source_name: Pt#16, CD34+ cells

source_name: Pt#16, T cells


title: Pt#9

source_name: Pt#9, CD34+ cells

source_name: Pt#9, T cells


title: Pt#14

source_name: Pt#14, CD34+ cells

source_name: Pt#14, T cells


title: Pt#10

source_name: Pt#10, CD34+ cells

source_name: Pt#10, T cells


title: Candida_albicans_normoxia_vs_hypoxia_rep6


title: Pt#13

source_name: Pt#13, CD34+ cells

source_name: Pt#13, T cells


title: Candida_albicans_normoxia_vs_hypoxia_rep1