title: TRPM2-AS siRNA rep4

city: Milano

first: Giovanni

last: Lavorgna

address: Via Olgettina, 60

country: Italy

institute: Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan 500 System.

data_processing: Data were normalized using the Rank Invariant normalization algorithm implemented on the Illumina BeadStudio software, using all probes on the array for the extraction of the rank invariant set of transcripts. After normalization, the expression dataset was further corrected by setting the bottom threshold signal to 140. This value was estimated from background noise obtained using Illumina negative controls, representing an estimation of both  the image background and the signals derived from non-specific binding or cross-hybridization. Differential expression of transcripts was assesed using the limma package (http://www.bioconductor.org/packages/release/bioc/html/limma.html).

source_name: TRPM2-AS siRNA

growth_protocol: Media: DMEM, 2mM L-Glutamine and 10% Fetal Bovine Serum.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PC3 cells were transfeted  either a non-specific siRNA or with a TRPM2-AS siRNA in replicates for 48 hours.

value: TRPM2-AS siRNA


title: norm-VUB-1008-AMQ-72-R-2-1_(HG-U133_Plus_2).CEL

status: Public on Sep 01 2014

type: RNA

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Treatment with AMQ

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. As the number of controls were less than the number of treatments, the same controls were used several to normalize data from several treatments.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepaRG cell line

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: The human hepatoma-derived HepaRG cells (Biopredic International, France) were cultivated as previously described  by A. Guillouzo et al. 168 (2007) 66-73.  and P. Gripon et al 99 (2002) 15655-15660. At day 13 of cultivation, dimethylsulfoxide (DMSO)-containing medium (2%) was added for 7 days . At day 19 exposure with the selected compounds was initiated.

extract_protocol: Samples for RNA isolation were collected after 24 and 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: The cells were individually exposed to 15 prototypical compounds for 24h and 72 hours at IC10 concentrations, i.e. 5 GTX (N-nitrosomorpholine, NMP, IC10=0.216mM; Hydroquinone, HQO, IC10=0.15mM; Hydrazine dihydrochloride, HHC, IC10=0.86mM; 2-acetylaminofluorene, TAF, IC10=0.0408mM; 2-amino-3-methylimidazo(4,5-f)quinoline, AMQ, IC10=0.003mM), 5 NGTX (Fumonisin B1, FMB, IC10=2.4mM; Cyclosporine A, CsA, IC10=0.0026mM; Acetamide, ACE, IC10=5.9; Diethylhexyl Phthalate, DHP, IC10=10mM; Ethanol, ETH, IC10=10mM), 5 NC (4-acetylaminofluorene, FAF, IC10=0.22; D,L-Menthol, DLM, IC10=1.2mM; Benzoin, BEN, IC10=0.345mM; Benzyl Alcohol, BEA, IC10=6.5mM; Triclosan, TRI, IC10=0.022mM).

tag: cell line

value: HepaRG cell line

tag: treatment

value: Treatment with AMQ

tag: replicate


title: TRPM2-AS siRNA rep2

label_protocol: Standard Illumina hybridization protocol.


title: norm-VUB-1007-AMQDMSO-72-R-1-1K_(HG-U133_Plus_2).CEL

description: Control AMQ

value: Control AMQ


title: norm-VUB-1007-BEA-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA

value: Treatment with BEA


title: synchronous colorectal cancer sample_5628

type: genomic

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: synchronous colorectal cancer :5628

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 and beta-value correction using metillumi R package

label: Cy5 and Cy3

molecule: genomic DNA

source_name: tumor colorectal tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Frozen samples were thawed and genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

extract_protocol: Frozen tumor colorectal tissues were obtained at surgery from all patients, and immediately stored at -80º until use. In patients with multiple lesions, tissue sample was obtained from one of the tumors (the most advanced or the largest one when multiple tumors had the same tumor stage)

treatment_protocol: Bisulfite treatment was carried out on genomic DNA using the EZ DNA Methylation-Gold Kit (Zymo Research, Orange, CA) according to the manufacturer’s protocol.

tag: type colorectal cancer

value: synchronous colorectal cancer

tag: gender

value: Male

tag: age (years)

tag: tumor location

value: distal

tag: cimp-h/l status

value: CIMP-H

tag: kras mutation status

value: wild type


title: norm-VUB-1009-AMQ-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with AMQ


title: norm-VUB-1009-BEA-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA


title: synchronous colorectal cancer sample_5063

description: synchronous colorectal cancer :5063

value: mutated


title: control siRNA rep2

source_name: control siRNA

value: control siRNA


title: control siRNA rep3


title: norm-VUB-1009-AMQDMSO-24-R-3-1A_(HG-U133_Plus_2).CEL

description: Control AMQ


title: control siRNA rep4


title: norm-VUB-1007-AMQ-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with AMQ


title: TRPM2-AS siRNA rep1


title: TRPM2-AS siRNA rep3


title: 2426 anoxic 4

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum regR mutant grown anoxically in completely filled bottles

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2.2 µg of labeled cDNA  were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium japonicum

source_name: B. japonicum regR mutant grown in anoxic conditions

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: B. japonicum cells were grown anoxically in Bergersen minimal medium (Bergersen 1977) with 10 mM succinate as carbon source and 10 mM nitrate (BSN minimal medium). Cells were first grown oxically in PSY medium, washed and further grown anoxically in BSN minimal medium to an optical density at 600 (OD600) of about 0.4. Anoxic conditions were obtained by incubation in completely filled bottles.

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

tag: strain

tag: genotype

value: delta regR mutant

tag: growth condition

value: anoxic

tag: medium

value: BSN


title: norm-VUB-1009-AMQDMSO-72-R-3-1F_(HG-U133_Plus_2).CEL

description: Control AMQ


title: 2426 anoxic 3


title: norm-VUB-1007-AMQDMSO-24-R-1-1E_(HG-U133_Plus_2).CEL

description: Control AMQ


title: norm-VUB-1008-AMQDMSO-24-R-2-1A_(HG-U133_Plus_2).CEL

description: Control AMQ


title: control siRNA rep1


title: norm-VUB-1008-AMQ-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with AMQ


title: norm-VUB-1007-AMQ-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with AMQ


title: norm-VUB-1009-DMSO-72-R-3-1F_(HG-U133_Plus_2).CEL

description: Control ACE

value: Control ACE


title: 2426 anoxic 1


title: norm-VUB-1009-AMQ-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with AMQ


title: 110spc4 anoxic 3

description: B. japonicum wild type grown anoxically in completely filled bottles

source_name: B. japonicum wildtype grown in anoxic conditions


title: 2426 anoxic 2


title: norm-VUB-1007-DMSO-24-R-1-1G_(HG-U133_Plus_2).CEL

description: Control BEA

value: Control BEA


title: 110spc4 anoxic 2


title: norm-VUB-1008-DMSO-72-R-2-1F_(HG-U133_Plus_2).CEL

description: Control ACE


title: 110spc4 anoxic 1


title: norm-VUB-1007-DMSO-72-R-1-1K_(HG-U133_Plus_2).CEL

description: Control ACE


title: norm-VUB-1009-ACE-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE

value: Treatment with ACE


title: 110spc4 anoxic 4


title: norm-VUB-1008-ACE-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE

value: HepaRG cell line


title: Whole blood_001-099-003-2007-B

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

country: USA

institute: Wayne State University

description: Dried blood spots for Pb and DNA methylation study

hyb_protocol: As described by Illumina for Human methylation 450K assay

data_processing:
Sample normalization done using Bioconductor package ChAMP. Type1 to type 2 probe bias correction was done using Beta mixed interquantile range normalization. Based on gender differences in DNA methylation profile the representative DNA methylation loci was divided into conserved female specific and male specific regions. The CpG sites show highly correlated changes in methylation signatures and can be defined as co-regulated regions. The co-regulated regions were assigned to specified clusters using the A-clustering algorithm (Sofer et al 2013). The association between Pb concentration measured in dried blood spot and DNA methylation of coregulated region for conserved female specific and male specific regions was calculated using Generalized estimating equations (GEE) (Sofer et al  2013)
Rawdata_signal_intensities.txt reports Unmethylated and methylated signal intensities (Pre-normalization)

label: Cy3, Cy5

source_name: whole blood (dried blood spots)

extract_protocol: DNA was isolated from dried blood spots with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. The Stains on Fabric preprocessing and Trace® (tip-dance) instrument protocol was used for isolation.

tag: race

tag: normalizedpbconc

tag: age (in months)

tag: mother's age (in months)

tag: gestational age (in months)

tag: smoking (0=no, 1=yes)


title: J_176_T1_pool10

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

description: Gene expression after 176 days in jejunum of T1 pigs

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies) The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The porcine Agilent microarray slides, G2519F Sus scrofa (035953; V2: 026440), harbouring 43,803 probes, were used and scanned using the DNA microarray scanner with Surescan high resolution Technology (Agilent Technologies). Agilent Scan Control with resolution of 5µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

organism: Sus scrofa

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling. The input was 10 ng of total RNA and 600 ng of labelled cRNA was used on the 8 pack array.

extract_protocol:
Blood: PAXgene Blood RNA tube from PreAnalytiX (a Qiagen/BD company). Tubes were thawed for 2 hours at room temperature (RT). Subsequently tubes were centrifuged at 3,200x g for 10 minutes at RT and the supernatant was discarded
Tissue: Total RNA was extracted from 50 to 100 mg tissue samples of jejunum and ileum. The jejunum and ileum samples were homogenized using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenized tissue samples were dissolved in 5ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube.

treatment_protocol: Treatment 1 (T1), no disturbance of piglets and only handled at the time of drawing blood at day 8. Treatment 2 (T2), injection (subcutaneously in the neck) with 0,1 ml Tulathromycine (dosage was 2.5 mg/kg [1mL/40 kg] body weight) at day 4 after birth. Treatment 3 (T3), injection with 0,1 ml Tulathromycine at day 4 and the standard management procedures (i.e. docking, clipping and weighing) used at that particular farm (VIC Sterksel, The Netherlands)

tag: tissue

value: jejunum

tag: treatment

tag: age

value: 176 days


title: J_176_T1_pool12


title: Whole blood_001-019-003-2007-B

scan_protocol: As described by Illumina for Human methylation 450K assay

tag: gender


title: J_176_T1_pool11


title: norm-VUB-1009-DMSO-24-R-3-1A_(HG-U133_Plus_2).CEL

description: Control ACE

tag: cell line

tag: replicate


title: norm-VUB-1007-ACE-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE


title: norm-VUB-1008-DMSO-24-R-2-1A_(HG-U133_Plus_2).CEL

description: Control ACE


title: norm-VUB-1007-DMSO-24-R-1-1E_(HG-U133_Plus_2).CEL

description: Control ACE


title: J_176_T2_pool8

description: Gene expression after 176 days in jejunum of T2 pigs


title: Whole blood_001-121-002-2007-B

label_protocol: As described by Illumina for Human methylation 450K assay

value: Female


title: J_176_T2_pool6


title: Whole blood_001-036-001-2007-B


title: norm-VUB-1009-ACE-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE


title: Whole blood_001-025-001-2007-B


title: Whole blood_001-019-001-2006-B


title: J_176_T2_pool5


title: J_176_T1_pool9


title: Whole blood_001-130-002-2007-B


title: norm-VUB-1008-ACE-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE


title: Whole blood_001-015-004-2008-B


title: Whole blood_001-036-003-2008-B


title: Whole blood_001-130-001-2007-B


title: norm-VUB-1007-ACE-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with ACE


title: J_176_T3_pool4

description: Gene expression after 176 days in jejunum of T3 pigs


title: J_176_T3_pool3


title: J_176_T3_pool1


title: Whole blood_001-092-001-2009-B


title: Whole blood_001-015-002-2010-B


title: I_176_T1_pool12

description: Gene expression after 176 days in ileum of T1 pigs

value: ileum


title: Whole blood_001-118-002-2009-B


title: I_176_T1_pool11


title: J_176_T3_pool2


title: I_176_T2_pool7

description: Gene expression after 176 days in ileum of T2 pigs


title: I_176_T1_pool10


title: I_176_T1_pool9


title: I_176_T2_pool8


title: Whole blood_001-015-006-2009-B


title: I_176_T2_pool5


title: Whole blood_001-095-001-2009-B

value: Male


title: Whole blood_001-036-005-2009-B


title: Whole blood_001-022-001-2008-B


title: I_176_T2_pool6


title: I_176_T3_pool3

description: Gene expression after 176 days in ileum of T3 pigs


title: J_55_T1_pool12

description: Gene expression after 55 days in jejunum of T1 pigs

value: 55 days


title: I_176_T3_pool2


title: Whole blood_001-122-001-2010-B


title: Whole blood_001-045-001-2008-B


title: Whole blood_001-079-002-2010-B


title: J_55_T1_pool10


title: J_55_T1_pool11


title: I_176_T3_pool4


title: Whole blood_001-082-001-2009-B


title: Whole blood_001-022-003-2010-B

value: Mixed


title: Whole blood_001-087-002-2010-B


title: Whole blood_001-085-002-2011-B


title: Whole blood_001-027-002-2010-B


title: J_55_T2_pool7

description: Gene expression after 55 days in jejunum of T2 pigs


title: J_55_T2_pool6


title: Whole blood_001-010-002-2009-B


title: Whole blood_001-092-003-2010-B


title: J_55_T1_pool9


title: Whole blood_001-033-002-2010-B


title: J_55_T2_pool5


title: J_55_T3_pool4

description: Gene expression after 55 days in jejunum of T3 pigs


title: Whole blood_001-095-003-2011-B


title: Whole blood_001-060-002-2010-B


title: Whole blood_001-084-001-2011-B


title: J_55_T3_pool1


title: I_55_T1_pool12

description: Gene expression after 55 days in ileum of T1 pigs


title: Whole blood_001-099-001-2011-B


title: J_55_T3_pool3


title: B728a-salA_Apoplastic_LabC_Rep2

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IA

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

institute: Iowa State University

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

hyb_protocol: Hybridization was performed by Roche NimbleGen Inc., Reykjavík, Iceland, 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:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance estimates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356).

organism: Pseudomonas syringae

source_name: Pseudomonas syringae B728a salA mutant, Apoplastic cells

label_protocol: Labeling was performed by Roche NimbleGen Inc., Reykjavík, Iceland, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown on solid King’s B medium containing rifampin (50 μg/ml).  Cells were transferred to liquid HMM and subcultured twice in HMM with aeration via shaking at 25°C.  HMM medium contained 0.2% D-fructose, 0.2% D-mannitol, 0.2% succinate, 10 mM L-glutamine, 10 µM FeCl3, 10 µM N-(β-ketocaproyl)-L-homoserine lactone (AHL), 50 mM potassium phosphate buffer, 7.6 mM (NH4)2SO4, 1.7 mM MgCl2, and 1.7 mM NaCl.   When the cells reached late-log phase (5x108 CFU/ml), they were collected by centrifugation at 5,000xg for 10 min.

extract_protocol: In the in vitro treatments, RNA was stabilized using RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA).  In the in planta treatments, RNA was stabilized using an acidic phenol RNA stabilizing solution due to the large volumes required.  Total RNA was extracted from the cells using a Qiagen RNeasy mini kit and DNA was removed using the on-column DNase I digestion with subsequent DNase I removal.  RNA integrity was evaluated using an Agilent 2100 bioanalyzer.

treatment_protocol:
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.  Two of the in vitro samples are missing; these are the B728a ∆rpoS cells in the basal medium (replicate 2) and the B728a ∆retS cells exposed to low N (replicate 2).
For the in planta treatments, the HMM-grown cells were suspended in water, which contained 0.01% of the biosurfactant Silwet L-77, to a density of 1x106 CFU/ml for B728a, ΔahlR, ΔaefR, ΔgacS, ΔsalA, and ΔretS, to a density of 1x107 CFU/ml for ΔrpoS and ΔalgU, to a density of 1x108 CFU/ml for ΔhrpL, and to a density of 1x109 CFU/ml for ΔrpoN. The higher inoculum densities were to compensate for the reduced growth of the mutants in planta and to ensure sufficient RNA recovery.  One of the in planta treatment samples is missing: the B728a ∆rpoN cells recovered from the apoplast (replicate 2).
To establish epiphytic populations, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml for B728a, ΔahlR, ΔaefR, ΔgacS, ΔsalA, and ΔretS, to a density of 1x107 CFU/ml for ΔrpoS and ΔalgU, to a density of 1x108 CFU/ml for ΔhrpL, and to a density of 1x109 CFU/ml for ΔrpoN. The higher inoculum densities were to compensate for the reduced growth of the mutants in planta and to ensure sufficient RNA recovery.  The bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.
To establish apoplastic populations, the HMM-grown cells were suspended in water, which contained 0.01% of the biosurfactant Silwet L-77, to the same densities as for the epiphytic treatment, with the exception of the ΔrpoS mutant, for which 106 cells/ml were used. The bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

value: B728a salA mutant


title: B728a-salA_Epiphytic_LabC_Rep2

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a salA mutant, Epiphytic cells


title: B728a-salA_Apoplastic_LabC_Rep1


title: Whole blood_001-036-002-2011-B


title: Whole blood_001-122-002-2011-B


title: Whole blood_001-130-003-2012-B


title: J_55_T3_pool2


title: B728a-salA_Epiphytic_LabC_Rep1


title: Whole blood_001-093-002-2011-B


title: I_55_T1_pool11


title: I_55_T1_pool10


title: Whole blood_001-058-004-2010-B


title: B728a-salA_Low Fe_LabC_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a salA mutant, Iron limited


title: Whole blood_001-001-001-2012-B


title: B728a-salA_H2O2_LabC_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a salA mutant, Oxidative stress


title: B728a-salA_H2O2_LabC_Rep1


title: B728a-salA_Low N_LabC_Rep1

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a salA mutant, Nitrogen limited


title: B728a-salA_Low Fe_LabC_Rep1


title: B728a-salA_Basal medium_LabC_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a salA mutant, Basal medium


title: B728a-salA_NaCl_LabC_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a salA mutant, Osmotic stress


title: B728a-salA_Basal medium_LabC_Rep1


title: Whole blood_001-009-001-2012-B

description: Dried blood spots for Pb and DNA methylation study


title: Whole blood_001-010-001-2012-B


title: Whole blood_001-113-002-2012-B


title: B728a-gacS_Low Fe_LabC_Rep2

source_name: Pseudomonas syringae B728a gacS mutant, Iron limited

value: B728a gacS mutant


title: B728a-gacS_Low N_LabC_Rep1

source_name: Pseudomonas syringae B728a gacS mutant, Nitrogen limited


title: I_55_T3_pool4

description: Gene expression after 55 days in ileum of T3 pigs


title: B728a-gacS_Low N_LabC_Rep2


title: B728a-gacS_Epiphytic_LabC_Rep1

source_name: Pseudomonas syringae B728a gacS mutant, Epiphytic cells


title: B728a-salA_NaCl_LabC_Rep1


title: I_55_T3_pool3


title: I_55_T2_pool6

description: Gene expression after 55 days in ileum of T2 pigs


title: I_55_T2_pool5


title: B728a-salA_Low N_LabC_Rep2


title: Whole blood_001-033-001-2012-B


title: B728a-gacS_Low Fe_LabC_Rep1


title: B728a-gacS_Apoplastic_LabC_Rep2

source_name: Pseudomonas syringae B728a gacS mutant, Apoplastic cells


title: B728a-gacS_Epiphytic_LabC_Rep2


title: B728a-gacS_Apoplastic_LabC_Rep1


title: I_55_T2_pool7


title: I_55_T1_pool9


title: B728a-gacS_H2O2_LabC_Rep2

source_name: Pseudomonas syringae B728a gacS mutant, Oxidative stress


title: I_55_T3_pool1


title: I_55_T3_pool2


title: I_8_T3_pool4

description: Gene expression after 8 days in ileum of T3 pigs

value: 8 days


title: I_8_T1_pool11

description: Gene expression after 8 days in ileum of T1 pigs


title: I_8_T2_pool7

description: Gene expression after 8 days in ileum of T2 pigs


title: I_8_T1_pool12


title: Whole blood_001-051-001-2011-B


title: I_8_T3_pool1


title: J_8_T1_pool10

description: Gene expression after 8 days in jejunum of T1 pigs


title: J_8_T1_pool12


title: B728a-gacS_NaCl_LabC_Rep2

source_name: Pseudomonas syringae B728a gacS mutant, Osmotic stress


title: B728a-gacS_H2O2_LabC_Rep1


title: I_8_T3_pool3


title: J_8_T1_pool11


title: I_8_T2_pool6


title: J_8_T1_pool9


title: I_8_T3_pool2


title: B728a-retS_Apoplastic_LabC_Rep1

source_name: Pseudomonas syringae B728a retS mutant, Apoplastic cells

value: B728a retS mutant


title: I_8_T2_pool5


title: I_8_T1_pool9


title: I_8_T1_pool10


title: B728a-gacS_Basal medium_LabC_Rep2

source_name: Pseudomonas syringae B728a gacS mutant, Basal medium


title: B728a-gacS_Basal medium_LabC_Rep1


title: B728a-gacS_NaCl_LabC_Rep1


title: B728a-retS_Epiphytic_LabC_Rep2

source_name: Pseudomonas syringae B728a retS mutant, Epiphytic cells


title: B728a-retS_Epiphytic_LabC_Rep1


title: J_8_T2_pool8

description: Gene expression after 8 days in jejunum of T2 pigs


title: B728a-retS_Low N_LabC_Rep1

source_name: Pseudomonas syringae B728a retS mutant, Nitrogen limited


title: J_8_T2_pool5


title: B728a-retS_Apoplastic_LabC_Rep2


title: J_8_T2_pool6


title: J_8_T2_pool7


title: J_8_T3_pool3

description: Gene expression after 8 days in jejunum of T3 pigs


title: B728a-retS_Low Fe_LabC_Rep2

source_name: Pseudomonas syringae B728a retS mutant, Iron limited


title: B728a-retS_H2O2_LabC_Rep2

source_name: Pseudomonas syringae B728a retS mutant, Oxidative stress


title: B728a-retS_Low Fe_LabC_Rep1


title: B728a-retS_H2O2_LabC_Rep1


title: B728a-retS_Basal medium_LabC_Rep2

source_name: Pseudomonas syringae B728a retS mutant, Basal medium


title: B728a-retS_NaCl_LabC_Rep2

source_name: Pseudomonas syringae B728a retS mutant, Osmotic stress


title: B728a-retS_NaCl_LabC_Rep1


title: J_8_T3_pool1


title: BL_8_T1_pool9

description: Gene expression after 8 days in blood of T1 pigs

value: whole blood


title: BL_8_T1_pool12


title: J_8_T3_pool4


title: J_8_T3_pool2


title: B728a-retS_Basal medium_LabC_Rep1


title: BL_8_T1_pool10


title: B728a-WT_Apoplastic_LabC_Rep1

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a wild type, Apoplastic cells

value: Wild type


title: B728a-WT_Apoplastic_LabC_Rep2


title: BL_8_T2_pool6

description: Gene expression after 8 days in blood of T2 pigs


title: BL_8_T2_pool8


title: Colon_VSL#3_Day14_mouse4

city: San Francisco

first: Jordan

middle: Samuel

last: Mar

state: Ca

address: 513 Parnassus Ave., S-357

department: Medicine, Division of Gastroenterology

institute: University Of California, San Francisco

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_vsl_1230M4

hyb_protocol: Next, the labeled DNA was denatured at 99C for 5 min and hybridized to custom-made Affymetrix GeneChips (16S rRNA genes PhyloChips) at 48ºC and 60 rpm for 16 h. PhyloChip washing and staining were performed according to the standard Affymetrix protocols described previously (Masuda and Church 2002).

scan_protocol: Each PhyloChip was scanned and recorded as a pixel image, and initial data acquisition and intensity determination were performed using standard Affymetrix software (GeneChip microarray analysis suite, version 5.1).

data_processing:
Fluorescence intensities were normalized to spike-in control oligonucleotides provided by SecondGenome, Inc. (San Bruno, CA, USA) using the proprietary PhyCA processing technique developed by SecondGenome, Inc, which utilizes aggregate measures (“r scores”) that incorporate mismatch probe fluorescence intensity as well as distribution of total chip fluorescence. Quartile r score cutoffs were chosen based on r scores retrieved for control probes spiked-in at known concentrations, as recorded from all Phylochip microarrays of the current study, and were as follows: rQ1 > .38, rQ2 > .57, rQ3 > .82. For more information on normalization procedure, see Ivanov, II, et al. Cell 2009; 139:485-98.
Values in the sample data table represent total, normalized flourescence intensities for each OTU (Operational taxonomic unit) found present in at least on sample. These values are untransformed and represent a the relative abundance of the OTU in question.

organism: Mus musculus

source_name: Colon harvested on day 14 from VSL#3 treated animals

label_protocol: 500 ng of pooled PCR amplicons of each sample were spiked with known concentrations of amplicons derived from yeast and bacterial metabolic genes. This mix was fragmented to 50Ð200 bp using DNase I (0.02 U ug-1 DNA, Invitrogen, Carlsbad, CA, USA) and One-Phor-All buffer (GE Healthcare, Piscataway, NJ, USA) following the manufacturer's protocols. The mixture was then incubated at 25ºC for 20 min and 98C for 10 min before biotin labeling with a GeneChip DNA labeling reagent kit (Affymetrix, Santa Clara, CA, USA) following the manufacturer's instructions.

extract_protocol: Murine tissue was transferred to Lysis Matrix E (MP Biomedicals, OH) tubes containing 600ul RLT buffer (Qiagen, CA). Samples were subjected to 30 seconds of bead beating at 5.5 m/second, followed by centrifugation for one minute at 2000 rpm. Supernatant was transferred to the AllPrep DNA (Qiagen, CA) spin column and nucleic acid purification was carried out according to the manufacturer's instructions. Nucleic acid concentrations were determined using a NanoDrop spectophotometer (Thermo Scientific, MA).

tag: strain backgroudn

tag: experiment group

tag: experiment day

value: Colon


title: B728a-WT_Epiphytic_LabC_Rep1

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a wild type, Epiphytic cells

tag: genotype

tag: strain


title: BL_8_T2_pool5


title: B728a-WT_Epiphytic_LabC_Rep2


title: B728a-WT_Low N_LabC_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a wild type, Nitrogen limited


title: B728a-WT_Low N_LabC_Rep1


title: BL_8_T3_pool4

description: Gene expression after 8 days in blood of T3 pigs


title: BL_8_T3_pool3


title: BL_8_T1_pool11


title: BL_8_T2_pool7


title: Colon_MSC_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_msc_1230M5

source_name: Colon harvested on day 14 from MSC treated animals

value: MSC


title: BL_8_T3_pool2


title: Colon_VSL#3_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_vsl_1230M5


title: B728a-WT_Low Fe_LabC_Rep1

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a wild type, Iron limited


title: Colon_MSC_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_msc_1230M4


title: B728a-WT_H2O2_LabC_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Oxidative stress


title: Colon_DSS_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_dss_1230M4

source_name: Colon harvested on day 14 from DSS only treated animals

value: DSS


title: Colon_DSS_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_dss_1230M5_2


title: Colon_MSC_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_msc_1230M3


title: B728a-WT_Low Fe_LabC_Rep2


title: B728a-WT_NaCl_LabC_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Osmotic stress


title: B728a-WT_H2O2_LabC_Rep2


title: B728a-WT_NaCl_LabC_Rep1


title: B728a-WT_Basal medium_LabC_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Basal medium


title: Colon_DSS_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_dss_1230M3


title: Colon_DSS_Day10_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_dss_12.26M5

source_name: Colon harvested on day 10 from DSS only treated animals


title: B728a-WT_Basal medium_LabC_Rep1


title: BL_8_T3_pool1


title: Colon_DSS_Day10_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_dss_12.26M4_redo


title: Colon_VSL#3_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_VSL_12.30_3


title: B728a-aefR_Apoplastic_LabB_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a aefR mutant, Apoplastic cells

value: B728a aefR mutant


title: B728a-aefR_Epiphytic_LabB_Rep2

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a aefR mutant, Epiphytic cells


title: B728a-aefR_Apoplastic_LabB_Rep1


title: Colon_VSL#3_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_VSL_12.30_1


title: P014ISA

city: Tartu

first: Tauno

last: Metsalu

address: Liivi 2

country: Estonia

institute: University of Tartu

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina HiScan scanner, analysis was done using Genome Studio 2010 Genotyping module 1.8.4

data_processing: SNP calling was performed with GenomeStudio (2010.3) using 95% call rate criterion.

source_name: blood

label_protocol: Illumina Infinium HD Assay Kit

extract_protocol: Total RNA extraction from frozen placental tissue was performed using mirVana™ miRNA Isolation Kit (Ambion®, Life Technologies™), according to the manufacturer’s instructions.

tag: trio

tag: person

value: father


title: P013ISA


title: 138 Area4

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

country: Canada

institute: University of Guelph

description: control_C5.2    Treatment_T5.2

hyb_protocol: The resulting antisense RNA (825 ng per replicate) was hybridized on the Agilent-manufactured EmbryoGENE design slides (GLE13226). The hybridizations were done using a two color design with full dye-swap. Hybridization took place for 17 h at 65°C after which slides were washed for 1 min in gene Expression Wash Buffer 1 at room temperature and 3 min in gene Expression Wash Buffer 2 (42°C) following 10 sec in 100% acetonitrile (room temperature) and finally 30 sec in Stabilization and Drying Solution (Agilent).

scan_protocol: Slides were scanned with PowerScanner (Tecan) and features extraction was done with Array-pro6. (MediaCybernetics).

data_processing: Microarray data analysis was performed using the Flex Array version 1.6, Data were submitted to a Normexp background subtraction, Loess within array normalization, and finally statistically analyzed using the Limma R package (R version 2.12.1 and Limma version 3). Genes were considered differentially expressed between TH treated and untreated groups at a fold-change greater than 1.5 with a P-value <0.05.

organism: Bos taurus

source_name: control

label_protocol:
To perform microarray hybridization, purified RNA was amplified by two rounds of in vitro T7 transcription using the RiboAmp HSPlus RNA Amplification Kit (Life Science)
Amplified RNA labeled with Cy3 and Cy5 using the ULS Fluorescent Labeling Kit (Kreatech, Durham, NC,USA)

growth_protocol: Domestic cattle (Bos taurus) ovaries were collected from a government inspected abattoir (Guelph, ON, Canada). Oocytes were aspirated and subjected to IVM, IVF and IVC as previously described by Mastromonaco et al. (2006) and Favetta et al. (2007). In brief, cumulus-oocyte complexes (COCs) were collected from visible ovarian follicles by aspiration into HEPES-buffered Ham's F-10 plus 2% steer serum (Cansera; Rexdale, ON, Canada). Oocytes with several layers of cumulus cells and homogenous cytoplasm were then randomly assigned into control and treated groups. COCs were matured in 80µl drops of TCM199 medium + 2% steer serum (IVM) supplemented with 1µg/ml of estradiol, 0.5µg/ml of bFSH and 1µg/ml of bLH (NIH, Washington, DC, USA) (IVM + H) under silicone oil (Paisley Products, Scarborough, ON, Canada) for 20-22 h at 38.5°C in 5% CO2 in air. The media used for treated groups were supplemented with 50 ng/ml of both T3 and T4. Co-incubation with sperm was carried out in 80µl drops of IVF TALP under silicone oil (Paisley Products, Scarborough, ON, Canada) for 18 h at 38.5°C in 5% CO2 in air. Frozen-thawed sperm was prepared by swim-up in 5 ml of sperm TALP and centrifugation at 2000 rpm for 10 min. The oocytes were inseminated with a final concentration of 1x10^6 motile frozen-thawed sperm/ml (Gencor, Guelph, ON, Canada). After 18-20 h, the presumptive zygotes were stripped of remaining cumulus cells by vortexing and cultured in 30µl drops of synthetic oviductal fluid (SOF) (Chemicon-Millipore, Billerica, MA, USA) plus 200µl of non-essential amino acids, 100µl of essential amino acids (Invitrogen), 5µl of gentamicin (Invitrogen), 560 µl of EFAF BSA 15% in SOF and 200 µl of bovine steer serum under silicone oil at 38.5°C in 5% CO2, 5% O2, 90% N2 for 8- 9 days.

extract_protocol: Total RNA from each replicate was extracted and purified using the PicoPure RNA Isolation Kit (Life Science) as described by Robert et al. (Mol Reprod Dev, 2011, 78:651-664). After DNase digestion (Qiagen), RNA concentration and quality was assessed using a Bioanalyzer 2100 (Agilent) and the remaining sample was stored at -80°C.

tag: sample type

tag: breed (cattle)

value: beef

tag: compound added

tag: number per pool

value: 50ng/ml T3_T4


title: Colon_MSC_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_MSC_12.30_2

tag: tissue


title: B728a-aefR_Epiphytic_LabB_Rep1


title: P008ISA


title: P005ISA


title: B728a-aefR_Low N_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a aefR mutant, Nitrogen limited


title: B728a-aefR_Low N_LabB_Rep1


title: Colon_DSS_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_DSS_12.30_2


title: P012ISA


title: 137 Area4

description: control_C5.2    Treatment_T5.2


title: 138 Area1

description: control_C2.2    Treatment_T2.1


title: 138 Area2

description: control_C3.2    Treatment_T3.2


title: P007ISA


title: B728a-aefR_Low Fe_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a aefR mutant, Iron limited


title: P009ISA


title: Colon_MSC_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_MSC_12.30_1


title: Colon_DSS_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_DSS_12.30_1


title: P012EMA

value: mother


title: B728a-aefR_Low Fe_LabB_Rep1


title: P013EMA


title: 137 Area3

description: control_C4.1    Treatment_T4.1


title: P001ISA


title: 138 Area3

description: control_C4.1    Treatment_T4.1


title: 137 Area2

description: control_C3.2    Treatment_T3.2


title: P002ISA


title: Colon_DSS_Day10_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_DSS_12.26_2


title: B728a-aefR_H2O2_LabB_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a aefR mutant, Oxidative stress


title: P007EMA


title: B728a-aefR_H2O2_LabB_Rep2


title: Colon_CNTL_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_1230M5

source_name: Colon harvested on day 14 from control animals

value: CNTL


title: 137 Area1

description: control_C2.2    Treatment_T2.1


title: P005EMA


title: P014EMA


title: B728a-aefR_NaCl_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a aefR mutant, Osmotic stress


title: Colon_DSS_Day10_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_DSS_12.26M3_2


title: B728a-aefR_NaCl_LabB_Rep1


title: Colon_CNTL_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.30_1B


title: Colon_CNTL_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.30_3


title: P006ISA


title: P008EMA


title: B728a-aefR_Basal medium_LabB_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a aefR mutant, Basal medium


title: P002EMA


title: Colon_CNTL_Day1_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.17_4

source_name: Colon harvested on day 1 from control animals


title: C_5

city: New York

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

description:
Deciduous versus permanent teeth cells
SlideNumber: 70
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190070

hyb_protocol: Samples were hybridized overnight to topic-defined PIQORTM Stem Cell Microarrays Human Antisense using the a-HybTM Hybridization Station. Control samples were labeled with Cy3 and experimental samples were labeled with Cy5.

scan_protocol: Signals were detected using a laser scanner from Agilent (Agilent Technologies) and ImaGene software (Biodiscovery).

data_processing: Expression intensities were background-corrected using a convolution of normal and exponential distributions (normexp option in limma function backgroundCorrect) with an offset of 50, which were then normalized within every slide using loess normalization. red and green channels were analysed separately using the mixed model method and a different groups were quantile-normalized separately (Tquantile option in limma function normalizeBetweenArrays). The correlation was computed between the two channels for the same spot. Differentially expressed genes were identified by computing the contrasts, fitting to a linear model, performing the hypothesis tests, and correcting for multiple testing by performing the false discovery rate using the Benjamini-Hochberg correction (p ≤ 0.05)

source_name: C

label_protocol: Sample labeling was performed according to the PIQORTM User manual.

extract_protocol: RNA was extracted from passage one cells with the Qiagen Rneasy minikit. At 90% confluency cells were washed with PBS and then placed with lysis buffer following manufacturer protocol.

value: tooth pulp

tag: tooth type

value: permanent

tag: developmental stage

value: adult  (> 38 years)

source_name: SHED

value: deciduous

value: child (3-12 years)


title: B728a-aefR_Basal medium_LabB_Rep1


title: B728a-ahlR_Apoplastic_LabB_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a ahlR mutant, Apoplastic cells

value: B728a ahlR mutant


title: Colon_CNTL_Day1_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.17_3


title: P006EMA


title: Colon_CNTL_Day1_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.17_5


title: P009EMA


title: C_4

description:
Deciduous versus permanent teeth cells
SlideNumber: 69
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190069


title: B728a-ahlR_Apoplastic_LabB_Rep1


title: P001EMA


title: Colon_CNTL_Day1_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.17_1B


title: C_2

description:
Deciduous versus permanent teeth cells
SlideNumber: 65
Batch: 1
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190065

value: adult (> 38 years)


title: C_3

description:
Deciduous versus permanent teeth cells
SlideNumber: 68
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190068


title: Colon_CNTL_Day1_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_CNTL_12.17_2


title: Colon_DUAL_Day14_Mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_BOTH_1230M4

source_name: Colon harvested on day 14 from Dual treatment (VSL3 + MSC) animals

value: DUAL


title: C_1

description:
Deciduous versus permanent teeth cells
SlideNumber: 64
Batch: 1
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190064


title: Colon_DUAL_Day14_Mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_BOTH_1230M5

value: Colon


title: B728a-ahlR_Low N_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a ahlR mutant, Nitrogen limited


title: B728a-ahlR_Epiphytic_LabB_Rep1

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a ahlR mutant, Epiphytic cells


title: B728a-ahlR_Epiphytic_LabB_Rep2


title: BC_3

description:
Old versus young permanent cells
SlideNumber: 73
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190073

source_name: B

value: adult (< 21 years)


title: Colon_DUAL_Day14_Mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_BOTH_12.30_3B


title: P014

value: child


title: BC_2

description:
Old versus young permanent cells
SlideNumber: 72
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190072


title: Colon_DUAL_Day14_Mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
proxcolon_BOTH_12.30_2


title: B728a-ahlR_Low N_LabB_Rep1


title: P012


title: P013


title: P009


title: Ileum_VSL#3_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
VSL_12.30_5.1_2

source_name: Ileum harvested on day 14 from VSL#3 treated animals

value: Ileum


title: B728a-ahlR_Low Fe_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a ahlR mutant, Iron limited


title: B728a-ahlR_H2O2_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a ahlR mutant, Oxidative stress


title: B_3

description:
Deciduous versus permanent teeth cells
SlideNumber: 74
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190074


title: B728a-ahlR_H2O2_LabB_Rep1


title: B_1

description:
Deciduous versus permanent teeth cells
SlideNumber: 62
Batch: 1
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190062


title: B728a-ahlR_Low Fe_LabB_Rep1


title: Ileum_VSL#3_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
VSL_12.30_1.1_2


title: Ileum_VSL#3_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
VSL_12.30_3.1_2


title: P007

source_name: blood


title: Ileum_MSC_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
MSC_12.30_5.1_3

source_name: Ileum harvested on day 14 from MSC treated animals

value: MSC


title: B728a-ahlR_NaCl_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a ahlR mutant, Osmotic stress


title: B728a-ahlR_NaCl_LabB_Rep1


title: P006


title: B728a-ahlR_Basal medium_LabB_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a ahlR mutant, Basal medium


title: P002


title: B_2

description:
Deciduous versus permanent teeth cells
SlideNumber: 63
Batch: 1
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190063


title: B728a-ahlR_Basal medium_LabB_Rep1


title: P008


title: P005


title: B728a-WT_Apoplastic_LabB_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a wild type, Apoplastic cells

value: Wild type


title: P001


title: Ileum_MSC_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
MSC_12.30_4.1_3


title: Ileum_MSC_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
MSC_12.30_3.1_3


title: Ileum_MSC_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
MSC_12.30_1.1_2


title: B728a-WT_Apoplastic_LabB_Rep1


title: Cecum_DUAL_Day14_Mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_9_redo

source_name: Cecum harvested on day 14 from Dual treatment (VSL3 + MSC) animals

value: Cecum


title: B728a-WT_Epiphytic_LabB_Rep2

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a wild type, Epiphytic cells


title: B728a-WT_Epiphytic_LabB_Rep1


title: B728a-WT_Low N_LabB_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a wild type, Nitrogen limited


title: Pig-24_liver_healthy_control

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: Expression profiles of porcine liver tissues were studied to indentify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same heard.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press the button on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press the button and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.1.0.4, Molecular Devices) using FeatureType = Irregular Filled and MorphologicalClosingFollowedByOpening as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.9.2 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.18.3) which is part of the Bioconductor project. Probes classified as “not found by GenePix, positive control probes, probes with a SNR value below 1, and probes with more than 50 % of saturated pixels were weighted “0 before the log2-transformed ratios of Alexa-555 to Alexa-647 (not background corrected) were normalized within-slide using global-loess with default parameters utilising the matrix of binary probe weights as implemented in Limma. This was followed by a scale normalisation between arrays to compensate for different spreads of M-values. All control probes were weighted “0 before further analysis. The individual probes were furthermore filtrated based on their representation across the arrays, such that probes not represented by at least two (in the control group) and two (in the challenge group) non-zero weighted measurements were excluded from the statistical analysis. Finally, probe pairs were excluded if one of the duplicates did not pass the filtration. The exclusions were performed by sub-setting the objects containing the normalised data. The normalized log-ratios were analyzed in Limma to identify genes being significantly differentially expressed between tissue of uninfected control animals and tissue of infected animals. The relative reliability of each array was estimated using the arrayWeights function of Limma. The function measures how well the expression values for the individual arrays follow the linear model. The matrix of spot weights was multiplied by the obtained vector of array weights to generate a final weight matrix which was applied to the statistical analysis. A pooled correlation estimate was used to take the duplicated elements into account. The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.05 was considered significant.

extract_protocol: RNeasy Midi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: Pigs assigned as healthy non-inoculated control animals were killed and sampled prior to inoculation of the infected group. Samples of approximately 500 mg were taken from liver tissue, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use. Pigs assigned as infected animals, were inoculated with Actinobacillus pleuropneumoniae 5b (strain L20) by dripping 1 ml bacterial suspension, (McFarland 0.5, mixed 1:1 with Brain Heart Infusion + 0.1 % NAD) containing approximately 0.7 x107 CFU, in each nostril during inhalation. Culture of bacteria as well as inoculation procedures has previously been described by (Kristensen et al., Vet. Microbiol. 98, 243-249, 2004). Animals were killed 14 – 18 hours post inoculation by means of captive bolt pistol followed by pitching and exsanguinations. All animal procedures were approved by the Danish Animal Experiments Inspectorate. Immediately after killing, lungs were inspected for sizes and numbers of pulmonary lesions. To verify the infection, samples from lung, liver, tonsil and spleen were cultivated on PPLO agar (BD, Brøndby, Denmark) to re-isolate the inoculation strain, which hereafter was serotyped using latex agglutination (Giese et al., Acta. Vet. Scand. 34, 223-225, 1993). From the infected animals, samples of approximately 500 mg were taken from liver tissue, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use.

tag: breed

value: Danish Landrace/Yorkshire/Duroc cross

tag: herd

value: high health free from A. pleuropneumoniae

tag: gender

value: castrated males

tag: age

value: 8-10 weeks

tag: treatment

value: healthy control

source_name: Reference, pool of equal amount of total-RNA from all liver samples balanced with respect to control and challenged animals.

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany). The labelled reference samples were mixed and divided into aliquots before combining it with a labelled sample.

value: pool of equal amount of total-RNA from all liver samples in experiment


title: Cecum_VSL#3_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_8_redo

source_name: Cecum harvested on day 14 from VSL#3 treated animals

tag: strain backgroudn

tag: experiment group

tag: experiment day


title: Pig-22_liver_healthy_control

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany).


title: Pig-32_liver_challenged

value: AP serotype 5b infected


title: Cecum_VSL#3_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_7_redo


title: B728a-WT_H2O2_LabB_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Oxidative stress

tag: genotype

tag: strain


title: Cecum_VSL#3_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_6_redo


title: Cecum_MSC_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_4

source_name: Cecum harvested on day 14 from MSC treated animals


title: B728a-WT_NaCl_LabB_Rep2

source_name: Pseudomonas syringae B728a wild type, Osmotic stress


title: Cecum_MSC_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_5


title: Cecum_MSC_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_3_redo


title: B728a-WT_H2O2_LabB_Rep2


title: Cecum_DSS_Day10_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_33

source_name: Cecum harvested on day 10 from DSS only treated animals

value: DSS


title: B728a-WT_Low Fe_LabB_Rep1

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a wild type, Iron limited


title: BC_1

description:
Old versus young permanent cells
SlideNumber: 71
Batch: 2
Raw data files named with _1b.txt are labeled with Cy3. Raw data files named with _2b.txt are labeled with Cy5.
M_7190071

source_name: C

value: tooth pulp

value: permanent

value: adult  (> 38 years)

source_name: B


title: Cecum_DSS_Day10_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_31_redo


title: Cecum_DSS_Day10_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_30_redo


title: Cecum_DSS_Day10_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_29_redo


title: B728a-WT_Low Fe_LabB_Rep2


title: B728a-WT_Low N_LabB_Rep1


title: B728a-WT_NaCl_LabB_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.


title: B728a-WT_Basal medium_LabB_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Basal medium


title: Cecum_CNTL_Day1_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_28

source_name: Cecum harvested on day 1 from control animals

value: CNTL


title: Cecum_CNTL_Day1_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_27


title: Cecum_DSS_Day10_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_32


title: B728a-rpoN_Epiphytic_LabA_Rep1

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a rpoN mutant, Epiphytic cells

value: B728a rpoN mutant


title: B728a-rpoN_Low N_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a rpoN mutant, Nitrogen limited


title: Cecum_CNTL_Day1_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_26


title: Cecum_CNTL_Day1_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_25


title: B728a-rpoN_Epiphytic_LabA_Rep2


title: B728a-rpoN_Low N_LabA_Rep1


title: B728a-rpoN_Apoplastic_LabA_Rep1

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a rpoN mutant, Apoplastic cells


title: Cecum_CNTL_Day1_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_24


title: Cecum_DSS_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_22_redo

source_name: Cecum harvested on day 14 from DSS only treated animals


title: B728a-WT_Basal medium_LabB_Rep1


title: Ileum_VSL#3_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
VSL_12.30_4.1_2

source_name: Ileum harvested on day 14 from VSL#3 treated animals

value: Ileum


title: Pig-20_liver_healthy_control

description: Expression profiles of porcine liver tissues were studied to indentify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same heard.

tag: sample type


title: SG200Dtin5 4dpi rep 2

city: Marburg

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Str.

department: Organismic Interactions

country: Germany

institute: Max Planck Institue for Terrestiral Microbiology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol Midi_Euk2V3.

scan_protocol: GeneChips were scanned on a Affymetrix GSC3000G scanner

data_processing: Date were analyzed with the GeneChip operating software (GCOS) 1.4 to generate CEL files.

label: Biotin

organism: Zea mays

source_name: maize seedling leave (leaf 3), 4 days after infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Maize plants (Early Golden Bantam) were grown in a phytochamer in a 15/9 hourd light/dark cycle. Temerature was 28°c and 20°c, relative humudity 40% and 60% during light and dark periods, respectively, with 1 hour ramping for both parameters.

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

treatment_protocol: Seedlings were inoculated 7 days after sawing with the respective U. maydis strains, resulting in an infection of the third seedling leaf. Samples were taken 4 days after fungal infection.

tag: cultivar/ecotype

value: Zea mays:Early Golden Bantam


title: SG200Dtin5 4dpi rep 3


title: SG200Dtin5 4dpi rep 1


title: B728a-rpoN_H2O2_LabA_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a rpoN mutant, Oxidative stress


title: 4_9_4

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing: Raw Ct values = 999 were converted to 0 (zero). Relative quantification of gene expression (log2 space) was obtained by subtracting the Ct values from the baseline value of 22. Values < 0 (zero) were converted to 0 (zero).

label: EvaGreen

source_name: pre-implantatio embryo

label_protocol: The cells and pools were subjected to reverse transcription with SuperScript®VILO™ cDNA Synthesis kit (Life Technologies) as recommended by the manufacturer. DELTAgene™ Assays were custom designed for 94 genes associated with embryo development or regulation of gene expression, and two controls. The cDNA from cells and pools were subjected to specific target amplification for 20 cycles. Pre-amplified template was diluted and subjected to primer specific amplification with SooFast™EvaGreen®Supermix (Biorad) on 96.96 array chip and BiomarkHD™ System (Fluidigm).

extract_protocol: Cell was lysed by freezing at -80  Celcius degree

tag: cell type


title: 4_9_3


title: 4_9_2


title: SG200Dtin4 4dpi rep 2


title: B728a-rpoN_H2O2_LabA_Rep2


title: SG200Dtin4 4dpi rep 1


title: Cecum_DSS_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_23_redo


title: Cecum_DSS_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_20


title: Cecum_DUAL_Day14_Mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_21

source_name: Cecum harvested on day 14 from Dual treatment (VSL3 + MSC) animals

value: DUAL


title: Cecum_MSC_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_2

source_name: Cecum harvested on day 14 from MSC treated animals

value: MSC

value: Cecum


title: SG200Dtin4 4dpi rep 3


title: B728a-rpoN_Low Fe_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a rpoN mutant, Iron limited


title: B728a-rpoN_Low Fe_LabA_Rep1


title: SG200Dtin3 4dpi rep 3


title: B728a-rpoN_NaCl_LabA_Rep1

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a rpoN mutant, Osmotic stress


title: B728a-rpoN_NaCl_LabA_Rep2


title: 4_8_4


title: 4_9_1


title: Cecum_MSC_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_1_redo


title: SG200Dtin3 4dpi rep 1


title: SG200Dtin3 4dpi rep 2


title: Cecum_DSS_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_19


title: 4_8_3


title: Cecum_CNTL_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_18_redo

source_name: Cecum harvested on day 14 from control animals


title: Cecum_CNTL_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_17


title: 4_8_2


title: B728a-rpoN_Basal medium_LabA_Rep1

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a rpoN mutant, Basal medium


title: SG200Dtin1 4dpi rep 3


title: SG200Dtin1 4dpi rep 2


title: 4_8_1


title: 4_7_4


title: B728a-rpoN_Basal medium_LabA_Rep2


title: Cecum_CNTL_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_16


title: SG200Dtin1 4dpi rep 1


title: Ileum_MSC_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
MSC_12.30_2.1_3

source_name: Ileum harvested on day 14 from MSC treated animals


title: B728a-hrpL_Apoplastic_LabA_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a hrpL mutant, Apoplastic cells

value: B728a hrpL mutant


title: Pig-28_liver_challenged

value: Danish Landrace/Yorkshire/Duroc cross

value: high health free from A. pleuropneumoniae

value: castrated males

source_name: Reference, pool of equal amount of total-RNA from all liver samples balanced with respect to control and challenged animals.


title: 4_7_3


title: 4_7_2


title: B728a-hrpL_Epiphytic_LabA_Rep1

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a hrpL mutant, Epiphytic cells


title: B728a-hrpL_Epiphytic_LabA_Rep2


title: Cecum_CNTL_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_14_redo


title: B728a-hrpL_Apoplastic_LabA_Rep1


title: 4_6_4


title: Cecum_CNTL_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_15_redo


title: 4_7_1


title: Cecum_DUAL_Day14_Mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_13


title: Cecum_DSS_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_12


title: Cecum_DUAL_Day14_Mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_11


title: SG200D19A 4dpi rep 1


title: SG200D19A 4dpi rep 2


title: Pig-27_liver_challenged

description: Expression profiles of porcine liver tissues were studied to indentify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same heard.

value: 8-10 weeks

value: pool of equal amount of total-RNA from all liver samples in experiment


title: B728a-hrpL_Low N_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a hrpL mutant, Nitrogen limited


title: B728a-hrpL_Low N_LabA_Rep1


title: SG200D19A 4dpi rep 3


title: B728a-hrpL_Low Fe_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a hrpL mutant, Iron limited


title: B728a-hrpL_Low Fe_LabA_Rep1


title: 4_6_3


title: Ileum_DSS_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.30_4.1_2

source_name: Ileum harvested on day 14 from DSS only treated animals

value: DSS


title: 4_6_1


title: 4_5_4


title: 4_6_2


title: B728a-hrpL_H2O2_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a hrpL mutant, Oxidative stress


title: B728a-hrpL_H2O2_LabA_Rep1


title: Ileum_DSS_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.30_5.1_2


title: Cecum_DUAL_Day14_Mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_Stemcells_10_redo


title: B728a-hrpL_NaCl_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a hrpL mutant, Osmotic stress


title: 4_5_2


title: Ileum_DSS_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.30_3.1


title: 4_5_3


title: B728a-hrpL_NaCl_LabA_Rep1


title: B728a-hrpL_Basal medium_LabA_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a hrpL mutant, Basal medium


title: Ileum_DSS_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.30_1.1_3


title: 4_5_1

source_name: pre-implantatio embryo


title: B728a-hrpL_Basal medium_LabA_Rep1


title: 4_4_3


title: 4_4_4


title: 4_4_2


title: Ileum_DSS_Day10_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.26_4.1

source_name: Ileum harvested on day 10 from DSS only treated animals


title: B728a-algU_Apoplastic_LabA_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a algU mutant, Apoplastic cells

value: B728a rpoS mutant


title: Ileum_DSS_Day10_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.26_3.1


title: Ileum_DSS_Day10_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.26_2.1_2


title: B728a-algU_Epiphytic_LabA_Rep2

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a algU mutant, Epiphytic cells


title: Ileum_DSS_Day10_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.26_5.1


title: B728a-algU_Apoplastic_LabA_Rep1


title: 4_4_1


title: 4_3_4


title: Ileum_CNTL_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.30_4

source_name: Ileum harvested on day 14 from control animals


title: 4_3_2


title: B728a-algU_Low N_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a algU mutant, Nitrogen limited


title: Ileum_CNTL_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.30_3


title: B728a-algU_Low N_LabA_Rep1


title: Ileum_DSS_Day10_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.26_1.1


title: B728a-algU_Low Fe_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a algU mutant, Iron limited


title: Ileum_CNTL_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.30_2


title: Ileum_DSS_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
DSS_12.30_2.1


title: B728a-algU_Epiphytic_LabA_Rep1


title: B728a-algU_Low Fe_LabA_Rep1


title: Ileum_CNTL_Day14_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.30_1


title: B728a-algU_H2O2_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a algU mutant, Oxidative stress


title: 4_2_4


title: 4_2_3


title: 4_3_1


title: Colorectal Tumor Tissue-112611-02TB-Affymetrix Human Exon 1.0 ST

city: Riyadh

first: Sathish

last: Periyasamy

state: Select a State or Province

department: Bioinformatics

country: Saudi Arabia

institute: NGHA

description: RMA expression value derived from AltAnalyze; core-exon analysis

hyb_protocol: GeneChip® Hybridization Wash and Stain Kit (cat # 900720) was procured from Affymetrix and used according the manufacturers protocol.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Data Processing using AltAnalyze Software. The default recommended settings by Altanalyze was used to analyze the data

source_name: Colorectal Tumor Tissue

label_protocol: Gene Chip WT Terminal Labelling and Controls Kit (cat # 951024) was procured from Affymetrix and used according the manufacturers protocol.

growth_protocol: NONE (Tissue samples were used)

extract_protocol: RNA was isolated from <30mg of biopsy and surgery derived tissues using Macherey Nagel (Germany) Trio Kit. Both DNA and RNA were extracted in the same protocol accoding to manufacturers protocol.

treatment_protocol: not applicable

value: Tumor

value: Male

value: Colon

tag: tnm

tag: Stage

value: II


title: Colorectal Tumor Tissue-121011-01TB-Affymetrix Human Exon 1.0 ST

tag: tissue

value: I


title: 4_2_2


title: Ileum_CNTL_Day1_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.17_3.1

source_name: Ileum harvested on day 1 from control animals

value: CNTL

value: Ileum


title: Colorectal Tumor Tissue-112611-01TB-Affymetrix Human Exon 1.0 ST

value: Female

value: Sigmoid

value: IV


title: Ileum_CNTL_Day1_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.17_4.1


title: B728a-algU_NaCl_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a algU mutant, Osmotic stress


title: B728a-algU_H2O2_LabA_Rep1


title: Colorectal Tumor Tissue-101011-01TB-Affymetrix Human Exon 1.0 ST


title: Ileum_CNTL_Day1_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.17_5.1


title: 4_3_3


title: 4_2_1


title: 4_1_4


title: Colorectal Tumor Tissue-101512-01TB-Affymetrix Human Exon 1.0 ST

value: Colon & Rectum


title: Colorectal Tumor Tissue-042412-01TB-Affymetrix Human Exon 1.0 ST

value: Recto-sigmoid

value: III


title: Ileum_CNTL_Day1_mouse1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Cntl_12.17_1.1


title: Colorectal Tumor Tissue-092811-01TB-Affymetrix Human Exon 1.0 ST

value: Rectal


title: B728a-algU_NaCl_LabA_Rep1


title: Colorectal Tumor Tissue-051611-01TB-Affymetrix Human Exon 1.0 ST


title: B728a-algU_Basal medium_LabA_Rep2

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a algU mutant, Basal medium


title: Colorectal Tumor Tissue-072711-01TB-Affymetrix Human Exon 1.0 ST


title: Colorectal Tumor Tissue-100811-01TB-Affymetrix Human Exon 1.0 ST


title: 4_1_3


title: Ileum_DUAL_Day14_mouse5

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Both_12.30_5_3

source_name: Ileum harvested on day 14 from Dual treatment (VSL3 + MSC) animals

value: DUAL


title: Ileum_DUAL_Day14_mouse4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Both_12.30_4_3


title: Colorectal Tumor Tissue-092611-01TB-Affymetrix Human Exon 1.0 ST


title: Ileum_DUAL_Day14_mouse3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Both_12.30_3_3


title: 4_1_1


title: B728a-algU_Basal medium_LabA_Rep1


title: 4_1_2


title: Colorectal Tumor Tissue-031912-01TB-Affymetrix Human Exon 1.0 ST


title: Colorectal Tumor Tissue-033112-01TB-Affymetrix Human Exon 1.0 ST


title: 2_20_1


title: B728a-rpoS_Apoplastic_LabA_Rep2

description: Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.

source_name: Pseudomonas syringae B728a rpoS mutant, Apoplastic cells


title: 2_20_2


title: B728a-rpoS_Apoplastic_LabA_Rep1


title: B728a-rpoS_Epiphytic_LabA_Rep2

description: Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.

source_name: Pseudomonas syringae B728a rpoS mutant, Epiphytic cells


title: Ileum_DUAL_Day14_mouse2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Both_12.30_2_3


title: Colorectal Tumor Tissue-011112-01TB-Affymetrix Human Exon 1.0 ST


title: 2_19_2


title: Colorectal Tumor Tissue-010912-01TB-Affymetrix Human Exon 1.0 ST


title: WT mouse, healthy (MZB cells)

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

description: MZB-WT

hyb_protocol: Affymetrix Hybridization Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=131467&categoryId=35807#1_1)

scan_protocol: Affymetrix Scan Protocol (Proprietary protocol information available at http://www.affymetrix.com/Auth/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf)

data_processing: Raw CEL data were RMA background corrected and then quantile-normalized and baseline-equalized between measurement groups. Probes were aggregated to Entrez Gene probesets as defined by the custom CDF [MoGene11stv1_Mm_ENTREZG_14.1.0] described in [PMID 16284200] via median polish.

source_name: healthy WT-mouse for reference

label_protocol: Affymetrix Labeling Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=prod110002&categoryId=35699#1_1)

growth_protocol: CD5+CD19+ tumor cells isolated from spleens of diseased mice. MZB cells isolated from spleens of healthy WT mice. B1 cells isolated form peritoneal cavity of healthy WT animals.

extract_protocol: Cells were isolated from mice, stained with respective antibodies and subsequently sorted by FACS

tag: strain background

tag: genotype/variation

value: healthy WT (for reference)

tag: disease class

value: healthy

value: MZB cells

tag: tumor load (in percent)

tag: measurement group


title: B728a-rpoS_Epiphytic_LabA_Rep1

value: B728a rpoS mutant


title: Colorectal Normal Tissue-010213-01TB-Affymetrix Human Exon 1.0 ST

value: Tumor

tag: gender

tag: age

value: IIIB


title: B728a-rpoS_Low N_LabA_Rep1

description: Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a rpoS mutant, Nitrogen limited


title: Colorectal Normal Tissue-123012-01TB-Affymetrix Human Exon 1.0 ST

value: Male

value: IIB


title: 2_19_1

source_name: pre-implantatio embryo


title: B728a-rpoS_Low Fe_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.

source_name: Pseudomonas syringae B728a rpoS mutant, Iron limited


title: B728a-rpoS_Low N_LabA_Rep2


title: WT mouse, healthy (B1 cells)

value: B1 cells


title: 2_18_1


title: WT mouse #7161 (replicate 2), healthy

tag: tissue type

value: laser-captured microdissected splenic follicular areas


title: WT mouse #7160 (replicate 2), healthy


title: Colorectal Normal Tissue-120112-01TB-Affymetrix Human Exon 1.0 ST

value: Not Available


title: 2_18_2


title: B728a-rpoS_Low Fe_LabA_Rep1


title: Colorectal Normal Tissue-080211-01TB-Affymetrix Human Exon 1.0 ST

value: Female

value: IV


title: WT mouse #7160, healthy


title: WT mouse #7158, healthy


title: 2_17_1


title: 2_16_2


title: B728a-rpoS_H2O2_LabA_Rep1

source_name: Pseudomonas syringae B728a rpoS mutant, Oxidative stress


title: B728a-rpoS_H2O2_LabA_Rep2


title: 2_16_1


title: WT mouse #7161, healthy


title: WT mouse #10331, EµTCL (pure tumor cells)

source_name: Emu-Tcl1 transgenic WT-mouse

value: Emu-Tcl1 transgenic WT

value: EµTCL

value: CD5+CD19+ tumor cells


title: B728a-rpoS_NaCl_LabA_Rep1

source_name: Pseudomonas syringae B728a rpoS mutant, Osmotic stress


title: 2_15_2


title: 2_17_2


title: 2_15_1


title: B728a-rpoS_Basal medium_LabA_Rep1

source_name: Pseudomonas syringae B728a rpoS mutant, Basal medium


title: Colorectal Normal Tissue-072511-01TB-Affymetrix Human Exon 1.0 ST

value: Colon & Rectum

value: III


title: B728a-WT_Apoplastic_LabA_Rep2

source_name: Pseudomonas syringae B728a wild type, Apoplastic cells

value: Wild type


title: Colorectal Normal Tissue-032612-01TB-Affymetrix Human Exon 1.0 ST

value: II


title: WT mouse #10763, EµTCL (pure tumor cells)


title: B728a-rpoS_NaCl_LabA_Rep2

value: B728a rpoS mutant


title: WT mouse #7032, EµTCL (pure tumor cells)


title: B728a-WT_Apoplastic_LabA_Rep1


title: WT mouse #7998, EµTCL (pure tumor cells)


title: Colorectal Normal Tissue-060612-01TB-Affymetrix Human Exon 1.0 ST

value: Tumor


title: B728a-WT_Epiphytic_LabA_Rep2

source_name: Pseudomonas syringae B728a wild type, Epiphytic cells


title: 2_14_1


title: Colorectal Normal Tissue-120511-01TB-Affymetrix Human Exon 1.0 ST

source_name: Colorectal Tumor Tissue


title: Colorectal Normal Tissue-121011-01NB-Affymetrix Human Exon 1.0 ST

source_name: Colorectal Normal Tissue

value: Adjacent Normal

value: Colon

value: I


title: Colorectal Normal Tissue-112611-02NB-Affymetrix Human Exon 1.0 ST

value: Male


title: 2_13_2


title: WT mouse #10333, EµTCL (pure tumor cells)


title: WT mouse #7029, EµTCL (pure tumor cells)


title: Colorectal Normal Tissue-120511-01NB-Affymetrix Human Exon 1.0 ST


title: Colorectal Normal Tissue-101011-01NB-Affymetrix Human Exon 1.0 ST

value: Sigmoid


title: B728a-WT_Epiphytic_LabA_Rep1


title: Colorectal Normal Tissue-120112-01NB-Affymetrix Human Exon 1.0 ST

value: Not Available


title: 2_12_2


title: B728a-WT_Low N_LabA_Rep2

source_name: Pseudomonas syringae B728a wild type, Nitrogen limited


title: B728a-WT_Low N_LabA_Rep1


title: 2_13_1


title: 2_12_1


title: Colorectal Normal Tissue-092811-01NB-Affymetrix Human Exon 1.0 ST

value: Female

value: Rectal


title: Colorectal Normal Tissue-100811-01NB-Affymetrix Human Exon 1.0 ST

value: Recto-sigmoid

value: IV


title: CXCR5-KO mouse #7078, EµTCL (pure tumor cells)

source_name: Emu-Tcl1 transgenic CXCR5-KO-mouse

value: Emu-Tcl1 transgenic CXCR5-KO

value: EµTCL

value: CD5+CD19+ tumor cells


title: CXCR5-KO mouse #8438, EµTCL (pure tumor cells)


title: B728a-WT_Low Fe_LabA_Rep2

source_name: Pseudomonas syringae B728a wild type, Iron limited

value: Wild type


title: 2_11_1


title: B728a-WT_Low Fe_LabA_Rep1


title: 2_10_2


title: Colorectal Normal Tissue-123012-01NB-Affymetrix Human Exon 1.0 ST

value: Colon & Rectum

value: IIB


title: Colorectal Normal Tissue-080211-01NB-Affymetrix Human Exon 1.0 ST


title: CXCR5-KO mouse #9049, EµTCL (pure tumor cells)


title: Colorectal Normal Tissue-092711-01NB-Affymetrix Human Exon 1.0 ST