title: B728a_NaCl_LabC_Rep2

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 mates 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); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_NaCl_LabC.txt  (linked as supplementary file on Series record).

source_name: Pseudomonas syringae B728a wild type, Osmotic stress

treatment_protocol:
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.
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.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, 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, 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: Osmotic stress


title: Wild type zymogenic cells

status: Public on Jan 12 2013

type: RNA

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

country: USA

institute: Baylor College of Medicine

description: Wild Type ZC

hyb_protocol: Biotinylated cRNA probes were hybridized to the GeneChips. Post hybridization staining/washing using Affymetrix (manufacturer?s) protocols using the Fluidics Station 450 instrument.

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner

data_processing: The setting for modeling on dChip was Model-based expression and background subtraction was by PM/MM difference, which are the default settings.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: zymogenic cells_wild type

label_protocol: total RNA pooled from multiple dissections and multiple mice to make ~100 ng RNA, which was then amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences).

extract_protocol: RNA was extracted by laser-capture microdissection, purified by PicoPure kit, RNA integrity verified on Agilent Bioanalyzer.

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue

value: adult stomach

tag: cell type

value: gastric epithelial zymogenic cells


title: Patient Derived Xenograft LTL-313H-G7

type: genomic

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: Sample 19

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924) or SurePrint G3 Human Catalog CGH 4x180K (Design ID 022060)

scan_protocol: scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing: quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1. FE files loaded into Nexus Copy Number Software v.6  (Biodiscovery Inc.) for analysis.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit

value: prostate cancer tumor

tag: patient source

tag: tumor foci

value: Patient Derived Xenograft

tag: host genetic background

value: NOD/SCID

source_name: male reference DNA (Promega Corp)

tag: sample type

value: male reference DNA (Promega Corp)


title: PLC_PTvsLM

city: Pokfulam, Hong Kong

first: Wing Lung

middle: Simon

last: Yau

address: 21 Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

description: Analysis carried out by comparing the primary tumor cell line established from primary liver tumor in mice and its corresponding lung metastatic tumor cell line

hyb_protocol: The two differentially labeled reactions were combined into one tube and the volume was reduced by half in a SpeedVac® Concentrator.  BSA (50mg/ml) was then added to a total volume of 28.5ul.  The samples were incubated with 28.5ul of 2X Enhanced hybridization buffer at 65oC for 10 min and then loaded onto NCode™ Multi-Species miRNA Microarrays V2.  The arrays were mounted with the Maui Mixer SL and hybridized overnight (16-20 h) at 52oC with constant mixing.

scan_protocol: The washes were performed following the standard protocol recommended in the NCode™ Rapid miRNA Labeling System Manual, and the arrays were scanned using a GenePix® 4000B microarray scanner (Molecular Devices).

data_processing: The scanned array images were annotated and analyzed using the GenePix software and the .GAL files containg the array list name for the human samples.Analysis was performed by Microsoft Excel

source_name: PLC-PT

label_protocol: Each total RNA sample, 1μl of NCode™ Multi-Species miRNA Microarray Controls (2fmol/ul) was spiked, and Poly (A) tailing reactions were set up following the protocol recommended in the NCode™ Rapid miRNA Labeling System Manual. The Poly (A) tailed reactions were ligated to labeled DNA polymers by using the 6X Alexa Fluor® 3 (A3) Rapid Ligation Mix or 6X Alexa Fluor® 5 (A5) Rapid Ligation Mix following the protocol recommended in the NCode™ Rapid miRNA Labeling System Manual.

growth_protocol: All cell lines are maintain at 37oC incubator with 5% CO2 with DMEM supplement with 10% FBS

extract_protocol: Total RNA were extracted by Trizol reagent accroding to manufacturer's protocol

value: Primary human HCC tumor cell line

tag: cell line (derived)

source_name: PLC-LM

value: Metastatic human HCC tumor cell line


title: Patient Derived Xenograft LTL-313H-G16

description: Sample 18


title: MIST1 knockout zymogenic cells

description: MIST1 KO ZC

source_name: zymogenic cells_MIST1 knockout

value: MIST1 knockout


title: Clinical Patient-927

data_processing:
quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1
FE files loaded into Nexus Copy Number Software v.6  (Biodiscovery Inc.) for analysis.

tag: individual

value: Clinical Patient


title: B728a_NaCl_LabC_Rep1

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IA

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

institute: Iowa State University

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.

organism: Pseudomonas syringae pv. syringae B728a

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.

tag: genotype

value: Wild type

tag: treatment

tag: lab

value: C


title: B728a_NaCl_LabB_Rep1

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 mates 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); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_NaCl_LabB.txt  (linked as supplementary file on Series record).

value: B


title: B728a_NaCl_LabB_Rep2


title: Wild type neck cells

description: Wild Type NC

source_name: mucous neck cells_wild type

value: gastric epithelial mucous neck cells


title: Patient Derived Xenograft LTL-311-G8

description: Sample 16


title: MIST1 knockout neck cells

description: MIST1 KO NC

source_name: mucous neck cells_MIST1 knockout


title: Clinical Patient-946


title: B728a_NaCl_LabA_Rep2

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 mates 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); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_NaCl_LabA.txt  (linked as supplementary file on Series record).

value: A


title: B728a_NaCl_LabA_Rep1

value: Osmotic stress


title: Patient Derived Xenograft LTL-418

value: Patient 1015


title: Patient Derived Xenograft LTL-412

value: Patient 1005


title: B728a_Basal medium_LabC_Rep2

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 mates 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); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
No .txt file.

source_name: Pseudomonas syringae B728a wild type, Basal medium

treatment_protocol:
Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.
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.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, 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, 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: Basal medium


title: Clinical Patient-1015

value: prostate cancer tumor


title: Patient Derived Xenograft LTL-313B-G8

description: Sample 17

value: Patient Derived Xenograft


title: Patient Derived Xenograft LTL-352

value: Patient 946

value: NOD/SCID


title: B728a_Basal medium_LabC_Rep1


title: Patient Derived Xenograft LTL-331

value: Patient 927

value: male reference DNA (Promega Corp)


title: Patient Derived Xenograft LTL-313B


title: Patient Derived Xenograft LTL-313H


title: Patient Derived Xenograft LTL-313C


title: TUMOR 1

status: Public on Jan 14 2013

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from normal tissue, untreated tumors, and tumors treated with rapamycin.

hyb_protocol: Agilent hybridization protocol 65C 10rpm 17 h.

scan_protocol: Agilent arrays were scanned using the Agilent Scanner G2565BA.

data_processing: The data was first processed by background correction and then quantile normalization.

label: Agilent  part #5190-0442 Quick-Amp Labeling kit 1-color.

source_name: Mus musculus

label_protocol: 300 ng of Qiagen-purified total RNA

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

tag: subtype

value: TUMOR


title: Patient Derived Xenograft LTL-370

value: Patient 972


title: Patient Derived Xenograft LTL-311


title: Patient Derived Xenograft LTL-313D


title: B728a_Basal medium_LabA_Rep1

value: Wild type


title: B728a_Basal medium_LabB_Rep1


title: Patient Derived Xenograft LTL-313A


title: B728a_Basal medium_LabB_Rep2


title: Insulinoma metastasis 19

status: Public on Jan 13 2013

city: Utrecht

first: Floryne

last: Buishand

address: Yalelaan 108

department: Clinical Sciences of Companion Animals

country: Netherlands

institute: Faculty of Veterinary Medicine, Utrecht University

description: Insulinoma liver metastasis from dog 19, DFI 122 days, ST 166 days

hyb_protocol: Microarray slides were washed for 1 min in 2x SSC containing 0.05% Sodium dodecyl sulphate (SDS) at room temperature (RT), incubated in 0.25% sodium borohydride and 0.25% SDS in 2x SSC for 30 min at 420C  and then rinsed 5 times in double distilled water at RT.  Slides were incubated for 45 minutes at 420C in pre-warmed pre-hybridization buffer (2X) consisting of 10xSSC, 25% formamide, 0.1% SDS and 1% BSA. Slides were washed 5 times in water followed by 5 times in isopropanol at RT and air dried. To 40 µl containing 2.5 µg of each Cy3 and Cy5 labeled RNA 40 µl hybridization buffer was added consisting of 50% formamide, 0.2% SDS and 200 µg/ml sheared herring sperm DNA. The mixture was heated at 95°C for 5 min, centrifuged for 2 min at 12,000xg and hybridized to the slides at 420C for 16 hours using hybridization chambers (Corning Life Sciences) in a water bath. After hybridization, slides were washed three times: first a low-stringency wash for 4 min at RT in 1xSSC and 0.2% SDS, next a high-stringency wash in 0.1% SDS and 0.2% SDS for 4 min and finally 2 washes in 0.1xSSC at room temperature. Slides were blown dry using compressed nitrogen.

scan_protocol: Slides were scanned using an Agilent G2565AA DNA microarray scanner (100% laser power, 30% photomultiplier tube).

data_processing: Image analysis was carried out using Imagene 5.0 software (Biodiscovery Inc). Data were normalized based on Lowess print-tip normalization by using the gene spots to calculate the Lowess line for each sub grid and then applying the these lines to all spots.

organism: Canis lupus familiaris

source_name: Insulinoma metastasis 19

label_protocol: Total RNA isolated from snap frozen insulinoma tissue was used for cRNA synthesis. About 2 µg total RNA was reverse transcribed using Superscript II reverse transcriptase and T7 promoter coupled poly T primers (5' GGCCAGTGAATTGTAATACGACTCACCTATAGGGAGG CGGT). After second strand synthesis, cDNA products were purified using QIAquick PCR Purification Kit and transcribed using the T7 Megascript kit (Ambion) using a UTP to 5-(3-aminoallyl)-UTP ratio of 1/3.5. The RNeasy mini kit (Qiagen) was used to clean the resulting cRNA. Three µg cRNA was coupled to Cy3 or Cy5 fluorophores. Labeled cRNA was cleaned using ChromaSpin-30 columns and cRNA samples with specific activity of 2-5% dye-labeled nucleosides were used for microarray hybridization.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Leusden, The Netherlands) according to the manufacturer’s protocol. To prevent contamination of the samples with genomic DNA, an on-column DNAse treatment was performed.

tag: dog id

value: Liver metastasis

tag: disease free interval (days)

tag: survival time (days)

tag: disease state

value: insulinoma

source_name: Reference pool

value: All 20 INS samples

value: primary and metastatic tumors


title: B728a_Basal medium_LabA_Rep2

value: A


title: CD-1 mice: Control vs. vitamin B6 diet

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: 1mg vitamin B6 diet

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: The mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNA of epididymal white adipose tissue were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Twenty-four mice were divided into two groups (n = 12) and fed either a 1 mg pyridoxine (PN) HCl /kg diet or a 35 mg PN HCl /kg diet for 8 weeks.

tag: strain

source_name: 35mg vitamin B6 diet


title: JAG1 overexpressed CL1-0, biological rep2

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from vector control transfectants and JAG1 overexpressed transfectants were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

source_name: Human lung adenocarcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human lung adenocarcinoma cell lines of CL1-0 JAG1-transfected and CL1-0 vector control were grown in DMEM with 10% fetal bovine serum at 37¢XC, 20% O2, 5% CO2 and 1000 £gg/ml G418.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

tag: cell line

tag: gender

value: male


title: JAG1 overexpressed CL1-0, biological rep3


title: IL8.3

status: Public on Jan 11 2013

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Av

department: Medicine- Digestive and Liver Diseases

institute: Columbia University

hyb_protocol: 12 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

source_name: IL8 human transgenic mouse colon cancer tumor (control)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

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

tag: genotype/variation

value: IL8 transgenic

tag: tissue

value: colon cancer tumor


title: JAG1 overexpressed CL1-0, biological rep1


title: IL8.2


title: CL1-0, biological rep3


title: ctrl.3

source_name: Colon cancer tumor (control)

value: wild type


title: CL1-0, biological rep1


title: blood CD1 24hrs Ecoli rep10 batch 9 batch 9 1545_4571_25352_Ecoli_10

city: Durham

first: Sun Hee

last: Ahn

state: NC

address: Stead Bldg, RM 1546A

department: Medicine

institute: Duke University

hyb_protocol: Biotin-labeled cDNA was hybridized to the arrays for 16 hours at 45°C according to the manufacturer’s instruction. Arrays were then washed and labeled with streptavidinphycoerythrin (strep-PE), and the signal was amplified using biotinylated antistreptavidin followed by another round of staining with strep-PE. These steps were performed on the Affymetrix fluidics station according to the recommended protocol.

scan_protocol: Amplification and microarray hybridization were performed at the Duke University Microarray Core. Labeled gene chips were scanned using an Affymetrix Genechip Scanner 7G (Santa Clara, CA).

data_processing: Data processing was conducted using the Robust Multichip Average (RMA) generated by Affymetrix Expression Console software. Microarray data was analyzed in two steps following the analysis strategy previously outlined and utilized (Zaas et al., 2010). First, a Bayesian sparse factor model was fit to the expression data without regard to phenotype (Carvalho et al., 2008; Wang et al., 2007). Second, factors were then used to build a probit regression with variable selection model (Hans et al., 2007) trained to identify S. aureus infection.

label: Biotin

source_name: blood CD1 mouse strain blood taken 24 hours after infection with E. coli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix).

growth_protocol: One methicillin-susceptible S. aureus strain (Sanger 476) and three methicillin-resistant S. aureus strains (USA100, USA300, and MW2) were used.  Overnight S. aureus cultures were inoculated into fresh tryptic soy broth and incubated aerobically at 30°C to log-phase growth (optical density 600nm of ~1.0) (Rice et al., 2003).  Cells were harvested by centrifugation, rinsed, and resuspended in phosphate-buffered saline (PBS).  E. coli O18:K1:H7 was grown at 30°C overnight in Luria Bertani broth (Miller et al., 1972).  Cultures were then diluted with fresh medium and grown for an additional 1 to 2 hours.  Upon reaching log phase, cells were harvested by centrifugation, washed, and resuspended in PBS.

extract_protocol: Total RNA was extracted from mouse blood using the Mouse RiboPure Blood RNA kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Globin mRNA was removed from whole blood RNA using the Globinclear kit (Ambion, Austin, TX). All samples passed the quality criteria of the Agilent Bioanalyzer and were used for microarray analysis. Since the total RNA yield of many samples was low, one round of linear amplification was performed for all samples using the MessageAmp Premier kit (Ambion, Austin, TX).

treatment_protocol: To mimic the natural course of S. aureus infection in humans, which typically arises from a primary focus of infection and disseminates to other sites, we employed an intraperitoneal (i.p.) route of infection in our animal model.

tag: host strain

tag: host gender

tag: host age (yr)

tag: pathogen

value: Escherichia  coli

tag: bacterial strain

tag: pathogen   dosage cfu/g

tag: inoculum route

value: peritoneum

tag: anatomic site of infection

tag: infection status

value: infected

tag: time after infection (h)

tag: replicate number

tag: experimental batch


title: CL1-0, biological rep2


title: ctrl.2

tag: strain


title: blood CD1 2hrs USA300 rep9 batch 9 batch 9 1545_4571_25349_USA_9

source_name: blood CD1 mouse strain blood taken 2 hours after infection with S. aureus USA300

value: Staphylococcus aureus


title: blood CD1 24hrs Ecoli rep9 batch 9 batch 9 1545_4571_25351_Ecoli_9


title: blood CD1 0hrs rep9 batch 9 batch 9 1545_4571_25345_control_9

source_name: blood CD1 mouse strain NOT infected


title: blood CD1 0hrs rep10 batch 9 batch 9 1545_4571_25346_control_10


title: blood CD1 2hrs Sanger rep10 batch 9 batch 9 1545_4571_25348_Sanger_10

source_name: blood CD1 mouse strain blood taken 2 hours after infection with S. aureus Sanger476


title: blood CD1 2hrs Sanger rep7 batch 9 batch 9 1545_4571_25339_Sanger_7


title: blood CD1 24hrs Ecoli rep8 batch 9 batch 9 1545_4571_25344_Ecoli_8


title: blood CD1 2hrs USA300 rep8 batch 9 batch 9 1545_4571_25342_USA_8


title: blood CD1 2hrs USA300 rep7 batch 9 batch 9 1545_4571_25341_USA_7


title: ctrl.1


title: blood CD1 2hrs Sanger rep9 batch 9 batch 9 1545_4571_25347_Sanger_9


title: blood CD1 2hrs Sanger rep8 batch 9 batch 9 1545_4571_25340_Sanger_8


title: IL8.1


title: blood CD1 2hrs USA300 rep10 batch 9 batch 9 1545_4571_25350_USA_10


title: blood CD1 24hrs Ecoli rep7 batch 9 batch 9 1545_4571_25343_Ecoli_7


title: blood CD1 2hrs USA300 rep6 batch 9 batch 9 1545_4571_25334_USA_6


title: blood CD1 24hrs Ecoli rep6 batch 9 batch 9 1545_4571_25336_Ecoli_6


title: blood CD1 0hrs rep7 batch 9 batch 9 1545_4571_25337_control_7


title: blood CD1 2hrs Sanger rep5 batch 9 batch 9 1545_4571_25331_Sanger_5


title: blood CD1 2hrs Sanger rep6 batch 9 batch 9 1545_4571_25332_Sanger_6


title: blood CD1 0hrs rep5 batch 9 batch 9 1545_4571_25329_control_5


title: blood CD1 2hrs USA300 rep3 batch 9 batch 9 1545_4571_25325_USA_3


title: blood CD1 24hrs Ecoli rep3 batch 9 batch 9 1545_4571_25327_Ecoli_3


title: blood CD1 0hrs rep8 batch 9 batch 9 1545_4571_25338_control_8


title: blood CD1 24hrs Ecoli rep4 batch 9 batch 9 1545_4571_25328_Ecoli_4


title: blood CD1 2hrs USA300 rep4 batch 9 batch 9 1545_4571_25326_USA_4


title: blood CD1 0hrs rep6 batch 9 batch 9 1545_4571_25330_control_6


title: blood CD1 2hrs USA300 rep5 batch 9 batch 9 1545_4571_25333_USA_5


title: blood CD1 2hrs Sanger rep3 batch 9 batch 9 1545_4571_25323_Sanger_3


title: blood CD1 24hrs Ecoli rep5 batch 9 batch 9 1545_4571_25335_Ecoli_5


title: Patient Derived Xenograft LTL-310

value: prostate cancer tumor

tag: patient source

tag: tumor foci

value: Patient Derived Xenograft

tag: host genetic background

value: NOD/SCID

source_name: male reference DNA (Promega Corp)

tag: sample type

value: male reference DNA (Promega Corp)


title: blood CD1 0hrs rep4 batch 9 batch 9 1545_4571_25322_control_4

tag: host strain


title: blood CD1 2hrs Sanger rep1 batch 9 batch 9 1545_4571_25315_Sanger_1

tag: host gender


title: blood CD1 2hrs Sanger rep2 batch 9 batch 9 1545_4571_25316_Sanger_2

tag: host age (yr)


title: blood CD1 2hrs USA300 rep2 batch 9 batch 9 1545_4571_25318_USA_2

tag: pathogen


title: blood CD1 24hrs Ecoli rep1 batch 9 batch 9 1545_4571_25319_Ecoli_1

tag: bacterial strain


title: blood C57BL/6J 6hrs Ecoli rep5 batch 8 batch 8 1545_6512_31141_BLEcol6h-5

source_name: blood C57BL/6J mouse strain blood taken 6 hours after infection with E. coli

tag: pathogen   dosage cfu/g


title: blood CD1 2hrs Sanger rep4 batch 9 batch 9 1545_4571_25324_Sanger_4

tag: inoculum route


title: blood C57BL/6J 12hrs Ecoli rep5 batch 8 batch 8 1545_6512_31142_BLEcol12h-5

source_name: blood C57BL/6J mouse strain blood taken 12 hours after infection with E. coli

tag: anatomic site of infection


title: blood CD1 0hrs rep1 batch 9 batch 9 1545_4571_25313_control_1

tag: infection status


title: blood CD1 24hrs Ecoli rep2 batch 9 batch 9 1545_4571_25320_Ecoli_2

tag: time after infection (h)


title: blood CD1 0hrs rep3 batch 9 batch 9 1545_4571_25321_control_3

tag: replicate number


title: blood C57BL/6J 24hrs Ecoli rep4 batch 8 batch 8 1545_6512_31133_BLEcol24h-4

source_name: blood C57BL/6J mouse strain blood taken 24 hours after infection with E. coli

tag: experimental batch


title: blood CD1 0hrs rep2 batch 9 batch 9 1545_4571_25314_control_2


title: blood C57BL/6J 24hrs Ecoli rep5 batch 8 batch 8 1545_6512_31143_BLEcol24h-5


title: blood C57BL/6J 12hrs Ecoli rep4 batch 8 batch 8 1545_6512_31132_BLEcol12h-4


title: blood A/J 12hrs Ecoli rep5 batch 8 batch 8 1545_6512_31137_AJEcol12h-5

source_name: blood A/J mouse strain blood taken 12 hours after infection with E. coli

value: A/J


title: blood C57BL/6J 6hrs Ecoli rep4 batch 8 batch 8 1545_6512_31131_BLEcol6h-4


title: blood A/J 24hrs Ecoli rep5 batch 8 batch 8 1545_6512_31138_AJEcol24h-5

source_name: blood A/J mouse strain blood taken 24 hours after infection with E. coli


title: blood C57BL/6J 2hrs Ecoli rep4 batch 8 batch 8 1545_6512_31130_BLEcol2h-4

source_name: blood C57BL/6J mouse strain blood taken 2 hours after infection with E. coli


title: blood C57BL/6J 0hrs rep5 batch 8 batch 8 1545_6512_31139_BLEcol0h-5

source_name: blood C57BL/6J mouse strain NOT infected


title: blood C57BL/6J 2hrs Ecoli rep5 batch 8 batch 8 1545_6512_31140_BLEcol2h-5

source_name: blood A/J mouse strain blood taken 2 hours after infection with E. coli


title: blood A/J 6hrs Ecoli rep5 batch 8 batch 8 1545_6512_31136_AJEcol6h-5

source_name: blood A/J mouse strain blood taken 6 hours after infection with E. coli


title: blood A/J 0hrs rep5 batch 8 batch 8 1545_6512_31134_AJEcol0h-5

source_name: blood A/J mouse strain NOT infected


title: blood A/J 2hrs Ecoli rep5 batch 8 batch 8 1545_6512_31135_AJEcol2h-5


title: blood A/J 24hrs Ecoli rep4 batch 8 batch 8 1545_6512_31128_AJEcol24h-4


title: blood C57BL/6J 0hrs rep4 batch 8 batch 8 1545_6512_31129_BLEcol0h-4


title: blood A/J 12hrs Ecoli rep4 batch 8 batch 8 1545_6512_31127_AJEcol12h-4


title: blood A/J 2hrs Ecoli rep4 batch 8 batch 8 1545_6512_31125_AJEcol2h-4


title: blood A/J 0hrs rep4 batch 8 batch 8 1545_6512_31124_AJEcol0h-4


title: blood A/J 6hrs Ecoli rep4 batch 8 batch 8 1545_6512_31126_AJEcol6h-4


title: blood CD1 2hrs USA300 rep1 batch 9 batch 9 1545_4571_25317_USA_1


title: blood C57BL/6J 12hrs Ecoli rep3 batch 8 batch 8 1545_6512_31122_BLEcol12h-3


title: blood C57BL/6J 2hrs Ecoli rep3 batch 8 batch 8 1545_6512_31120_BLEcol2h-3


title: blood A/J 24hrs Ecoli rep3 batch 8 batch 8 1545_6512_31118_AJEcol24h-3


title: blood C57BL/6J 24hrs Ecoli rep2 batch 8 batch 8 1545_6512_31113_BLEcol24h-2


title: blood A/J 12hrs Ecoli rep3 batch 8 batch 8 1545_6512_31117_AJEcol12h-3


title: blood A/J 6hrs Ecoli rep3 batch 8 batch 8 1545_6512_31116_AJEcol6h-3


title: blood C57BL/6J 6hrs Ecoli rep3 batch 8 batch 8 1545_6512_31121_BLEcol6h-3


title: blood A/J 2hrs Ecoli rep3 batch 8 batch 8 1545_6512_31115_AJEcol2h-3


title: blood A/J 0hrs rep3 batch 8 batch 8 1545_6512_31114_AJEcol0h-3


title: blood C57BL/6J 0hrs rep2 batch 8 batch 8 1545_6512_31109_BLEcol0h-2


title: blood C57BL/6J 6hrs Ecoli rep2 batch 8 batch 8 1545_6512_31111_BLEcol6h-2


title: blood C57BL/6J 2hrs Ecoli rep2 batch 8 batch 8 1545_6512_31110_BLEcol2h-2


title: blood C57BL/6J 0hrs rep3 batch 8 batch 8 1545_6512_31119_BLEcol0h-3


title: blood C57BL/6J 12hrs Ecoli rep2 batch 8 batch 8 1545_6512_31112_BLEcol12h-2


title: blood A/J 0hrs rep2 batch 8 batch 8 1545_6512_31104_AJEcol0h-2


title: blood C57BL/6J 12hrs Ecoli rep1 batch 8 batch 8 1545_6512_31102_BLEcol12h-1


title: blood A/J 2hrs Ecoli rep2 batch 8 batch 8 1545_6512_31105_AJEcol2h-2


title: blood A/J 12hrs Ecoli rep2 batch 8 batch 8 1545_6512_31107_AJEcol12h-2


title: blood A/J 12hrs Ecoli rep1 batch 8 batch 8 1545_6512_31097_AJEcol12h-1


title: blood A/J 24hrs Ecoli rep1 batch 8 batch 8 1545_6512_31098_AJEcol24h-1


title: blood C57BL/6J 24hrs Ecoli rep1 batch 8 batch 8 1545_6512_31103_BLEcol24h-1


title: blood C57BL/6J 2hrs Ecoli rep1 batch 8 batch 8 1545_6512_31100_BLEcol2h-1


title: blood A/J 6hrs Ecoli rep2 batch 8 batch 8 1545_6512_31106_AJEcol6h-2


title: blood A/J 0hrs rep1 batch 8 batch 8 1545_6512_31094_AJEcol0h-1


title: blood A/J 24hrs Ecoli rep2 batch 8 batch 8 1545_6512_31108_AJEcol24h-2


title: blood A/J 2hrs Ecoli rep1 batch 8 batch 8 1545_6512_31095_AJEcol2h-1


title: blood A/J 6hrs Ecoli rep1 batch 8 batch 8 1545_6512_31096_AJEcol6h-1


title: blood C57BL/6J 24hrs Ecoli rep3 batch 8 batch 8 1545_6512_31123_BLEcol24h-3


title: blood NOD/ShiLtJ 2hrs Sanger rep1 batch 2 batch 2 1545_4182_22008_NOD-2ht-1set

source_name: blood NOD/ShiLtJ mouse strain blood taken 2 hours after infection with S. aureus Sanger476

value: NOD/ShiLtJ


title: blood NOD/ShiLtJ 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22036_NOD-2ht-3set


title: blood NOD/ShiLtJ 0hrs rep2 batch 2 batch 2 1545_4182_22021_NOD-cont-2set

source_name: blood NOD/ShiLtJ mouse strain NOT infected


title: blood C57BL/6J 12hrs Sanger rep5 batch 1 batch 1 1545_3293_16135_49

source_name: blood C57BL/6J mouse strain blood taken 12 hours after infection with S. aureus Sanger476


title: blood NOD/ShiLtJ 0hrs rep3 batch 2 batch 2 1545_4182_22035_NOD-cont-3set


title: blood NOD/ShiLtJ 0hrs rep1 batch 2 batch 2 1545_4182_22007_NOD-cont-1set


title: blood C57BL/6J 0hrs rep1 batch 8 batch 8 1545_6512_31099_BLEcol0h-1


title: blood C57BL/6J 12hrs Sanger rep4 batch 1 batch 1 1545_3293_16134_48


title: blood C57BL/6J 12hrs Sanger rep3 batch 1 batch 1 1545_3293_16133_47


title: blood C57BL/6J 12hrs Sanger rep4 batch 2 batch 2 1545_4008_20950_B12h-6set


title: blood NOD/ShiLtJ 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22022_NOD-2ht-2set


title: blood C57BL/6J 12hrs Sanger rep2 batch 1 batch 1 1545_3293_16132_46


title: blood C57BL/6J 6hrs Ecoli rep1 batch 8 batch 8 1545_6512_31101_BLEcol6h-1


title: blood C57BL/6J 12hrs Sanger rep3 batch 2 batch 2 1545_4008_20940_B12h-3set


title: blood C57BL/6J 12hrs Sanger rep1 batch 1 batch 1 1545_3293_16136_45


title: blood C57BL/6J 12hrs Sanger rep5 batch 2 batch 2 1545_4008_20960_B12h-5set


title: blood C57BL/6J 4hrs Sanger rep5 batch 2 batch 2 1545_4008_20958_B4h-5set

source_name: blood C57BL/6J mouse strain blood taken 4 hours after infection with S. aureus Sanger476


title: blood C57BL/6J 12hrs Sanger rep2 batch 2 batch 2 1545_4008_20929_B12h-2set


title: blood C57BL/6J 6hrs Sanger rep5 batch 2 batch 2 1545_4008_20959_B6h-5set

source_name: blood C57BL/6J mouse strain blood taken 6 hours after infection with S. aureus Sanger476


title: blood C57BL/6J 4hrs Sanger rep4 batch 2 batch 2 1545_4008_20948_B4h-4set


title: blood C57BL/6J 12hrs Sanger rep1 batch 2 batch 2 1545_3968_20732_B12h-1set


title: blood C57BL/6J 4hrs Sanger rep3 batch 2 batch 2 1545_4008_20938_B4h-3set


title: blood C57BL/6J 6hrs Sanger rep2 batch 2 batch 2 1545_4008_20928_B6h-2set


title: blood C57BL/6J 4hrs Sanger rep2 batch 2 batch 2 1545_4008_20925_B4h-2set


title: blood C57BL/6J 6hrs Sanger rep4 batch 2 batch 2 1545_4008_20949_B6h-4set


title: blood C57BL/6J 2hrs Sanger rep5 batch 2 batch 2 1545_4008_20957_B2h-5set

source_name: blood C57BL/6J mouse strain blood taken 2 hours after infection with S. aureus Sanger476


title: blood C57BL/6J 6hrs Sanger rep3 batch 2 batch 2 1545_4008_20939_B6h-3set


title: blood C57BL/6J 4hrs Sanger rep1 batch 2 batch 2 1545_3968_20730_B4h-1set


title: blood C57BL/6J 2hrs Sanger rep3 batch 2 batch 2 1545_4008_20937_B2h-3set


title: blood C57BL/6J 2hrs Sanger rep4 batch 2 batch 2 1545_4008_20947_B2h-4set


title: blood C57BL/6J 6hrs Sanger rep1 batch 2 batch 2 1545_3968_20731_B6h-1set


title: blood C57BL/6J 2hrs Sanger rep1 batch 2 batch 2 1545_3968_20729_B2h-1set


title: blood C57BL/6J 24hrs Ecoli rep5 batch 1 batch 1 1545_3617_18185_BE5


title: blood C57BL/6J 0hrs rep5 batch 2 batch 2 1545_3967_20733_18Bcontrol


title: blood C57BL/6J 24hrs Ecoli rep2 batch 1 batch 1 1545_3617_18182_BE2


title: blood C57BL/6J 24hrs Ecoli rep4 batch 1 batch 1 1545_3617_18184_BE4


title: blood C57BL/6J 0hrs rep4 batch 2 batch 2 1545_4008_20952_B4cont


title: blood C57BL/6J 0hrs rep1 batch 2 batch 2 1545_4182_22003_B-cont-1set


title: blood C57BL/6J 0hrs rep2 batch 2 batch 2 1545_4182_22017_B-cont-2set


title: blood C57BL/6J 0hrs rep4 batch 1 batch 1 1545_3293_16117_19


title: blood C57BL/6J 24hrs Ecoli rep1 batch 1 batch 1 1545_3617_18181_BE1


title: blood C57BL/6J 0hrs rep3 batch 2 batch 2 1545_4008_20942_B3cont


title: blood C57BL/6J 0hrs rep2 batch 2 batch 2 1545_4008_20932_B2cont


title: blood C57BL/6J 24hrs Ecoli rep3 batch 1 batch 1 1545_3617_18183_BE3


title: blood C57BL/6J 0hrs rep5 batch 1 batch 1 1545_3293_16123_20


title: blood C57BL/6J 2hrs Sanger rep2 batch 2 batch 2 1545_4008_20927_B2h-2set


title: blood C57BL/6J 0hrs rep3 batch 2 batch 2 1545_4182_22031_B-cont-3set


title: blood C57BL/6 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22032_B2h-3set


title: blood C57BL/6J 0hrs rep1 batch 2 batch 2 1545_4008_20926_B1cont


title: blood C57BL/6 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22018_B2h-2set


title: blood C3H/HeJ 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22034_C3H-2h-3set

source_name: blood C3H/HeJ mouse strain blood taken 2 hours after infection with S. aureus Sanger476


title: blood C3H/HeJ 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22020_C3H-2h-2set


title: blood C3H/HeJ 2hrs Sanger rep1 batch 2 batch 2 1545_4182_22006_C3H-2h-1set


title: blood C57BL/6J 2hrs Sanger rep1 batch 2 batch 2 1545_4182_22004_B2h-1set


title: blood C3H/HeJ 0hrs rep2 batch 2 batch 2 1545_4182_22019_C3H-cont-2set

source_name: blood C3H/HeJ mouse strain NOT infected


title: blood C57BL/6J 0hrs rep2 batch 1 batch 1 1545_3293_16115_17


title: blood C3H/HeJ 0hrs rep3 batch 2 batch 2 1545_4182_22033_C3H-cont-3set


title: blood C57BL/6J 0hrs rep1 batch 1 batch 1 1545_3293_16114_16


title: blood C3H/HeJ 0hrs rep1 batch 2 batch 2 1545_4182_22005_C3H-cont-1set


title: blood C57BL/6J 0hrs rep3 batch 1 batch 1 1545_3293_16116_18


title: blood BALB/cByJ 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22030_BALB-2h-3set

source_name: blood BALB/cBy mouse strain blood taken 2 hours after infection with S. aureus Sanger476

value: BALB/cByJ


title: blood BALB/cByJ 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22016_BALB-2h-2set


title: blood BALB/cByJ 0hrs rep3 batch 2 batch 2 1545_4182_22029_BALB-cont-3set

source_name: blood BALB/cBy mouse strain NOT infected


title: blood BALB/cByJ 2hrs Sanger rep1 batch 2 batch 2 1545_4182_22002_BALB-2h-1set


title: blood BALB/cByJ 0hrs rep1 batch 2 batch 2 1545_4182_22001_BALB-cont-1set


title: blood BALB/cByJ 0hrs rep2 batch 2 batch 2 1545_4182_22015_BALB-cont-2set


title: blood AKR/J 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22014_AKR-2h-2set

source_name: blood AKR/J mouse strain blood taken 2 hours after infection with S. aureus Sanger476

value: AKR/J


title: blood AKR/J 0hrs rep2 batch 2 batch 2 1545_4182_22013_AKR-cont-2set

source_name: blood AKR/J mouse strain NOT infected


title: blood A/J 2hrs USA100 rep3 batch 6 batch 6 1545_4319_23521_AJ-usa-100-5

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus USA100


title: blood A/J 2hrs USA300 rep2 batch 6 batch 6 1545_4319_23518_AJ-usa-300-4

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus USA300


title: blood A/J 12hrs Sanger rep5 batch 1 batch 1 1545_3293_16137_40

source_name: blood A/J mouse strain blood taken 12 hours after infection with S. aureus Sanger476


title: blood A/J 2hrs USA300 rep1 batch 6 batch 6 1545_4319_23510_AJ-usa-300-2


title: blood A/J 12hrs Sanger rep1 batch 1 batch 1 1545_3293_16128_36


title: blood A/J 12hrs Sanger rep3 batch 1 batch 1 1545_3293_16130_38


title: blood A/J 2hrs USA300 rep3 batch 6 batch 6 1545_4319_23520_AJ-usa-300-5


title: blood A/J 12hrs Sanger rep2 batch 1 batch 1 1545_3293_16129_37


title: blood A/J 12hrs Sanger rep4 batch 1 batch 1 1545_3293_16131_39


title: blood AKR/J 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22028_AKR-2h-3set


title: blood A/J 12hrs Sanger rep4 batch 2 batch 2 1545_4008_20946_A12h-4set


title: blood AKR/J 0hrs rep1 batch 2 batch 2 1545_4182_21999_AKR-cont-1set


title: blood A/J 12hrs Sanger rep5 batch 2 batch 2 1545_4008_20956_A12h-5set


title: blood A/J 2hrs USA100 rep2 batch 6 batch 6 1545_4319_23519_AJ-usa-100-4


title: blood AKR/J 2hrs Sanger rep1 batch 2 batch 2 1545_4182_22000_AKR-2h-1set


title: blood A/J 12hrs Sanger rep1 batch 2 batch 2 1545_3968_20728_A12h-1set


title: blood A/J 2hrs USA100 rep1 batch 6 batch 6 1545_4319_23511_AJ-usa-100-2


title: blood A/J 6hrs Sanger rep1 batch 2 batch 2 1545_3968_20727_A6h-1set

source_name: blood A/J mouse strain blood taken 6 hours after infection with S. aureus Sanger476


title: blood A/J 4hrs Sanger rep4 batch 2 batch 2 1545_4008_20944_A4h-4set

source_name: blood A/J mouse strain blood taken 4 hours after infection with S. aureus Sanger476


title: blood A/J 4hrs Sanger rep3 batch 2 batch 2 1545_4008_20934_A4h-3set


title: blood A/J 12hrs Sanger rep2 batch 2 batch 2 1545_4008_20924_A12h-2set


title: blood AKR/J 0hrs rep3 batch 2 batch 2 1545_4182_22027_AKR-cont-3set


title: blood A/J 6hrs Sanger rep4 batch 2 batch 2 1545_4008_20945_A6h-4set


title: blood A/J 6hrs Sanger rep5 batch 2 batch 2 1545_4008_20955_A6h-5set


title: blood A/J 6hrs Sanger rep3 batch 2 batch 2 1545_4008_20935_A6h-3set


title: blood A/J 12hrs Sanger rep3 batch 2 batch 2 1545_4008_20936_A12h-3set


title: blood A/J 4hrs Sanger rep5 batch 2 batch 2 1545_4008_20954_A4h-5set


title: blood A/J 6hrs Sanger rep2 batch 2 batch 2 1545_4008_20923_A6h-2set


title: blood A/J 2hrs Sanger rep3 batch 6 batch 6 1545_4319_23522_AJ-sanger-5

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus Sanger476


title: blood A/J 4hrs Sanger rep1 batch 2 batch 2 1545_3968_20726_A4h-1set


title: blood A/J 2hrs Sanger rep2 batch 6 batch 6 1545_4319_23515_AJ-sanger-3


title: blood A/J 2hrs Sanger rep1 batch 2 batch 2 1545_4182_21998_A2h-1set


title: blood A/J 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22026_A2h-3set


title: blood A/J 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22012_A2h-2set


title: blood A/J 2hrs Sanger rep1 batch 6 batch 6 1545_4319_23512_AJ-sanger-2


title: blood A/J 4hrs Sanger rep2 batch 2 batch 2 1545_4008_20922_A4h-2set


title: blood A/J 2hrs Sanger rep2 batch 2 batch 2 1545_4008_20930_A2h-2nd


title: blood A/J 2hrs Sanger rep3 batch 2 batch 2 1545_4008_20933_A2h-3set


title: blood A/J 24hrs Ecoli rep4 batch 1 batch 1 1545_3617_18179_AE4

source_name: blood A/J mouse strain blood taken 24 hours after infection with E. coli


title: blood A/J 2hrs MW2 rep3 batch 6 batch 6 1545_4319_23523_AJ-nw2-4

source_name: blood A/J mouse strain blood taken 2 hours after infection with S. aureus MW2


title: blood A/J 0hrs rep1 batch 2 batch 2 1545_4182_21997_A-cont-1set

source_name: blood A/J mouse strain NOT infected


title: blood A/J 24hrs Ecoli rep5 batch 1 batch 1 1545_3617_18180_AE5


title: blood A/J 2hrs Sanger rep5 batch 2 batch 2 1545_4008_20953_A2h-5set


title: blood A/J 2hrs MW2 rep1 batch 6 batch 6 1545_4319_23513_AJ-nw2-2


title: blood A/J 2hrs Sanger rep4 batch 2 batch 2 1545_4008_20943_A2h-4set


title: blood A/J 2hrs Sanger rep1 batch 2 batch 2 1545_3968_20725_A2h-1set


title: blood A/J 24hrs Ecoli rep1 batch 1 batch 1 1545_3617_18176_AE1


title: blood A/J 24hrs Ecoli rep2 batch 1 batch 1 1545_3617_18177_AE2


title: blood A/J 24hrs Ecoli rep3 batch 1 batch 1 1545_3617_18178_AE3


title: blood A/J 2hrs MW2 rep2 batch 6 batch 6 1545_4319_23516_AJ-nw2-3


title: blood A/J 0hrs rep3 batch 2 batch 2 1545_4182_22025_A-cont-3set


title: blood A/J 0hrs rep2 batch 2 batch 2 1545_4008_20931_A2cont


title: blood A/J 0hrs rep3 batch 2 batch 2 1545_4008_20941_A3cont


title: blood A/J 0hrs rep5 batch 1 batch 1 1545_3293_16122_7


title: blood A/J 0hrs rep1 batch 2 batch 2 1545_4008_20921_A1cont


title: blood A/J 0hrs rep2 batch 2 batch 2 1545_4182_22011_A-cont-2set


title: blood A/J 0hrs rep5 batch 2 batch 2 1545_3968_20724_6Acontrol


title: blood A/J 0hrs rep3 batch 1 batch 1 1545_3293_16120_3


title: blood A/J 0hrs rep1 batch 1 batch 1 1545_3293_16118_1


title: blood A/J 0hrs rep2 batch 1 batch 1 1545_3293_16119_2


title: blood A/J 0hrs rep4 batch 2 batch 2 1545_4008_20951_A4cont


title: blood A/J 0hrs rep1 batch 6 batch 6 1545_4319_23514_AJ-control-2


title: blood 129S1/SvImJ 2hrs Sanger rep3 batch 2 batch 2 1545_4182_22024_129-2h-3set

source_name: blood 129S1/SvImJ mouse strain blood taken 2 hours after infection with S. aureus Sanger476


title: blood A/J 0hrs rep4 batch 1 batch 1 1545_3293_16121_6


title: blood 129S1/SvImJ 2hrs Sanger rep2 batch 2 batch 2 1545_4182_22010_129-2h-2set


title: blood 129S1/SvImJ 0hrs rep3 batch 2 batch 2 1545_4182_22023_129-cont-3set

source_name: blood 129S1/SvImJ mouse strain NOT infected


title: blood 129S1/SvImJ 0hrs rep2 batch 2 batch 2 1545_4182_22009_129-cont-2set


title: blood 129S1/SvImJ 2hrs Sanger rep1 batch 2 batch 2 1545_4182_21996_129-2h-1set


title: blood A/J 0hrs rep3 batch 6 batch 6 1545_4319_23524_AJ-control-5


title: blood A/J 0hrs rep2 batch 6 batch 6 1545_4319_23517_AJ-control-3


title: blood 129S1/SvImJ 0hrs rep1 batch 2 batch 2 1545_4182_21995_129-cont-1set


title: HSP-MCAO-1

city: Stanford

first: Robin

last: White

state: CA

address: Grant Building S272, 300 Pasteur Drive

department: Anesthesia

institute: Stanford University

hyb_protocol: Standard hybridization for Affymetrix 430_2 was used.

scan_protocol: The Affymetrix Genechip Scanner 3000 7G was used for scanning.  Raw image files were processed using Affymetrix GCOS software.

data_processing: The Significance Analysis of Microarrays (SAM) method was used to determine genes that were significantly expressed between treatments.  For SAM analysis, initial chip processing and signal calling was done with R and Bioconductor.  The RMA background correction method, quantile normalization and the median polish probeset summary method were employed.

source_name: Ischemic hemisphere 24H

label_protocol: The Affymetrix IVT labeling kit was used according to the manufacturer's protocol.

extract_protocol: Mice were deeply anesthetized with isofluorane and sacrificed 24h after MCAO or sham surgery.  Brains were rapidly removed, divided into hemispheres and RNA was extracted from the ischemic hemisphere or for sham animals the ipsilateral hemisphere using Qiagen RNeasy Midi Kit.

tag: gender

tag: genotype

tag: treatment

value: MCAO

tag: hemisphere

value: Ischemic


title: WT-MCAO-2

value: male

value: WT


title: WT-MCAO-3


title: 6 weeks transfer-G64

city: Shreveport

first: Kevil

middle: G

last: Christopher

state: LA

address: 1501 Kings Highway

department: Pathology

institute: Louisiana State University Health Science Center, Shreveport

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 500 as normalization method.

source_name: colon

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

growth_protocol: The mouse were housed in specific pathogen-free conditions according to Institutional Animal Care and Use Committee (IACUC) regulations and the National Research Council's Guide for the Care and Use of Laboratory Animals.

extract_protocol: Total RNA was extracted by using Rneasy isolation kit (Qiagen).

treatment_protocol: Half a million CD4+CD45RBhigh T cells from healthy wild type C57BL/6 male mice were transferred to male (Rag-/-) mice on C57BL/6 background. The mice were sacrificed and the colon tissue were collected at week 0, 2, 4 and 6.

tag: tissue

value: colon

value: T cell transfer

tag: time

value: 6 weeks

tag: genetic background


title: HSP-SHAM-2

source_name: Control hemisphere, 24H

value: sham

value: control


title: 6 weeks transfer-G61


title: 6 weeks transfer-G62


title: 4 weeks transfer-G4B3

value: 4 weeks


title: HSP-MCAO-2


title: WT-SHAM-1


title: 4 weeks transfer-G41


title: WT-SHAM-2


title: 4 weeks transfer-G43


title: 2 weeks transfer-G26

value: 2 weeks


title: HSP-SHAM-1


title: WT-MCAO-1


title: HSP-MCAO-3


title: 6 weeks transfer-G63


title: 4 weeks transfer-G44


title: Lung cancer saliva-9

city: Los Angeles

first: Hua

last: Xiao

address: 10833 Le Conte Ave

institute: UCLA

description: Gene expression data from human saliva

hyb_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

data_processing: The CEL files from all datasets (array data from 10 lung cancer saliva samples and 10 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.

source_name: saliva

label_protocol: Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

extract_protocol: Ten Lung cancer samples and 10 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMax Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). Equal amounts of labeled RNA (20 mg) were subsequently fragmented and sent to the UCLA microarray core facility for chip hybridization and scanning. The Affymetrix Human Genome U133 Plus 2.0 Array was applied in the salivary transcriptomic profiling.

tag: disease status

value: Lung Cancer


title: Lung cancer saliva-7

description: Gene expression data from human saliva

scan_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)


title: Lung cancer saliva-8

description: Gene expression data from human saliva


title: 2 weeks transfer-G23


title: 2 weeks transfer-G24


title: Normal colon-G06

value: 0 week


title: 2 weeks transfer-G22


title: Normal colon-G04


title: Lung cancer saliva-10

description: Gene expression data from human saliva


title: Lung cancer saliva-6

description: Gene expression data from human saliva


title: Lung cancer saliva-4

description: Gene expression data from human saliva


title: Lung cancer saliva-3

description: Gene expression data from human saliva


title: Lung cancer saliva-1

description: Gene expression data from human saliva


title: Lung cancer saliva-5

description: Gene expression data from human saliva


title: Lung cancer saliva-2

description: Gene expression data from human saliva


title: Healthy control saliva-lc6

description: Gene expression data from human saliva

value: Healthy Control


title: Healthy control saliva-lc3

description: Gene expression data from human saliva


title: Healthy control saliva-lc5

description: Gene expression data from human saliva


title: Healthy control saliva-lc4

description: Gene expression data from human saliva


title: CPC 3-5 patient pool 4

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: labeled miRNA was hybridized onto Agilent's Human miRNA Microarrays V3, Release 12.0 (P/N G4471A, AMADID 021827) annotated against the Sanger miRBASE 12.0 database of miRNAs. according to the manufacturer's instructions.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner

data_processing: The scanned images were analyzed with GenePix Pro 6.0 analysis software using default parameters to obtain background subtracted signal intensities. The data was normalized with quantile method using R Limma package.

source_name: CPC 3-5 patient plasma pool

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from total RNA of 400µL plasma using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

extract_protocol: mirVana Ambion

value: plasma


title: CPC 3-5 patient pool 5


title: Healthy control saliva-lc1

description: Gene expression data from human saliva


title: CPC 3-5 patient pool 3


title: Healthy control saliva-lc7

description: Gene expression data from human saliva


title: Healthy control saliva-lc8

description: Gene expression data from human saliva


title: Healthy control saliva-lc2

description: Gene expression data from human saliva


title: Healthy control saliva-lc10

description: Gene expression data from human saliva


title: CPC 3-5 patient pool 2


title: Healthy control saliva-lc9

description: Gene expression data from human saliva


title: CPC 3-5 patient pool 1


title: CPC 1-2 patient pool 5

source_name: CPC 1-2 patient plasma pool


title: CPC 1-2 patient pool 3


title: CPC 1-2 patient pool 4


title: CPC 1-2 patient pool 2


title: CPC 1-2 patient pool 1


title: Con rep 3

city: Bonn

first: Moritz

last: Kebschull

address: Welschnonnenstr. 17

department: Department of Periodontology

country: Germany

institute: University of Bonn

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Data were analyzed using R/Bioconductor and limma.

source_name: bone-marrow derived dendritic cells

label_protocol: Standard Illumina labeling protocol

growth_protocol: BMDCs were raised from C57BL6 wildtype mouse bone marrow in the presence of GMCSF (20 ng/ml, 6 days). A. actinomycetemcomtans Y4 was cultivated on blood agar plates at 37°C, 5% CO2. P. gingivalis 381 was anaerobically cultivated on blood agar plates.

extract_protocol: Total RNA was extracted from BMDCs using Trizol and subsequent RNAeasy Mini Kit (Qiagen) column cleanup.

treatment_protocol: Bacteria were harvested, quantified at OD600 using established growth curves and diluted in AB-free DMEM/5% FCS. BMDCs were infected at MOI 10 for 24h.

value: uninfected

tag: strain


title: Con rep 2

description: replicate 2


title: Con rep 1

description: replicate 1


title: P.g. rep 2

description: replicate 2

value: Porphyromonas gingivalis infected


title: P.g. rep 1

description: replicate 1


title: A.a. rep 2

description: replicate 2


title: P.g. rep 3

description: replicate 3


title: A.a. rep 3

description: replicate 3


title: A.a. rep 1

description: replicate 1


title: Normal colon-G01


title: T_tumor_NP_77

city: Duarte

first: Peter

middle: P

last: Lee

address: 1500 E Duarte Rd.

department: Cancer Immunotherapeutics and Tumor Immunology

institute: City of Hope

description:
251485020791-1.txt test label is Cy3, ref is Cy5; 251485020791-2.txt test label is Cy5, ref is Cy3
gene expression

hyb_protocol: standard Agilent hyb protocol

scan_protocol: Agilent Microarray Scanner G2505B

data_processing: Quantile normalization and LOESS normalization were used to normalize the raw data. After normalization, the generalized log ratio values for each gene were taken to obtain a relative expression level in samples over UHR. Multiple probes for the same genes were averaged when they were highly correlated; otherwise they were left as is. Probes without entrez ID or Gene Ontology annotation were removed. Variance filtering was used to remove genes which showed little to no variabilty. The R version used is 2.15.1, and the log base transformation of the normalized data is log2

label: Cy3, Cy5

source_name: primary tumor

label_protocol: Material  was labeled with CY3/CY5. Cy-labeled patient samples were mixed with the same amount of reverse color Cy-labeled universal human reference (UHR) cRNA. Dye incorporation and cRNA yield were checked with a NanoDrop Spectrophotometer.

extract_protocol: Total RNA was extracted using the TRIzol method and  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer. cRNA was amplified using TrueLabeling Pico-AMP kit.

treatment_protocol: Primary tumor and tumor-positive lymph nodes were enzymatically digested with Collagenase III and DNAse, and mechanically disaccociated. Cells were strained  through a 70um filter followed by 40um filter. Cells were purified by FACS sorting and homogenized in TRIzol.

tag: cell type

value: tumor cells

value: primary tumor

tag: node status (np or nn for positive or negative, respectively)

value: NP

label: Cy5, Cy3

source_name: universal human reference (UHR)

tag: reference

value: universal human reference (UHR)


title: Normal colon-G05

value: colon


title: T_tumor_NP_81

description:
251485020028-3.txt test label is Cy3, ref is Cy5; 251485020028-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_70

description:
251485033384-1.txt test label is Cy3, ref is Cy5; 251485033384-2.txt test label is Cy5, ref is Cy3
gene expression

value: immune cells


title: T_tumor_NP_78

description:
251485033401-1.txt test label is Cy3, ref is Cy5; 251485033401-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NP_82.2

description:
251485020793-3.txt test label is Cy3, ref is Cy5; 251485020793-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NN_73

description:
251485025870-3.txt test label is Cy3, ref is Cy5; 251485025870-4.txt test label is Cy5, ref is Cy3
gene expression

value: NN


title: T_tumor_NP_76

description:
251485020665-3.txt test label is Cy3, ref is Cy5; 251485020665-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_65.2

description:
251485020793-1.txt test label is Cy3, ref is Cy5; 251485020793-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_69

description:
251485020665-1.txt test label is Cy3, ref is Cy5; 251485020665-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NP_80

description:
251485025872-3.txt test label is Cy3, ref is Cy5; 251485025872-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NP_79

description:
251485025842-1.txt test label is Cy3, ref is Cy5; 251485025842-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_66

description:
251485020790-1.txt test label is Cy3, ref is Cy5; 251485020790-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_71

description:
251485020028-1.txt test label is Cy3, ref is Cy5; 251485020028-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_68

description:
251485025872-1.txt test label is Cy3, ref is Cy5; 251485025872-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_67

description:
251485025841-1.txt test label is Cy3, ref is Cy5; 251485025841-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NN_72

description:
251485020027-3.txt test label is Cy3, ref is Cy5; 251485020027-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NN_75

description:
251485025890-1.txt test label is Cy3, ref is Cy5; 251485025890-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NN_74

description:
251485020666-3.txt test label is Cy3, ref is Cy5; 251485020666-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_tumor_NP_82.1

description:
251485025845-3.txt test label is Cy3, ref is Cy5; 251485025845-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_NN_64

description:
251485025794-3.txt test label is Cy3, ref is Cy5; 251485025794-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_NP_65.1

description:
251485025845-1.txt test label is Cy3, ref is Cy5; 251485025845-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_60

description:
251485026234-3.txt test label is Cy3, ref is Cy5; 251485026234-4.txt test label is Cy5, ref is Cy3
gene expression

source_name: peripheral blood

value: peripheral blood


title: T_NN_63

description:
251485020666-1.txt test label is Cy3, ref is Cy5; 251485020666-2.txt test label is Cy5, ref is Cy3
gene expression


title: T_NN_61

description:
251485020027-1.txt test label is Cy3, ref is Cy5; 251485020027-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_59

description:
251485026235-3.txt test label is Cy3, ref is Cy5; 251485026235-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_56

description:
251485020252-3.txt test label is Cy3, ref is Cy5; 251485020252-4.txt test label is Cy5, ref is Cy3
gene expression


title: T_NN_62

description:
251485025870-1.txt test label is Cy3, ref is Cy5; 251485025870-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_54

description:
251485033076-3.txt test label is Cy3, ref is Cy5; 251485033076-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_55

description:
251485025807-3.txt test label is Cy3, ref is Cy5; 251485025807-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_57

description:
251485026253-3.txt test label is Cy3, ref is Cy5; 251485026253-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_52

description:
251485025794-1.txt test label is Cy3, ref is Cy5; 251485025794-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_58

description:
251485033079-3.txt test label is Cy3, ref is Cy5; 251485033079-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_51

description:
251485025806-1.txt test label is Cy3, ref is Cy5; 251485025806-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_48

description:
251485020794-3.txt test label is Cy3, ref is Cy5; 251485020794-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_42

description:
251485033318-1.txt test label is Cy3, ref is Cy5; 251485033318-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_43

description:
251485025891-3.txt test label is Cy3, ref is Cy5; 251485025891-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_46

description:
251485033432-1.txt test label is Cy3, ref is Cy5; 251485033432-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_39.2

description:
251485026251-3.txt test label is Cy3, ref is Cy5; 251485026251-4.txt test label is Cy5, ref is Cy3
gene expression

source_name: non-sentinel lymph node

value: non-sentinel lymph node


title: T-_NSLN_NP_39.4

description:
251485026252-1.txt test label is Cy3, ref is Cy5; 251485026252-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_39.1

description:
251485026251-1.txt test label is Cy3, ref is Cy5; 251485026251-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_40

description:
251485020026-3.txt test label is Cy3, ref is Cy5; 251485020026-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_49

description:
251485025841-3.txt test label is Cy3, ref is Cy5; 251485025841-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_45

description:
251485033504-3.txt test label is Cy3, ref is Cy5; 251485033504-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_38.4

description:
251485020251-3.txt test label is Cy3, ref is Cy5; 251485020251-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_44

description:
251485020788-3.txt test label is Cy3, ref is Cy5; 251485020788-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_38.3

description:
251485020243-1.txt test label is Cy3, ref is Cy5; 251485020243-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_41

description:
251485033400-1.txt test label is Cy3, ref is Cy5; 251485033400-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_39.3

description:
251485026253-1.txt test label is Cy3, ref is Cy5; 251485026253-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NN_47

description:
251485026235-1.txt test label is Cy3, ref is Cy5; 251485026235-2.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_50

description:
251485025844-3.txt test label is Cy3, ref is Cy5; 251485025844-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_38.1

description:
251485020243-3.txt test label is Cy3, ref is Cy5; 251485020243-4.txt test label is Cy5, ref is Cy3
gene expression


title: PB_NP_53

description:
251485033501-1.txt test label is Cy3, ref is Cy5; 251485033501-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_38.5

description:
251485020250-3.txt test label is Cy3, ref is Cy5; 251485020250-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_38.2

description:
251485020244-1.txt test label is Cy3, ref is Cy5; 251485020244-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_37.2

description:
251485025804-3.txt test label is Cy3, ref is Cy5; 251485025804-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_37.3

description:
251485025805-1.txt test label is Cy3, ref is Cy5; 251485025805-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.4

description:
251485033075-3.txt test label is Cy3, ref is Cy5; 251485033075-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.6

description:
251485033076-1.txt test label is Cy3, ref is Cy5; 251485033076-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_37.1

description:
251485025805-3.txt test label is Cy3, ref is Cy5; 251485025805-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.1

description:
251485033075-1.txt test label is Cy3, ref is Cy5; 251485033075-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.3

description:
251485033403-1.txt test label is Cy3, ref is Cy5; 251485033403-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_35.4

description:
251485033387-3.txt test label is Cy3, ref is Cy5; 251485033387-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.5

description:
251485033402-3.txt test label is Cy3, ref is Cy5; 251485033402-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_35.1

description:
251485033388-3.txt test label is Cy3, ref is Cy5; 251485033388-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_25.3

description:
251485020029-3.txt test label is Cy3, ref is Cy5; 251485020029-4.txt test label is Cy5, ref is Cy3
gene expression

source_name: sentinel lymph node

value: sentinel lymph node


title: T-_SLN_NP_28

description:
251485025687-1.txt test label is Cy3, ref is Cy5; 251485025687-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_36.2

description:
251485033403-3.txt test label is Cy3, ref is Cy5; 251485033403-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_26

description:
251485033435-1.txt test label is Cy3, ref is Cy5; 251485033435-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_25.2

description:
251485020663-1.txt test label is Cy3, ref is Cy5; 251485020663-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_22.4

description:
251485025793-3.txt test label is Cy3, ref is Cy5; 251485025793-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_NSLN_NP_35.2

description:
251485033388-1.txt test label is Cy3, ref is Cy5; 251485033388-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_23

description:
251485025807-1.txt test label is Cy3, ref is Cy5; 251485025807-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_25.1

description:
251485020663-3.txt test label is Cy3, ref is Cy5; 251485020663-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_24

description:
251485020246-3.txt test label is Cy3, ref is Cy5; 251485020246-4.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 4, Mucosa 1

city: Richmond

first: Santanu

last: Dasgupta

state: VA

address: 1220 E Broad Street

institute: Virginia Commonwealth University

hyb_protocol: The biotinylated DNA was added to a hybridization solution and hybridized overnight at 49°C using standard Affymetrix protocol.

scan_protocol: Hybridized arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix Inc).

data_processing:
SNP 250K-NSpI array analysis: We used the 250K-Nsp I array platform from the Affymetrix 500K array set for genotyping each sample.  The genotype call was automatically detected by the Affymetrix’ Genotype Analysis (GTYPE) Software.  Data were analyzed with dChip using HMM model. Nexus program was also used in parallel.  Individual genes were identified based on the SNP ID.

Determination of loss of heterozygosity (LOH) and copy number variation (CNV): The resulting data was anlyzed using both dChip (www.dchip.org) and Nexus software package (http://www.snp-nexus.org) for the determination of LOH and CNV respectively. Intensity (.CEL) files was normalized and modeled using the PM-MM difference modeling method. Array normalization and quality control was performed as per the Affymetrix protocol and requirement. A region of "LOH" was designated when there was a consicutive loss of at least 10 SNPs. The Nexus program was utilized parallely to identify the copy neutral and copy number losses/gains as well as homozygous deletion based on the standard data interpretation criteria.

source_name: surgical biopsy, Patient 4, Mucosa 1

label_protocol: Two hundred fifty nanograms of genomic DNA was digested with Nsp I and ligated to adaptors that recognize the cohesive four base-pair (bp) overhangs. All fragments resulting from restriction enzyme digestion was then ligated using T4 ligase and PCR-amplified using an Applied Biosystems  Thermal Cycler I (9700) to achieve a size range of 200–1,100 bp. Amplified DNA was then pooled, concentrated and cleaned up. The amplified and cleaned product was fragmented using DNaseI (Affymetrix Inc.) and subsequently labeled and denatured using standard Affymetrix protocol.

growth_protocol: None, surgical biopsies

extract_protocol: Genomic DNA was extracted from surgical specimens following standard phenol/chloroform protocol

treatment_protocol: None, surgical biopsies

tag: patient

tag: age (years)

value: F

tag: tumor node metastisis (tnm)

tag: Stage

value: IIB

tag: location

value: Right upper lobe, left lower lobe

tag: diagnosis

value: PDSCC (poorly differentiated squamous cell carcinoma)/MDSCC (moderately differentiated squamous cell carcinoma)

tag: smoking rate

value: 1-2 packs/day

tag: duration

value: 35 yrs

value: Mucosa


title: T-_SLN_NP_22.1

description:
251485025791-1.txt test label is Cy3, ref is Cy5; 251485025791-2.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_27

description:
251485033078-3.txt test label is Cy3, ref is Cy5; 251485033078-4.txt test label is Cy5, ref is Cy3
gene expression


title: T-_SLN_NP_22.2

description:
251485025793-1.txt test label is Cy3, ref is Cy5; 251485025793-2.txt test label is Cy5, ref is Cy3
gene expression


title: T+_SLN_NP_14

description:
251485033078-1.txt test label is Cy3, ref is Cy5; 251485033078-2.txt test label is Cy5, ref is Cy3
gene expression


title: T+_SLN_NP_13

description:
251485033434-3.txt test label is Cy3, ref is Cy5; 251485033434-4.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 4, Normal lymph node

source_name: surgical biopsy, Patient 4, Normal lymph node

tag: gender

value: Normal lymph node


title: Patient 3, Mucosa 3

source_name: surgical biopsy, Patient 3, Mucosa 3

value: Left lung

value: PDSCC (poorly differentiated squamous cell carcinoma)

value: 40 yrs

tag: tissue


title: T+_SLN_NP_12

description:
251485025806-3.txt test label is Cy3, ref is Cy5; 251485025806-4.txt test label is Cy5, ref is Cy3
gene expression

value: NP

value: universal human reference (UHR)


title: T-_SLN_NP_21

description:
251485020791-3.txt test label is Cy3, ref is Cy5; 251485020791-4.txt test label is Cy5, ref is Cy3
gene expression

value: immune cells


title: Patient 4, Carcinoma_1

source_name: surgical biopsy, Patient 4, Carcinoma_1

value: Carcinoma


title: Patient 4, Mucosa 3

source_name: surgical biopsy, Patient 4, Mucosa 3


title: T+_SLN_NP_11.1

description:
251485033384-3.txt test label is Cy3, ref is Cy5; 251485033384-4.txt test label is Cy5, ref is Cy3
gene expression


title: T+_SLN_NP_10

description:
251485020254-1.txt test label is Cy3, ref is Cy5; 251485020254-2.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 4, Mucosa 2

source_name: surgical biopsy, Patient 4, Mucosa 2


title: T+_SLN_NP_9

description:
251485020792-1.txt test label is Cy3, ref is Cy5; 251485020792-2.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 3, Mucosa 1

source_name: surgical biopsy, Patient 3, Mucosa 1


title: T+_SLN_NP_8

description:
251485020794-1.txt test label is Cy3, ref is Cy5; 251485020794-2.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_7

description:
251485033431-3.txt test label is Cy3, ref is Cy5; 251485033431-4.txt test label is Cy5, ref is Cy3
gene expression

value: NN


title: SLN_NN_6.4

description:
251485033504-1.txt test label is Cy3, ref is Cy5; 251485033504-2.txt test label is Cy5, ref is Cy3
gene expression

value: sentinel lymph node


title: SLN_NN_5.2

description:
251485020788-1.txt test label is Cy3, ref is Cy5; 251485020788-2.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_6.1

description:
251485033501-3.txt test label is Cy3, ref is Cy5; 251485033501-4.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_6.2

description:
251485033502-1.txt test label is Cy3, ref is Cy5; 251485033502-2.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_6.3

description:
251485033502-3.txt test label is Cy3, ref is Cy5; 251485033502-4.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 3, Carcinoma_1

source_name: surgical biopsy, Patient 3, Carcinoma_1

value: F


title: Patient 3, Mucosa 2

source_name: surgical biopsy, Patient 3, Mucosa 2

value: IIB


title: T+_SLN_NP_11.2

description:
251485033500-1.txt test label is Cy3, ref is Cy5; 251485033500-2.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 3, Normal lymph node

source_name: surgical biopsy, Patient 3, Normal lymph node


title: Patient 2, Mucosa 3

source_name: surgical biopsy, Patient 2, Mucosa 3

value: M

value: IB

value: Right upper lobe

value: MDSCC (moderately differentiated squamous cell carcinoma)

value: 2-3 packs/day

value: 30 yrs


title: SLN_NN_5.1

description:
251485025795-3.txt test label is Cy3, ref is Cy5; 251485025795-4.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 2, Mucosa 5

source_name: surgical biopsy, Patient 2, Mucosa 5

value: Mucosa


title: SLN_NN_3.3

description:
251485033316-3.txt test label is Cy3, ref is Cy5; 251485033316-4.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_3.2

description:
251485033315-1.txt test label is Cy3, ref is Cy5; 251485033315-2.txt test label is Cy5, ref is Cy3
gene expression


title: SLN_NN_1.3

description:
251485020026_1.txt test label is Cy3, ref is Cy5; 251485020026-2.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 2, Mucosa 2

source_name: surgical biopsy, Patient 2, Mucosa 2


title: SLN_NN_3.1

description:
251485020667-3.txt test label is Cy3, ref is Cy5; 251485020667-4.txt test label is Cy5, ref is Cy3
gene expression

source_name: universal human reference (UHR)


title: SLN_NN_4

description:
251485025891-1.txt test label is Cy3, ref is Cy5; 251485025891-2.txt test label is Cy5, ref is Cy3
gene expression


title: Patient 2, Normal lymph node

source_name: surgical biopsy, Patient 2, Normal lymph node

value: Normal lymph node


title: Patient 2, Carcinoma_1

source_name: surgical biopsy, Patient 2, Carcinoma_1


title: Patient 2, Mucosa 4

source_name: surgical biopsy, Patient 2, Mucosa 4


title: T-_SLN_NP_22.3

description:
251485025792-1.txt test label is Cy3, ref is Cy5; 251485025792-2.txt test label is Cy5, ref is Cy3
gene expression

source_name: sentinel lymph node


title: Patient 1, Mucosa 4

source_name: surgical biopsy, Patient 1, Mucosa 4

value: IA

value: 1-2 packs/day

value: 10 yrs


title: SLN_NN_1.2

description:
251485020025-3.txt test label is Cy3, ref is Cy5; 251485020025-4.txt test label is Cy5, ref is Cy3
gene expression

value: immune cells

value: universal human reference (UHR)


title: Patient 2, Mucosa 1

source_name: surgical biopsy, Patient 2, Mucosa 1


title: Serum sample from Advanced Adenoma after removal (X629)

city: Barcelona

first: María Dolores

last: Giráldez

state: Barcelona

address: Villarroel 170

department: Gastroenterology

country: Spain

institute: Hospital Clínic

description: Serum sample from Advanced Adenoma after removal group (X629)

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: serum plasma sample

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: 20 ml of whole blood from each participant were collected in EDTA tubes. Blood samples were left at 4ºC until plasma separation and plasma was frozen within 6 h of the blood draw. Briefly, samples were centrifuged at 1,600 x g for 10 min at 4 ºC to spin down blood cells, and plasma was transferred into new tubes, followed by further centrifugation at 16,000 x g for 10 minutes at 4ºC to completely remove cellular components. Plasma was then aliquoted and stored at -80°C until use.

tag: disease state

value: Advanced Adenoma after removal

tag: sample type

value: serum


title: Serum sample from Advanced Adenoma group (X623)

value: Advanced Adenoma


title: Serum sample from Advanced Adenoma group (X700)


title: Serum sample from Advanced Adenoma group (X620)


title: Patient 1, Mucosa 5

source_name: surgical biopsy, Patient 1, Mucosa 5


title: Serum sample from colorectal cancer after surgical intervention group (X566)


title: Patient 1, Mucosa 3

source_name: surgical biopsy, Patient 1, Mucosa 3


title: SLN_NN_2

description:
251485025871-1.txt test label is Cy3, ref is Cy5; 251485025871-2.txt test label is Cy5, ref is Cy3
gene expression

value: sentinel lymph node

value: NN


title: blood patient with E. coli bacteremia [DU09-03S96738]

description: Enrollment protocol: Subjects were enrolled at Duke University Medical Center (DUMC; Durham, NC) as part of a prospective, NIH-sponsored study to develop novel diagnostic tests for severe sepsis and community-acquired pneumonia (ClinicalTrials.gov NCT00258869).  Enrolled patients had a known or suspected infection a exhibited two or more Systemic Inflammatory Response Syndrome criteria. Patients were excluded if they had an imminently terminal co-morbid condition, advanced AIDS (CD4 count < 50), were receiving antibiotics prior to enrollment, or were enrolled in another clinical trial. Subjects in the current report had culture-confirmed monomicrobial BSI due to S. aureus (n=26; median age 55 years; range 40-91) or E. coli (n=14; median age 51.5 years; range 25-91). Uninfected controls (n=44; median age 26 years; range 20-59) were enrolled at DUMC as part of study investigating the effect of aspirin on platelet function among healthy.

hyb_protocol: Target was prepared and hybridized according to the "Affymetrix Technical Manual". The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in an GeneChip® Scanner 3000 and expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix).  All GeneChips were scaled to a median intensity setting of 500.

data_processing: Data processing was conducted using the Robust Multichip Average (RMA) generated by Affymetrix Expression Console software.   Microarray data was analyzed in two steps following the analysis strategy.  First, a Bayesian sparse factor model was fit to the expression data without regard to phenotype. Second, factors were then used as independent variables to build a penalized binary regression with variable selection model trained to identify S. aureus infection. In order to minimize issues with overfitting, batch was not included in the regression models. This approach also allows for model averaging, which properly accounts for uncertainty in the choice of predictors and typically outperforms the single best model in predictive accuracy. Genes were filtered for analysis using non-specific filtering for genes with high mean expression and high variance across samples. Samples with a high number of outlying genes were removed during the factor analysis. Mice were batched into discrete experiments with each experiment containing the relevant controls to avoid confounding. Using the same murine experimental data, another classifier was derived to classify methicillin-resistant vs. methicillin-sensitive S. aureus infection. The methodology was otherwise the same as that described above.  We fit a factor model on the human data independently from the mouse data. The factor model was fit to 8,892 genes after non-specific filtering to remove unexpressed and uniformly expressed genes. The factor model was trained on the 95 samples from three batches of expression data, and this resulted in 77 factors. These 77 factors were then projected onto the full data set with the goal of distinguishing S. aureus BSI from healthy controls or E. coli BSI. Leave-one-out cross-validation was utilized in order to control for overfitting of the penalized binary regression model. In order to minimize issues with overfitting, batch was not included in the regression models. Matlab scripts to perform these operations are available.

source_name: blood patient with E. coli bacteremia prior antibiotic treatment (Emergency Department)

label_protocol: The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc).  The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).

extract_protocol: Total RNA was extracted from human blood using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) following the manufacturer’s recommended protocol including DNase treatment.  Following isolation, RNA quantity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). A set of four peptide nuleic acid (PNA) oligomers (Applied Biosystems, Foster City, CA) with sequences complimentary to globin mRNA were added to 2.5 ug of total RNA to reduce globin RNA transcription, then converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).   After first strand synthesis, residual RNA was degraded by the addition of RNaseH and a double-stranded cDNA molecule was generated using DNA Polymerase I and DNA Ligase. The cDNA was then purified and concentrated using a phenol:chloroform extraction followed by ethanol precipitation.

tag: ethnicity

value: White

tag: host gender

value: Male

tag: host age (yr)

tag: pathogen

value: Escherichia coli

tag: anatomic site of infection

value: Urinary Tract

tag: experimental batch


title: embryo of Pax6 mutant, biological rep1

city: Sendai

first: Takako

last: Kikkawa

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip Rat Genome 230 2.0 Array (GPL1355). Washing and staining were performed after hybridization under Affymetrix fluidics station protocol.

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

data_processing: The data were analyzed with the GC content-adjusted robust-multi-array (GC-RMA) algorithm using the R statistical software with Bioconductor packages as normalization method.

organism: Rattus norvegicus

source_name: Pax6 mutant rat (rSey2/rSey2) telencephalon at E11.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: The midday of the vaginal plug was designated as embryonic day 0.5 (E0.5).

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

treatment_protocol: Rat telencephalon at E11.5 were disscted under the stereomicroscope. Selected tissues were rinsed with PBS and placed on ice in the TRIZOL Reagent (Invitrogen).

value: telencephalon

tag: genotype

value: Pax6 mutant rat (rSey2/rSey2)

tag: age

tag: genetic background

value: Sprague-Dawley


title: embryo of WT, biological rep2

source_name: WT rat telencephalon at E11.5

value: wild type rat


title: blood patient with E. coli bacteremia [DU10-01S06732]

value: Female


title: embryo of Pax6 mutant, biological rep2


title: blood patient with E. coli bacteremia [DU09-03S07915]


title: embryo of WT, biological rep1


title: blood patient with E. coli bacteremia [DU10-01S02093]


title: SLN_NN_1.1

description:
251485020025-1.txt test label is Cy3, ref is Cy5; 251485020025-2.txt test label is Cy5, ref is Cy3
gene expression

tag: cell type

tag: node status (np or nn for positive or negative, respectively)

tag: reference


title: Serum sample from Advanced Adenoma group (X626)


title: Serum sample from Advanced Adenoma after removal (X632)

description: Serum sample from Advanced Adenoma after removal group (X632)


title: Patient 1, Mucosa 1

source_name: surgical biopsy, Patient 1, Mucosa 1

tag: patient

tag: age (years)

value: M

tag: tumor node metastisis (tnm)

tag: Stage

value: IA

tag: location

value: Right upper lobe

tag: diagnosis

value: MDSCC (moderately differentiated squamous cell carcinoma)

tag: smoking rate

value: 1-2 packs/day

tag: duration

value: 10 yrs

value: Mucosa


title: blood patient with S. aureus bacteremia [DU09-03S95905]

source_name: blood patient with S. aureus bacteremia prior antibiotic treatment (Emergency Department)

tag: ethnicity

tag: host gender

tag: host age (yr)

tag: pathogen

value: Staphylococcus aureus

value: CNS


title: Patient 1, Mucosa 2

source_name: surgical biopsy, Patient 1, Mucosa 2

tag: gender

tag: tissue


title: Serum sample from Advanced Adenoma after removal (X577)

description: Serum sample from Advanced Adenoma after removal group (X577)

tag: disease state

value: Advanced Adenoma after removal

tag: sample type

value: serum


title: Serum sample from colorectal cancer group (X540)

value: colorectal cancer


title: Serum sample from Advanced Adenoma group (X542)

value: Advanced Adenoma


title: Serum sample from Advanced Adenoma after removal (X576)

description: Serum sample from Advanced Adenoma after removal group (X576)


title: blood patient with S. aureus bacteremia [DU09-03S92423]

value: White

value: Male

tag: anatomic site of infection

value: Skin or Skin Structure

tag: experimental batch


title: Serum sample from colorectal cancer group (X493)


title: Serum sample from Advanced Adenoma group (X492)


title: blood patient with S. aureus bacteremia [DU09-03S93303]

value: Black


title: Patient 1, Normal lymph node

source_name: surgical biopsy, Patient 1, Normal lymph node

tag: patient

tag: age (years)

value: M

value: Normal lymph node


title: Patient 1, Carcinoma_1

source_name: surgical biopsy, Patient 1, Carcinoma_1

tag: tumor node metastisis (tnm)

tag: Stage

value: IA

value: Right upper lobe

value: Carcinoma


title: Serum sample from Advanced Adenoma group (X491)


title: Serum sample from Advanced Adenoma group (X489)


title: blood healthy control [DU09-01S01276.CEL]

source_name: blood human NOT infected

value: black

value: Female


title: blood patient with E. coli bacteremia [DU10-01S03145]

value: Escherichia coli

value: Urinary Tract


title: Serum sample from colorectal cancer group (X488)