title: C2_SA1076

value: Test

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

value: F

tag: tissue

tag: illness

value: Arthritis/No bacteremia

value: yes

value: MRSA

value: IV

value: III

tag: cluster

tag: mdth

value: Invasive

value: Osteoarticular

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: bands

value: Missing Data

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)


title: C2_SA1032

status: Public on Apr 04 2012

type: RNA

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with BeadArray Reader 500X

data_processing: The data were normalised using average normalisation with Genome Studio

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted with MagMAX™ RNA Isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia, osteomyelitis

value: no

value: No Isolate

value: No Data

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: eosinophils (%)

tag: basophils (%)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology

value: abnormal


title: C2_SA1007

value: Test

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

value: Groin abscess, complex s/p surgical i&d 1/20/08, elevated CRP (42)

value: yes

value: MRSA

value: IV

value: I

tag: cluster

tag: mdth

value: Mild

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)


title: Sample-121-control

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: Two hundred ng of total RNA from each sample were labeled and hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

scan_protocol: Illumina BeadArray Reader with standard scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R

label: biotin

source_name: blood

extract_protocol: Total RNA, including miRNA from plasma, was isolated using the miRNeasy kit (Qiagen) with minor modifications. The quality and quantity of the RNA was evaluated by 260/280 ratio using NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc.) and Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: pNZ8900 vs pNZ-ykrK rep2

city: Groningen

first: Bogumila

last: Marciniak

address: Nijenborgh 7

department: Department of Genetics

country: Netherlands

institute: Rijksuniversiteit Groningen

hyb_protocol: The labelled cDNA was hybridized to oligo DNA microarray in Ambion Slidehyb #1 buffer (Ambion Eurpe Ltd) at 48°C for 18 hours. Next, microarray slides were washed in 2 × SSC with 0.5% SDS, 1 × SSC with 0.25% SDS and 1 × SSC with 0.1% SDS and dried by centrifugation.

scan_protocol: Images were acquired with GeneTac LS IV confocal laser scanner (Genomics Solutions).

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP (van Hijum et. al. (2003) Appl. Bioinformatics 2, 241-244). Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of overexpression mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data

organism: Bacillus subtilis

source_name: Net intensity (tr.mean) {B}

label_protocol: 16 μg of total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a CyScribe GFX purification kit (Amersham Biosciences).

growth_protocol: 50 ml of LB was inoculated with over/night cultures to an OD600=0.05 and cultures were grown under vigurous shaking (225 rpm) at 37°C.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) according to the manufacturer's instruction. Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures and from one culture of each strain an additional sample was collected for technical replicate.

treatment_protocol: When cells reached OD600=0.8, 0.1% subtilin (subtilin containing supernatant of subtilin producing B. subtilis strain ATCC 6633). 30 minuts after subtilin induction, 13 OD units of each culture were collected for total RNA isolation (1 OD unit = 1 ml of a culture of an OD600 = 1.0).

tag: genotype

value: Wild Type

tag: strain

tag: plasmid

source_name: Net intensity (tr.mean) {A}

value: test

value: YkrK Overexpression Mutant

value: pNZ-ykrK


title: RAW264.7 cells, Tbc1d23 overexpression, 1 hrs post-LPS, replicate 1

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

description: cSA2 - A - 1hr

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using RMA and log2-transformed in Partek software (St. Louis, MO)

organism: Mus musculus

source_name: LPS-stimulated RAW264.7 macrophages

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM + 10% FBS + 400 ug/ml G418 (Invitrogen).  The cultures were grown at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using Qiagen RNeasy miniprep kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RAW264.7 cells harboring constructs that either overexpress Tbc1d23 or Chloramphenicol Acetyltransferase (CAT) were exposed to 20 ng/ml LPS for the indicated times - either 1,3, or 5 hrs or were left unexposed (0 hrs) and then cells were lysed and RNA was prepared.

tag: construct

tag: lps exposure time


title: Sample-119-control

label_protocol: Two hundred ng of total RNA from each sample were labeled and hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).


title: C2_H939

tag: disease

value: Healthy

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

value: Missing Data

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: mchc (g/dl)


title: C2_SA1024

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

value: abscess, SST, PICU (serious)

value: Quarter 2

value: Tier 1

tag: cluster

tag: mdth

value: Severe

value: Invasive

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology

value: abnormal


title: Sample-116-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: Sample-117-control


title: C2_H938

tag: disease

value: Healthy

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mchc (g/dl)


title: pNZ8900 vs pNZ-ykrK rep1

tag: genotype

value: Wild Type

tag: strain

tag: plasmid

tag: sample type

value: test

value: YkrK Overexpression Mutant

value: pNZ-ykrK


title: Sample-120-control

tag: disease state

tag: cell type


title: C2_H936

value: Test

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)


title: Sample-118-case

tag: disease state

value: familial ovarian cancer

tag: sample type

value: case

tag: cell type


title: Sample-114-control


title: Sample-113-control


title: Sample-112-control


title: Sample-109-control


title: Sample-110-control


title: Sample-108-control


title: C2_H934

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H1357

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-107-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-115-control


title: C2_H1358

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H2003.1

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-111-case

tag: disease state

tag: sample type

tag: cell type


title: C2_H1321

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H1353

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C2_H924

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H1355

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C2_H1354

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H1359

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C2_H1299

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: Sample-105-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: Sample-103-control


title: Sample-106-case


title: C2_H1261.1

tag: disease

value: Healthy

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-104-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-102-control


title: C2_H1260

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: C2_H1278

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C2_H1244

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: Sample-101-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-99-case


title: C2_H1285

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-97-control

tag: disease state

tag: sample type

tag: cell type


title: C2_H1284

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)


title: Sample-96-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-98-control


title: Sample-100-control


title: Sample-95-control


title: C2_H1191

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-92-control

tag: disease state

tag: sample type

tag: cell type


title: C1_SA954

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

value: Bacteremia

value: yes

value: MRSA

value: II

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Cefazolin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-94-control

tag: disease state

tag: sample type

tag: cell type


title: C1_SA953

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: IV

value: I

value: Quarter 2

tag: cluster

tag: mdth

value: Osteoarticular

tag: treatment

value: Vancomycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

value: Missing Data

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA949

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

tag: illness

value: Bacteremia x 3d (19,20,22)/Suppurative Arthritis (knee)

tag: cluster

tag: mdth

value: Severe

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA952

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

value: Bacteremia/Pneumonia/Cellulitis

value: yes

value: MRSA

value: Tier 2

tag: cluster

tag: mdth

value: Pneumonia

tag: treatment

value: Vancomycin/Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA960

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Pneumonia/Empyema

value: IV

value: I

tag: cluster

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Vancomycin/Bactrimycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-93-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: C1_SA909

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: Disseminated disease

value: Quarter 2

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Clindamycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-90-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-88-case

value: familial ovarian cancer

value: case


title: Sample-87-control


title: C1_SA944

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Osteomyelitis

value: yes

value: MRSA

value: IV

value: I

value: Quarter 3

value: Tier 2

tag: cluster

tag: mdth

value: Osteoarticular

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-91-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: C1_SA943

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

tag: illness

value: Osteomyelitis/Suppurative Arthritis

value: Quarter 2

tag: cluster

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA908

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/SST Abscess/Cellulitis

value: yes

value: MSSA

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Cefazolin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA907

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

tag: illness

value: Bacteremia

value: MRSA

value: IV

value: I

value: Quarter 3

value: Tier 3

tag: cluster

value: MQ

tag: mdth

value: Unclassified

value: Bacteremia only

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: Sample-86-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: Sample-85-control


title: C1_SA633

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Osteomyelitis/Pyomyositis

value: yes

value: Quarter 2

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA999

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: F

tag: tissue

tag: illness

value: Osteomyelitis/Pyomyositis/SST Abscess

value: MRSA

value: IV

value: I

value: Tier 2

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA1267

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Pneumonia

value: no

value: No Isolate

value: No Data

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA619

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia/Osteomyelitis

value: yes

value: MSSA

value: II

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA632

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Osteomyelitis/Pyomyositis

value: MRSA

value: IV

value: I

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA617

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

tag: illness

value: Osteomyelitis/Suppurative Arthritis

value: yes

value: MSSA

tag: cluster

value: MQ

tag: mdth

value: Moderate

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_SA1276

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Osteomyelitis/DVT

value: no

value: No Isolate

value: MRSA

value: No Data

value: Tier 3

tag: cluster

tag: mdth

value: Invasive

value: Osteoarticular

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-89-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: Sample-83-control


title: C2_H1053

value: Test

tag: disease

value: Healthy

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-84-control

tag: disease state

tag: sample type

tag: cell type


title: Sample-81-case

value: familial ovarian cancer

value: case


title: Sample-80-control


title: Sample-79-control


title: Sample-78-control


title: Sample-75-control


title: Sample-77-control


title: Sample-76-control


title: Sample-74-case


title: C1_SA1263

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Pneumonia

value: Quarter 1

value: Tier 2

tag: cluster

tag: mdth

value: Moderate

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-82-control

tag: disease state

value: control

tag: sample type

tag: cell type


title: Sample-73-case

value: lymphoblastoid cell line


title: C1_SA1142

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: Bacteremia/Suppurative Arthritis

value: no

value: No Isolate

value: MSSA

value: No Data

value: Quarter 2

tag: cluster

value: MQ

tag: mdth

value: Invasive

value: Osteoarticular

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1117

value: Training

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Osteomyelitis/Pyomyositis

value: yes

value: I

value: Quarter 3

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Cefazolin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

value: Missing Data

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1122

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: MRSA

value: IV

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1152

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

value: no

value: No Isolate

value: MSSA

value: No Data

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1257

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Cellulitis/Meningitis

value: yes

value: I

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Disseminated

value: Meningitis

tag: treatment

value: Vanco/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-72-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: C1_SA1155

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia/Osteomyelitis

value: MSSA

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Oxacillin/Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

value: Missing Data

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1118

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Suppurative Arthritis elbow/Osteomyelitis (humerus)

value: yes

value: MRSA

value: IV

value: I

value: Quarter 3

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-71-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: C1_SA1141

value: Training

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia/Suppurative Arthritis

value: III

value: Tier 3

tag: cluster

value: MQ

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

value: Missing Data

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1228

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: yes

value: MSSA

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1204

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: Bacteremia/Osteomyelitis

value: no

value: No Isolate

value: MRSA

value: No Data

value: Quarter 3

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1154

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: yes

value: MSSA

value: I

value: Missing Data

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-70-control

tag: disease state

value: control

tag: sample type

tag: cell type

value: lymphoblastoid cell line


title: Sample-68-case

value: familial ovarian cancer

value: case


title: Sample-69-control


title: Sample-67-control


title: Sample-66-case


title: Sample-65-case


title: C1_SA1115

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

value: MRSA

value: IV

value: Tier 3

tag: cluster

value: MQ

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-64-control

tag: disease state

tag: sample type

tag: cell type


title: C1_SA1083

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: Bacteremia/Pyomyositis

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Severe

value: Invasive

value: Osteoarticular

tag: treatment

value: Oxacillin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1081

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia (3d)/Osteomyelitis (femur)/Suppurative Arthritis (hip)

value: yes

value: I

tag: cluster

tag: mdth

tag: treatment

value: Vancomycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

value: Missing Data

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1109

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: Bacteremia (4d)/Suppurative Arthritis (R elbow and shoulder)/Osteomyelitis

value: no

value: No Isolate

value: MRSA

value: No Data

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1078

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: Pneumonia

value: MSSA

value: Tier 3

tag: cluster

value: MQ

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Cephalexin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1075

value: Training

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Osteomyelitis/Pyomyositis/no bacteremia

value: yes

value: IV

value: I

tag: cluster

tag: mdth

value: Osteoarticular

tag: treatment

value: Vancomycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1069

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: MRSA

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_SA1066

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

value: Osteomyelitis/Suppurative Arthritis

value: MSSA

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: C1_SA1070

value: Training

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia (2d)/Suppurative Arthritis/Pyomyositis (iliopsoas)

value: yes

value: II

tag: cluster

value: MQ

tag: mdth

tag: treatment

value: Cefazolin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-63-case

tag: disease state

value: familial ovarian cancer

tag: sample type

value: case

tag: cell type

value: lymphoblastoid cell line


title: C1_SA1056

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Pneumonia/Empyema

value: MRSA

value: IV

value: I

value: Tier 3

tag: cluster

tag: mdth

value: Pneumonia

tag: treatment

value: Vancomycin/Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

value: Missing Data

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-59-case

tag: disease state

tag: sample type

tag: cell type


title: Sample-61-case


title: Sample-60-case


title: Sample-57-case


title: Sample-55-case


title: Sample-54-case


title: Sample-56-case


title: Sample-58-case


title: C1_SA1033

value: Training

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia

value: yes

value: Quarter 3

tag: cluster

tag: mdth

value: Unclassified

value: Bacteremia only

tag: treatment

value: Oxacillin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-62-case

tag: disease state

value: familial ovarian cancer

tag: sample type

value: case

tag: cell type

value: lymphoblastoid cell line


title: Sample-53-case


title: Sample-52-case


title: Sample-51-case


title: Sample-49-case


title: C1_H288

tag: disease

value: Healthy

tag: age

tag: ethnicity

value: AA

tag: gender

value: F

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)


title: Sample-48-case

tag: disease state

tag: sample type

tag: cell type


title: Sample-50-case


title: C1_H646

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)


title: C1_H275

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_H289

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: eosinophils (%)

tag: basophils (%)

tag: bands

value: Missing Data

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: platelets (103/mm3)


title: C1_H287

value: Training

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: rdw (%)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Sample-47-case

tag: disease state

tag: sample type

tag: cell type


title: C1_H332

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)


title: C1_H241

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_H229

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)


title: C1_H153

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)


title: C1_H213

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)


title: C1_H226

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)


title: C1_H240

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C1_H205

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)


title: Sample-44-case

tag: disease state

tag: sample type

tag: cell type


title: C1_H231

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)


title: Sample-46-case

tag: disease state

tag: sample type

tag: cell type


title: C1_H996

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)


title: C1_H220

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)


title: Sample-43-case

tag: disease state

tag: sample type

tag: cell type


title: Sample-40-case


title: Sample-39-case


title: Sample-42-case


title: Sample-41-case


title: Sample-45-case


title: C1_H127

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)


title: C1_H1181

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)


title: C1_H1242

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)


title: JF5 late-log replicate 1

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

description: JF5_1 late-log.CEL

hyb_protocol: Arrays were hybridized using streptavidin phycoerythrin according to Affymetrix protocol ProkGE-WS2v3_450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing:
Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetix, Inc.)  GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies)
Normalization was done per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples.  The cross-gene error model was operating based on replicates.  The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering

organism: Neisseria gonorrhoeae

source_name: cells harvested at late-log phase; OD600 = 0.8

label_protocol: Biotinylated cRNA was prepared according to Affymetrix Genechip® Expression Analysis Technical Manual prokaryotic protocol from 10ug of total RNA

growth_protocol: Isolates were grown to mid-log and late-log phase in GC broth @ 37°C with supplements and sodium bicarbonate: Shafer, W.M., L. F. Guymon, I. Lind, and P. F. Sparling. 1984. Identification of an envelope mutation (env-10) resulting in increased antibiotic susceptibilit

extract_protocol: RNA was isolated by a hot phenol method according to: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005.  Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol.

treatment_protocol: Gene expression of FA19 MpeR mutant JF5 mid-log replicates were compared to previously deposited WT FA19 mid-log samples (GSM318543, GSM318544, and GSM318545)

tag: strain

value: FA19mpeR mutant


title: AML-9

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

hyb_protocol: The amplified cRNA samples were hybridized overnight and then washed based on the protocol of the Agilent Oligo Microarray (One-Color Microarray-Based Gene Expression Analysis V5.7, GE 8x15K, Gene Expression Hybridization Kit).

scan_protocol: Array slides were scanned on a GenePix 4000B scanner at 570 PMT and 100% Power standard setting according to the manufacturer’s instruction (Molecular Devices Corporation, Sunnyvale, CA, USA).

data_processing: Array slide images were then analyzed using Agilent Feature Extraction software (9.5.1.1) to obtain gene expression signals and array QC reports. Partek Genomics Suite (Partek Inc., St. Louis, MO, USA) were used for the data normalization. Briefly, background-adjustment, quantile normalization, and log2-transformation were used to normalize and treat gene expression intensities, and then median-centering genes for each array and median-centering each gene across all arrays were conducted.

source_name: AML

label_protocol: 0.5ug total RNA per sample was reverse transcribed, amplified and labeled with Cy3 using the Agilent one-color amplification protocol (Agilent Quick-Amp Labeling Kit, One-color; One-Color Microarray-Based Gene Expression Analysis).

extract_protocol: Blasts and mononuclear cells were purified by use of NycoPrep 1.077A (Axis-Shield, Oslo, Norway) according to the manufacturer’s manual. Total RNA was isolated from each sample using the miRNeasy Mini Kit (Qiagen), Trizol reagent (Invitrogen), or guanidinium thiocyanate followed by cesium chloride-gradient purification.

tag: gender

value: male

tag: age (yrs)

tag: tissue

value: bone marrow (BM)

tag: disease state

value: acute myeloid leukemia (AML)

tag: abnormality


title: JF5 late-log replicate 3

description: JF5_3 late-log.CEL


title: Sample-37-case

value: familial ovarian cancer

tag: sample type

tag: cell type


title: Sample-36-case

value: case


title: Sample-38-case

value: lymphoblastoid cell line


title: JF5 late-log replicate 2

description: JF5_2 late-log.CEL


title: AML-8

tag: subtype


title: AML-7

value: peripheral blood (PB)


title: C1_H1183

tag: disease

value: Healthy

tag: age

tag: ethnicity

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: neutrophil (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)


title: JF5 mid-log replicate 2

description: JF5_2 mid-log.CEL

source_name: cells harvested at mid-log phase; OD600 = 0.6

tag: strain


title: Sample-35-case

tag: disease state

tag: sample type

tag: cell type


title: JF5 mid-log replicate 1

description: JF5_1 mid-log.CEL


title: Rybp binding in Dnmt1-KO ESCs_Promoter [Agilent-014716]

type: genomic

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: Microarray 1 of 2

hyb_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

scan_protocol: ChIP-v1_10_Apr08, Agilent DNA Microarray Scanner G2505C, Agilent Scan Control (Ver. A.8.4.1)

data_processing: Scanned images were quantified with Agilent Feature Extraction software 9.5.3.1 under standard conditions. Each signal was normalized using linear transformation to fit representing probes extracted using rank consistency filter algorithm.

molecule: genomic DNA

source_name: Input from Dnmt1-KO ESCs

growth_protocol: ES cells were cultured in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.

extract_protocol: ES cells were subjected to ChIP assay using a Rybp antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008).

treatment_protocol: ES cells were treated with 1 % formaldehyde/PBS for 10 min at room temperature. Cells were washed with PBS, collected and resuspended in swelling buffer [20 mM Hepes (pH 7.8), 1.5 mM MgCl2, 10 mM KCl, 0.1 % NP-40, and 1 mM DTT] by pipetting and then kept on ice for 10 min. After Dounce homogenizing 10-20 times, the cells were centrifuged and then the pellets were resuspended in RIPA buffer [20 mM Tis-HCl (pH 8.0), 1 mM EDTA, 140 mM NaCl, 1 % Triton X-100, 0.1 % SDS, and 0.1 % deoxycholic acid] containing protease inhibitors and sonicated into fragments with an average length of 0.3-0.5 kb. After centrifugation, the supernatants were subjected to IP with specific antibodies as previously described (Orlando et al., 1997)

value: embryonic stem cells

tag: genotype/variation

value: Dnmt1 constitutive KO

value: input DNA from whole cell extract

source_name: Immunoprecipitated DNA with anti-Rybp from Dnmt1-KO ESCs

value: Immunoprecipitated DNA

tag: chip antibody

value: Rybp antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody catalog number


title: JF5 mid-log replicate 3

description: JF5_3 mid-log.CEL


title: FA19 late-log replicate 2

description: FA19_2 late-log.CEL


title: C1_H1245

value: Training

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

value: Missing Data

tag: hemoglobin (g/dl)

tag: mpv (um3)


title: FA19 late-log replicate 1

description: FA19_1 late-log.CEL

tag: strain


title: FA19 late-log replicate 3

description: FA19_3 late-log.CEL


title: Sample-34-case

tag: disease state

tag: sample type

tag: cell type


title: AML-64

tag: gender

value: male

tag: age (yrs)

tag: tissue

value: acute myeloid leukemia (AML)

tag: subtype

tag: abnormality


title: C1_H1239

tag: disease

tag: age

tag: ethnicity

tag: illness

tag: cluster

tag: mdth

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)


title: Rybp binding in Eed-KO ESCs_Promoter [Agilent-014716]

description: Microarray 1 of 2

source_name: Input from Eed-KO ESCs

label_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

tag: cell type

tag: genotype/variation

value: Eed constitutive KO

tag: sample type

source_name: Immunoprecipitated DNA with anti-Rybp from Eed-KO ESCs

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody catalog number


title: Rybp binding in WT ESCs_Promoter [Agilent-014716]

description: Microarray 1 of 2

source_name: Input from WT ESCs

value: wild type

source_name: Immunoprecipitated DNA with anti-Rybp from WT ESCs


title: Sample-33-case

tag: disease state

value: familial ovarian cancer

value: case

value: lymphoblastoid cell line


title: AML-65

tag: gender

tag: age (yrs)

tag: tissue

value: bone marrow (BM)

tag: subtype

tag: abnormality

value: NK


title: Sample-32-case


title: Sample-31-case


title: 126

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

description:
3C
Used in analysis: yes
WK_4_2_4.txt

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with a 8x15k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, and hen dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, the edwards method for background correction was used (min. offset = 30), and global loess normalizion (MAANOVA) was done.

organism: Folsomia candida

source_name: 30 animals, field soil, 3C

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil. 20 adult animals were incubated per container, which contained a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle.

extract_protocol: Total RNA was extracted from all animals (~30) per jar using the SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at the same conditions as incubation. After exposure, the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: age

value: 23 days

value: whole body

tag: treatment

value: field soil

tag: copper level

tag: ph

value: C


title: AML-62


title: AML-61


title: Sample-30-case


title: AML-60


title: 103

description:
4C
Used in analysis: yes
WK_4_2_4.txt

source_name: 30 animals, field soil, 4C


title: FA19 mid-log replicate 2

data_processing: Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetrix, Inc.)  GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies) and normalized per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples.  The cross-gene error model was operating based on replicates.  The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering.

source_name: FA19 cells harvested at mid-log phase; 0.6 @600 OD

growth_protocol: Isolates were grown to mid-log phase in GC broth @ 37°C with supplements and sodium bicarbonate: Shafer, W.M., L. F. Guymon, I. Lind, and P. F. Sparling. 1984. Identification of an envelope mutation (env-10) resulting in increased antibiotic susceptibilit

tag: strain


title: FA19 mid-log replicate 1


title: 46

description:
2B
Used in analysis: no
WK_4_2_3.txt

source_name: 30 animals, field soil, 2B

value: B


title: FA19 mid-log replicate 3


title: AML-63


title: 24

description:
3D
Used in analysis: no
WK_4_2_3.txt

source_name: 30 animals, field soil, 3D

value: D


title: 102

description:
2A
Used in analysis: no
WK_4_2_1.txt

source_name: 30 animals, field soil, 2A

value: A


title: Sample-29-case

source_name: blood

tag: cell type


title: AML-6

value: female


title: Sample-28-case


title: Sample-27-case


title: 112

description:
4A
Used in analysis: yes
WK_4_1_4.txt

source_name: 30 animals, field soil, 4A


title: AML-59

value: male


title: AML-58

value: acute myeloid leukemia (AML)


title: 28

description:
3B
Used in analysis: yes
WK_4_2_2.txt

source_name: 30 animals, field soil, 3B


title: 32

description:
1D
Used in analysis: yes
WK_4_2_2.txt

source_name: 30 animals, field soil, 1D


title: 27

description:
2D
Used in analysis: yes
WK_4_1_4.txt

source_name: 30 animals, field soil, 2D


title: 105

description:
1A
Used in analysis: no
WK_4_2_1.txt

source_name: 30 animals, field soil, 1A


title: Sample-25-case


title: 6

description:
4B
Used in analysis: yes
WK_4_1_3.txt

source_name: 30 animals, field soil, 4B


title: AML-57


title: 125

description:
2C
Used in analysis: yes
WK_4_1_2.txt

source_name: 30 animals, field soil, 2C


title: 20

description:
4D
Used in analysis: yes
WK_4_1_3.txt

source_name: 30 animals, field soil, 4D


title: Sample-24-case


title: Sample-23-case


title: AML-55


title: AML-54

value: MLL


title: AML-53


title: 44

description:
2D
Used in analysis: no
WK_3_2_4.txt


title: 101

description:
2C
Used in analysis: no
WK_3_2_2.txt


title: AML-56

value: peripheral blood (PB)


title: 109

description:
3A
Used in analysis: no
WK_4_1_1.txt

source_name: 30 animals, field soil, 3A


title: 42

description:
3B
Used in analysis: yes
WK_3_2_2.txt


title: Sample-26-case

value: familial ovarian cancer


title: 75

description:
2B
Used in analysis: yes
WK_3_2_3.txt


title: 66

description:
1B
Used in analysis: yes
WK_4_1_2.txt

source_name: 30 animals, field soil, 1B


title: 77

description:
3A
Used in analysis: yes
WK_3_2_3.txt


title: 38

description:
4C
Used in analysis: yes
WK_3_2_4.txt


title: 83

description:
1C
Used in analysis: yes
WK_4_1_1.txt

source_name: 30 animals, field soil, 1C


title: Sample-22-case

value: case


title: AML-52


title: 59

description:
4D
Used in analysis: no
WK_3_2_1.txt


title: 94

description:
1A
Used in analysis: yes
WK_3_2_1.txt


title: Sample-20-case

value: lymphoblastoid cell line


title: Sample-21-case


title: AML-51

value: bone marrow (BM)


title: 87

description:
2A
Used in analysis: no
WK_3_1_4.txt


title: Sample-19-case


title: AML-5

value: NK


title: 90

description:
4A
Used in analysis: no
WK_3_1_4.txt

value: 23 days


title: AML-50


title: Sample-16-case


title: Sample-18-case


title: Sample-17-case


title: 29

description:
4B
Used in analysis: no
WK_3_1_3.txt

value: whole body


title: AML-48


title: AML-47


title: 61

description:
1D
Used in analysis: yes
WK_3_1_3.txt

value: field soil


title: AML-49


title: Sample-14-case


title: Whole plant_Long-days_25C_rep2

city: Canberra

first: Megan

middle: Natalie

last: Hemming

state: ACT

address: GPO Box 1600

country: Australia

institute: CSIRO Division of Plant Industry

hyb_protocol: The fragmented Cy3 labelled cRNA was prepared for hybridisation to the arrays using the GX hybridisation kit (Agilent, 5188-5242) where each hybridisation reaction had a final volume of 70µL.  The Agilent hybridisation chambers were prepared according to manufacturer’s instructions. Hybridisation chambers were placed in a rotating hybridisation oven at 65°C for 17 hours. After hybridisation, the arrays were washed according to manufacturer’s instructions using GX washing buffers (Agilent, 5188-5327).

scan_protocol: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v1_95_Feb07 and Grid: 021623_D_F_20100204) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The microarray dataset was analysed in R v2.7.1 using packages from Bioconductor (Gentleman et al. 2004 (Genome Biol 5:R80); http://www.bioconductor.org/). Scale normalisation (Smyth and Speed 2003 Methods 31:181-192) was carried out using the ‘normalizeBetweenArrays’ function in limma and differentially expressed probes were identified across the normalised datasets for biological replicates using linear modelling in limma (Smyth 2005 limma: Linear Models for Microarray Data).

organism: Hordeum vulgare

source_name: whole plant, 16 hour photoperiod, 25°C, replicate2

label_protocol: 500ng RNA was labelled using the Ambion Total Prep RNA amplification kit (Applied Biosystems, AMIL1791). The quantity of amplified product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. 750ng of amplified cRNA was used for the Cy3 coupling process using an ULS labelling kit (Kreatech, EA-006). After coupling the dye, the reaction was cleaned using the KREApure columns in the kit. The Cy3 labelled cRNA samples were then fragmented using the Ambion fragmentation kit (Applied Biosystems, AM8740). The fragmented cRNA was quality checked using the Agilent Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: Plants were grown in Conviron PGC20 Plant Growth Chambers (Conviron). Light was provided by 40 Phillips 54W 840 cool white fluorescent tubes (Philips Electronics) and 7 Sylvania Reflector 60W incandescent bulbs (Sylvania). Total light intensity was 600µmol m-2 s-2 at plant height. Plants were grown in pots in Debco Seed Raising Mix (Debco) supplemented with 2g/L Mini-Osmocote (Scotts Australia). Plants were maintained in a fully-watered state throughout the experiment.

extract_protocol: RNA was extracted from whole plants, minus roots, using the protocol of Chang et al. 1993 (Plant Mol. Biol. Report 11:113-116) and then further purified using RNeasy columns (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Seeds of barley cultivar Sonja were germinated and grown in darkness at 2 ±1.5°C for 9 weeks and then transferred to growth chambers at constant temperatures of 15°C or 25°C and either a short-day treatment of 8 hours light/16 hours dark or a long-day treatment of 16 hours light/8 hours dark. Plants were grown until the fourth leaf was visible on the main stem.

value: whole plant, minus roots

tag: day length

value: 16 hours

tag: temperature


title: Whole plant_Long-days_25C_rep3

source_name: whole plant, 16 hour photoperiod, 25°C, replicate3


title: Sample-15-case

tag: sample type


title: 81

description:
1B
Used in analysis: yes
WK_3_1_2.txt

value: B


title: Sample-13-case


title: AML-45


title: 93

description:
3D
Used in analysis: no
WK_3_1_2.txt

value: D


title: 69

description:
1C
Used in analysis: yes
WK_3_1_1.txt

value: C


title: AML-43

value: male


title: AML-44

value: female

value: acute myeloid leukemia (AML)


title: AML-46

source_name: AML

value: peripheral blood (PB)

value: MLL


title: 86

description:
3C
Used in analysis: yes
WK_3_1_1.txt

source_name: 30 animals, field soil, 3C


title: Whole plant_Long-days_15C_rep2

source_name: whole plant, 16 hour photoperiod, 15°C, replicate2


title: 62

description:
2D
Used in analysis: yes
WK_2_2_4.txt


title: Whole plant_Long-days_25C_rep1

source_name: whole plant, 16 hour photoperiod, 25°C, replicate1


title: Whole plant_Long-days_15C_rep3

source_name: whole plant, 16 hour photoperiod, 15°C, replicate3


title: Sample-12-case

source_name: blood

value: familial ovarian cancer

value: case


title: Sample-11-case

value: lymphoblastoid cell line


title: 51

description:
1C
Used in analysis: yes
WK_2_2_4.txt


title: Whole plant_Short-days_25C_rep3

source_name: whole plant, 8 hour photoperiod, 25°C, replicate3

value: 8 hours


title: Whole plant_Long-days_15C_rep1

source_name: whole plant, 16 hour photoperiod, 15°C, replicate1


title: 54

description:
3A
Used in analysis: yes
WK_2_2_3.txt

value: 23 days

value: A


title: AML-42

value: bone marrow (BM)

value: NK


title: Whole plant_Short-days_25C_rep2

source_name: whole plant, 8 hour photoperiod, 25°C, replicate2

value: whole plant, minus roots


title: AML-41


title: Whole plant_Short-days_15C_rep3

source_name: whole plant, 8 hour photoperiod, 15°C, replicate3


title: Whole plant_Short-days_25C_rep1

source_name: whole plant, 8 hour photoperiod, 25°C, replicate1


title: Sample-9-case


title: Sample-10-case


title: Sample-8-case


title: AML-4


title: AML-40


title: AML-39


title: 95

description:
2C
Used in analysis: no
WK_2_2_2.txt

source_name: 30 animals, field soil, 2C

value: whole body

value: field soil


title: Whole plant_Short-days_15C_rep1

source_name: whole plant, 8 hour photoperiod, 15°C, replicate1


title: 45

description:
4B
Used in analysis: no
WK_2_2_2.txt

source_name: 30 animals, field soil, 4B

value: B


title: 91

description:
4D
Used in analysis: no
WK_2_2_1.txt

source_name: 30 animals, field soil, 4D

value: D


title: 63

description:
1B
Used in analysis: yes
WK_2_2_3.txt

source_name: 30 animals, field soil, 1B


title: Sample-5-case


title: Sample-6-case


title: AML-37

value: male


title: 58

description:
4A
Used in analysis: yes
WK_2_2_1.txt

source_name: 30 animals, field soil, 4A


title: Whole plant_Short-days_15C_rep2

source_name: whole plant, 8 hour photoperiod, 15°C, replicate2


title: AML-36

value: female

value: acute myeloid leukemia (AML)


title: AML-38


title: 57

description:
2A
Used in analysis: yes
WK_2_1_4.txt

source_name: 30 animals, field soil, 2A


title: Sample-7-case


title: AML-35


title: Sample-3-case


title: DNA methylation analysis of parental cell line

city: Philadelphia

first: Noel

middle: J-M

last: Raynal

state: Pennsylvania

address: 3307 N. Broad Street

department: Fels Institute for Cancer and Molecular Biology

institute: Temple University

description: SW48 colon cancer cells (parental cells of YB5)

hyb_protocol: Microarray protocols including the hybridization and post-hybridization procedures are according to protocols developed by DeRisi et al. (1996), except for washing steps, which were extended to 10 min each to decrease background.

scan_protocol: Agilent whole genome array (G4497A) that was scanned using the Agilent G2505B scanner

data_processing: Two-step global lowess normalization was done using the background-subtracted median intensity of each spot

source_name: SW48 colon cancer cells

label_protocol: Incorporation of amino-allyl dUTP (aa-dUTP; Sigma) into 600 ng each of tumor DNA and normal DNA was conducted using the Bioprime DNA-labeling system protocol (Life Technologies) (Weinmann et al. 2002).

growth_protocol: SW48 cell line was cultured in L-15 medium with 10% fetal bovine serum and 100 μg/mL Penicillin-Streptomycin solution.

extract_protocol: 5 μg of DNA was digested with 100 units of SmaI for 16 h (all restriction enzymes were from New England Biolabs), followed by digestion with 20 units of XmaI for 6 h. DNA fragments were then precipitated with ethanol.

value: Unmethylated DNA

tag: cell line

value: Methylated DNA


title: Sample-4-case

value: familial ovarian cancer

value: case


title: Sample-2-case

value: lymphoblastoid cell line


title: 104

description:
2B
Used in analysis: yes
WK_2_1_3.txt

source_name: 30 animals, field soil, 2B

value: 23 days


title: Hif1a-/- LSC, biological rep2

city: Worcester

first: shaoguang

last: li

state: MA

address: 364 Plantation street

department: medicine

institute: Umass medical school

description:
DNA microarray analysis was carried out to compare gene expression between BCR-ABL-expressing WT LSCs and BCR-ABL-expressing Hif1a-/- LSCs.
Gene expression data from BCR-ABL-expressing Hif1a-/- LSCs.

hyb_protocol: Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and CEL files generated, which are then used for analysis.

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method, which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: Hif1a-/- leukemia stem cell

label_protocol: The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.

growth_protocol: We used the bone marrow transplantation mouse model of CML as an assay system, in which bone marrow cells from donor mice pre-treated with 5-fluorouracil (5-FU) and transduced with BCR-ABL result in development of CML in recipient mice. We transduced bone marrow cells from C57BL/6 (B6) mice or Hif1a-/- mice with retrovirus containing BCR-ABL/GFP under conditions for induction of CML, followed by transplantation of the transduced cells into B6 recipient mice. 14 days after BMT, bone marrow cells were isolated and subsequently sorted by FACS for LSCs (GFP+Lin-c-Kit+Sca-1+) .

extract_protocol: Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.), between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double-stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place, incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.

tag: genotype

value: leukemia stem cells (LSCs)

value: 8 weeks


title: AML-34

value: bone marrow (BM)

tag: disease state

value: NK


title: 78

description:
3B
Used in analysis: yes
WK_2_1_4.txt

source_name: 30 animals, field soil, 3B

value: whole body


title: AML-33

tag: gender


title: WT LSC, biological rep2

description:
DNA microarray analysis was carried out to compare gene expression between BCR-ABL-expressing WT LSCs and BCR-ABL-expressing Hif1a-/- LSCs.
Gene expression data from BCR-ABL-expressing WT LSCs.

source_name: WT leukemia stem cell

value: WT


title: 18

description:
4C
Used in analysis: yes
WK_2_1_2.txt

source_name: 30 animals, field soil, 4C

value: field soil

value: C


title: AML-32

tag: age (yrs)


title: WT LSC, biological rep1


title: Hif1a-/- LSC, biological rep1


title: AML-30

value: male

tag: tissue


title: WT HSC, biological rep2

description:
DNA microarray analysis was carried out to compare gene expression between WT HSCs and Hif1a-/- HSCs.
Gene expression data from WT HSCs (Lin-c-Kit+Sca-1+).

source_name: WT HSC

growth_protocol: Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+).

value: hematopoietic stem cells (HSCs)


title: 36

description:
1A
Used in analysis: no
WK_2_1_1.txt

source_name: 30 animals, field soil, 1A

value: A


title: 68

description:
3C
Used in analysis: no
WK_2_1_1.txt

source_name: 30 animals, field soil, 3C


title: Sample-1-case

source_name: blood


title: 55

description:
3C
Used in analysis: yes
WK_1_2_4.txt


title: 99

description:
1D
Used in analysis: yes
WK_2_1_3.txt

source_name: 30 animals, field soil, 1D

value: D


title: AML-28

value: acute myeloid leukemia (AML)

tag: subtype


title: AML-3

tag: abnormality


title: Hif1a-/- HSC, biological rep1

description:
DNA microarray analysis was carried out to compare gene expression between WT HSCs and Hif1a-/- HSCs.
Gene expression data from Hif1a-/- HSCs (Hif1a-/- Lin-c-Kit+Sca-1+).

source_name: Hif1a-/- HSC

tag: age


title: WT HSC, biological rep1


title: Hif1a-/- HSC, biological rep2


title: AML-26

value: peripheral blood (PB)


title: AML-31

value: female


title: 52

description:
4B
Used in analysis: no
WK_1_2_3.txt

source_name: 30 animals, field soil, 4B

tag: treatment

value: B


title: 108

description:
3D
Used in analysis: yes
WK_2_1_2.txt

source_name: 30 animals, field soil, 3D

value: 23 days

tag: copper level


title: 25

description:
1B
Used in analysis: yes
WK_1_2_4.txt

source_name: 30 animals, field soil, 1B

tag: ph


title: AML-25


title: 127

description:
3D
Used in analysis: no
WK_1_2_3.txt


title: 116

description:
1D
Used in analysis: yes
WK_1_2_2.txt


title: 21

description:
4A
Used in analysis: yes
WK_1_2_2.txt

source_name: 30 animals, field soil, 4A


title: AML-29


title: AML-27


title: 4

description:
2A
Used in analysis: yes
WK_1_2_1.txt

source_name: 30 animals, field soil, 2A


title: 96

description:
3B
Used in analysis: yes
WK_1_1_4.txt


title: 5

description:
1C
Used in analysis: yes
WK_1_2_1.txt

source_name: 30 animals, field soil, 1C


title: AML-21


title: AML-24


title: AML-22


title: AML-23


title: 100

description:
4D
Used in analysis: no
WK_1_1_4.txt

source_name: 30 animals, field soil, 4D


title: AML-20

value: MLL


title: AML-2