title: Genmascq_Pig_LL_242


title: Pf-5_Cu adapted_replicate 1

status: Public on Apr 05 2012

type: RNA

city: Sydney

first: amy

middle: k

last: cain

state: NSW

address: Building E8A

department: CBMS

country: Australia

institute: Macquarie University

description: Biological replicate 3

hyb_protocol: Microarray slides were immersed in pre-hybridization buffer (1 % BSA, 5X SSC, 0.1 % SDS, 0.45 mm-filtered) before hybridization. Slides were washed with sterile water (4x) and isopropanol (3x), spin-dried and covered with lifterslip. cDNA probes were dried using Speedvac and then resuspended in hybridization buffer (50 % formamide, 5X SSC, 0.1 % SDS, 0.45 mm-filtered). Probes were heated at 95 degrees Celcius (15 min) before applying to the slides. Hybridization was performed overnight at 42 degrees Celcius. After hybridization, slides were washed with the following steps: 2x wash buffer 1 (1X SSC, 0.2% SDS) at 42 degrees Celcius, 1x wash buffer 2 (0.1X SSC, 0.1% SDS) and 3x wash buffer 3 (0.1X SSC, 0.1% SDS).

scan_protocol: Images were scanned with Axon 4000B scanner and GenePix 4.0 software

data_processing: The microarray data was analyzed with Spotfinder (TIGR) and normalized using the LOWESS algorithm in the TIGR-MIDAS package with block mode and smoothing parameter value of 0.33

label: Alexa fluor 555

molecule: total RNA

organism: Pseudomonas protegens Pf-5

source_name: Pseudomonas fluorescens Pf-5, CuSO4 treated

label_protocol: Reverse transcription of RNA samples was performed using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) with random hexamer primers. Approximately 7 µg of total RNA was used for cDNA synthesis in each reaction. cDNA samples were labeled with either Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen) according to manufacturer's instruction. Spike-in controls were made from RNA transcribed from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) with the MegaScript Kit (Ambion). Spike-in control were prepared as follow. For Alexa Fluor 555 pool,  0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.06 ng ltp6 RNA, 0.25 ng crp1 RNA, 0.95 ng nac RNA, 0.08 ng xcp2 RNA, 0.17 ng prk RNA and 0.21 ng tim RNA. For Alexa Fluor 647 pool, 0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.02 ng ltp6 RNA, 0.08 ng crp1 RNA, 0.31 ng nac RNA, 0.25 ng xcp2 RNA, 0.50 ng prk RNA and 0.63 ng tim RNA.

growth_protocol: Pseudomonas fluorescens Pf-5 was grown in Mueller Hinton rich media in triplicate and another set of 3 were supplemented 1/2 MIC concentration of CuSO4 (3.2mM). The cultures were grown aerobically with shaking at 25'C until early log phase (an OD600=0.5+/- 0.02)

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and and treated with RNAse-free DNAse (Ambion) as per manufacturer's instruction

treatment_protocol: The +Cu cultures were supplemented with 3.2mM copper sulfate (1/2 MIC) whereas the no Cu were not treated with anythings, just MH media

tag: treatment

label: Alexa fluor 647

source_name: Pseudomonas fluorescens Pf-5, non-Cu treated


title: Genmascq_Pig_LL_197

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

organism: Sus scrofa

source_name: Longissimus lumborum

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

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

tag: tissue

value: Longissimus lumborum

tag: ChIP


title: Pf-5_Cu adapted_replicate 2

description: Biological replicate 1


title: Pf-5_Cu adapted_replicate 5

description: Technical replicate 2 of biological replicate 3


title: Genmascq_Pig_LL_248


title: Genmascq_Pig_LL_259


title: Genmascq_Pig_LL_184


title: ZH11 rep2

city: shanghai

first: linlin

last: yin

address: 300 fenglin road

country: China

institute: SIPPE

description: Gene expression in nucellar projection of 3 DAF ZH11 seed

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4*44K Microarrays 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 (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 015241_D_F_20081112) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Oryza sativa

source_name: Nucellar projection cells, ZH11,3 DAF, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 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: ZH11 and A-OsMADS29 (line2 and line14) were growth in the same conditon.The rice seeds were germinated in sterilized water and then grown in pots in a phytotron with a 12-h light (26℃) / 12-h dark (18℃) cycle.

extract_protocol: Nucellar projection cells of seeds at 3 DAF were isolated using a Veritas Microdissection System (Arcturus/Molecular Devices).The RNA was extracted with the PicoPure RNA Isolation Kit (Arcturus/Molecular Devices) and amplified using a TargetAmp 2-round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies) following the manufacturer's recommendations. RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genetic background

tag: genotype

value: wild type

tag: source tissue

value: seed

tag: cell type

value: Nucellar projection cells

tag: age

value: 3 DAF


title: Pf-5_Cu adapted_replicate 3

description: Biological replicate 2


title: Pf-5_Cu adapted_replicate 4

description: Technical replicate 2 of biological replicate 1


title: Pf-5_Cu adapted_replicate 6

description: Technical replicate 3 of biological replicate 3


title: A-OsMADS29 (line2) rep1

description: Gene expression in nucellar projection of 3 DAF A-OsMADS29 (line2) seed

source_name: Nucellar projection cells, A-OsMADS29 (line2),3 DAF, replicate 1

value: OsMADS29 mutant


title: Genmascq_Pig_LL_247


title: Genmascq_Pig_LL_181


title: low Nkx2-1 rep1

city: New York

first: steve

last: shen

state: NY

address: 545 First Ave

department: Biochemistry

country: USA

institute: New York University

description:
mouse differentiated ES cells
Derivation of purified Nkx2-1+ endodermal lung and thyroid progenitors via directed differentiation of mouse ES cells

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

organism: Mus musculus

source_name: GFP- samples are the three sorted samples with the low Nkx2-1 expression levels

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated from three biological replicates corresponding to different cell and tissue types using miRNeasy Mini Kit (Qiagen,217004) according to the manufacturer’s protocol, and the WT-OvationTM Pico RNA amplification system (Nugen) was used to amplify the RNA

value: ES cells


title: Genmascq_Pig_LL_173


title: Genmascq_Pig_LL_176


title: low Nkx2-1 rep2


title: tumor metformin3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

organism: Homo sapiens

source_name: tumor metformin

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: cell line: Cells were grown in RPM I 1640 supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C. Tumor(mouse): Each mouse was inoculated with MKN74 cells (5×106 cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: cell line: MKN74 cells were treated with 10 mM metformin or without metformin for 72 h. Tumor: The metformin-treated group was injected 5 times a week intraperitoneally (i.p.) at 1 mg/body or 2 mg/body per day for 4 weeks.

value: tumor

tag: disease type

value: gastric cancer


title: Genmascq_Pig_LL_169


title: Genmascq_Pig_LL_182


title: Genmascq_Pig_LL_159


title: high Nkx2-1 rep3

source_name: GFP+ samples are the three sorted samples with the high Nkx2-1 expression levels


title: Genmascq_Pig_LL_167


title: Genmascq_Pig_LL_168


title: Genmascq_Pig_LL_170


title: Genmascq_Pig_LL_161


title: Genmascq_Pig_LL_166


title: high Nkx2-1 rep2


title: tumor control3

source_name: tumor control


title: Genmascq_Pig_LL_158


title: Genmascq_Pig_LL_171


title: Genmascq_Pig_LL_165


title: Genmascq_Pig_LL_163


title: tumor metformin2


title: Genmascq_Pig_LL_183


title: tumor metformin1


title: tumor control2


title: Genmascq_Pig_LL_155


title: Genmascq_Pig_LL_154


title: SD8 skin fibroblasts- biological replicate 1

city: Vancouver

first: Alireza

last: Baradaran-Heravi

state: BC

address: 950 West 28th Avenue, Room 218

department: Medical Genetics

country: Canada

institute: UBC

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
Bioconductor GCRMA
An ANOVA model was fit to each genotype (Y=Genotype + Error), where Y is the normalized expression measure for a gene on a particular microarray. The model was fit using the LIMMA R package.

label_protocol: One-cycle target labeling

growth_protocol: Primary human skin fibroblasts from control and SIOD patients were cultured in DMEM (Gibco/Invitrogen) containing 15% fetal bovine serum (Gibco/Invitrogen) and 1% antibiotic/antimycotic (Gibco/Invitrogen) at 37°C and 5% CO2.

extract_protocol: QIAGEN RNeasy Mini Kit

treatment_protocol: Not applicable.

tag: gender

value: male

value: skin fibroblast


title: SD60 skin fibroblasts- biological replicate 2

description: SD600-2_skin-fib_lal_BC_1707_H2_6992.CEL


title: high Nkx2-1 rep1


title: SD8 skin fibroblasts- biological replicate 2


title: Genmascq_Pig_LL_153


title: Control human skin fibroblasts- biological replicate 3

source_name: Control


title: SD60 skin fibroblasts- biological replicate 1

description: SD600-1_skin-fib_lal_BC_1707_H2_6991.CEL


title: low Nkx2-1 rep3


title: Control human skin fibroblasts- biological replicate 2


title: cell line control4

source_name: cell line control

value: cell line


title: tumor control1


title: cell line metformin4

source_name: cell line metformin


title: cell line metformin3


title: Genmascq_Pig_LL_148


title: Genmascq_Pig_LL_146


title: cell line control3


title: cell line control2


title: PLC8024 CD133-, RMA

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: RMA

hyb_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached) According to Affymetrix protocol

data_processing: The data were analyzed with RMA using GCOS Affymetrix default analysis settings and global scaling as normalization method.

label_protocol:
Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached)
Ambion MessageAmp II-Biotin Enhanced (Cat #1791)

growth_protocol: CD133+ and CD133- cells sorted from PLC8024 HCC cells using flow cytometry cell sorting technique

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

value: HCC

tag: cell line


title: Genmascq_Pig_LL_145


title: Genmascq_Pig_LL_138


title: Genmascq_Pig_LL_143


title: cell line metformin1


title: Control human skin fibroblasts- biological replicate 1


title: Genmascq_Pig_LL_144


title: Genmascq_Pig_LL_142


title: cell line control1


title: PLC8024 CD133-, MAS5

scan_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached) According to Affymetrix protocol

data_processing: The data were analyzed with MAS5 using GCOS Affymetrix default analysis settings and global scaling as normalization method.


title: PLC8024 CD133+, RMA

description: RMA


title: Huh7 CD133-, RMA

description: RMA

source_name: Huh7 CD133-

growth_protocol: CD133+ and CD133- cells sorted from Huh7 HCC cells using flow cytometry cell sorting technique


title: cell line metformin2


title: PLC8024 CD133+, MAS5


title: Genmascq_Pig_LL_134


title: Huh7 CD133+, RMA

description: RMA

source_name: Huh7 CD133+


title: Genmascq_Pig_LL_132


title: Genmascq_Pig_LL_133


title: Huh7 CD133-, MAS5


title: C3 sex vs C5 veg 2

city: Uppsala

first: Nicklas

last: Samils

address: Almas allé 5

department: Forest Mycology and Plant Pathology

country: Sweden

institute: Swedish University of Agricultural Sciences

description:
sex_mc vs veg_mc
dye-swap

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora intermedia

source_name: Mycelia

label_protocol: 2 µg of mRNA were primed with .5 µg of Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 40 U SuperScript II RTase (Invitrogen), and .8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Vegetative Nutrient Medium (Vogel's Medium)

treatment_protocol: Constant Darkness

tag: type

value: sexual mycelium

value: vegetative mycelium


title: C3 sex vs C5 veg 1

description:
sex_mc1 vs veg_mc_1
dye-swap


title: Genmascq_Pig_LL_383


title: Genmascq_Pig_LL_293


title: C3 veg vs C5 sex 1

description:
veg_mc1 vs sex_mc_1
dye-swap


title: C3 veg vs C5 sex 2

description:
veg_mc vs sex_mc
dye-swap


title: HESC_cAME_si(KLF9+PGR)_pool2

status: Public on Apr 04 2012

city: Little Rock

first: Rosalia

middle: CM

last: Simmen

state: Arkansas

address: 15 Children's Way Slot 512-20B

department: Physiology and Biophysics

institute: University of Arkansas for Medical Sciences

description:
Endometrial stromal cell gene expression
siKP_2
KP2.CEL

hyb_protocol: Fifteen microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (N = 2/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring GX v 11
Summarization Algorithm: GCRMA
Technology: Affymetrix.GeneChip.HG-U133_Plus_2
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: Human endometrial stromal cells-human

label_protocol: First- and second- strand cDNA synthesis (from 0.1 ug total RNA), biotin-labeled aRNA synthesis, and fragmentation of cRNA  reactions were performed following protocols described by Affymetrix. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated from HESC using RNeasy Plus kit with genomic DNA eliminator column (Qiagen)

value: Endometrium

value: Stromal cell


title: HESC_vehicle_non-target-siRNA_pool1

description:
Endometrial stromal cell gene expression
vehicle_1
N1.CEL


title: HESC_cAME_siPGR_pool1

description:
Endometrial stromal cell gene expression
siPGR_1
PT1.CEL


title: HESC_cAME_siKLF9_pool2

description:
Endometrial stromal cell gene expression
siKLF9_2
KT2.CEL


title: HESC_cAME_siKLF9_pool1

description:
Endometrial stromal cell gene expression
siKLF9_1
KT1.CEL


title: HESC_cAME_non-target-siRNA_pool1

description:
Endometrial stromal cell gene expression
NT_1
T1.CEL


title: HESC_cAME_siPGR_pool2

description:
Endometrial stromal cell gene expression
siPGR_2
PT2.CEL


title: Huh7 CD133+, MAS5


title: HESC_vehicle_non-target-siRNA_pool2

description:
Endometrial stromal cell gene expression
vehicle_2
N2.CEL


title: leukemia-92

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

hyb_protocol: Samples were analyzed using the Affymetrix GeneChip Human Exon 1.0 ST Array (Affymetirx, Santa Clara, CA) according to the manufacturer's instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix).

data_processing:
After background correction according to the standard protocols, the quantified signals were normalized using Robust Multi-array Average (RMA), which is a robust algorithm of background-adjustment, quantile normalization, and log2-transformation. Partek Genomics Suite (Partek Inc., St. Louis, MI) was used for the analysis of the normalized data.

Exons included in analysis: core
Genome build: hg18
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix), and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Blasts and mononuclear cells were purified by use of NycoPrep 1.077A (Axis-Shield, Oslo, Norway) according to the manufacturer’s manual. RNA was isolated with the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

tag: age (yrs)

tag: tissue source

value: peripheral blood (PB)

tag: disease state

value: acute myeloid leukemia (AML)

tag: subtype

tag: abnormality


title: leukemia-91

value: female


title: leukemia-88


title: HESC_cAME_si(KLF9+PGR)_pool1

description:
Endometrial stromal cell gene expression
siKP_1
KP1.CEL


title: leukemia-90


title: HESC_cAME_non-target-siRNA_pool2

description:
Endometrial stromal cell gene expression
NT_2
T2.CEL


title: leukemia-93


title: leukemia-89


title: leukemia-85

value: bone marrow (BM)


title: leukemia-86


title: leukemia-83


title: leukemia-84


title: leukemia-87


title: Tetracycline-inducible glioma cells dox 3

city: Columbus

first: Amy

last: Haseley

state: OH

department: Neurological Surgery

institute: The Ohio State University

description: gene expression was measured 24 hours + induction of Cyr61 protein in glioma cells

hyb_protocol: 15ug of labeled and fragmented cRNA was hybridized at 45C for 16 hours at 60rpm. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer’s protocol

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Raw data files were generated and processed with Affymetrix AGCC software.

data_processing: The data were analyzed through Bioconductor package, RMA method was used as the background-correction, normalization, and probe summarization method.

source_name: Glioma cells expressing Cyr61

label_protocol: 1ug RNA was used to generate cRNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual

growth_protocol: Cy-1 cells were maintainted in Dulbecco’s modified minimal essential medium (DMEM) supplemented with 2% fetal bovine serum, 100U/ml penicillin, and 100ug/ml streptomycin in a 37C incubator with 5% CO2

extract_protocol: RNA was extracted using Qiashredders and Rneasy Mini Kit per manufacturer's protocol

treatment_protocol: Cells were treated ± doxycycline (1ug/ml) for 24 hours

tag: expression


title: leukemia-82


title: Tetracycline-inducible glioma cells dox 1


title: Tetracycline-inducible glioma cells no dox 3

description: gene expression was measured 24 hours - induction of Cyr61 protein in glioma cells

source_name: Glioma cells not expressing Cyr61

value: control


title: Tetracycline-inducible glioma cells dox 2


title: Tetracycline-inducible glioma cells no dox 1


title: Tetracycline-inducible glioma cells no dox 2


title: leukemia-81


title: leukemia-80


title: leukemia-76


title: leukemia-77


title: leukemia-79


title: leukemia-78


title: leukemia-71


title: leukemia-70


title: leukemia-60


title: leukemia-57


title: leukemia-56


title: leukemia-67


title: leukemia-55


title: leukemia-65


title: leukemia-75


title: leukemia-73


title: leukemia-61


title: leukemia-74


title: leukemia-58


title: leukemia-62


title: leukemia-69


title: leukemia-72


title: leukemia-54


title: leukemia-63


title: leukemia-64


title: leukemia-52


title: leukemia-49


title: leukemia-53


title: leukemia-50


title: leukemia-68


title: leukemia-59


title: leukemia-48


title: leukemia-47


title: leukemia-51


title: leukemia-41


title: leukemia-42


title: leukemia-43


title: leukemia-46


title: S.sanguinis_ΔluxS_3

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

country: Germany

institute: hospital university rostock

description: This sample is of S. sanguinis SK36 ΔluxS.

hyb_protocol: Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

scan_protocol: Scanning was performed with the DNA Microarray Scanner (Agilent) at a resolution of 5 µm and NimbleScanTM version 2.4 software

data_processing: The raw data (.pair file) were checked for inhomogenous hybridization and probes with a high intensity caused by wash artefacts were deleted. Probes not belonging to S. sanguinis SK36 or RANDOM were excluded from analysis. The remaining probes were quantile normalized, background corrected, and sumarized with NimbleScan Software RMA, and subsequently analysed with GeneSpring GX 11.0, Agilent Technologies. Gene-signal intensities are quantile normalized, and background corrected with RMA over all samples, averaged of three technical on chip replikates, and displayed in log2 scale.

organism: Streptococcus sanguinis SK36

source_name: 8 hours culture of S.sanguinis SR ΔluxS

label_protocol: Labeling with Cy3 was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)

growth_protocol: Bacterial cells were cultured under anaerobic conditions (10% CO2; 10% H2; 80% N2) at 37°C in chemical defined medium sublemented with 50 mM succrose for 8 h.

extract_protocol: RNA was extracted out of 100 mg harvested cells using the Fast RNA Pro Blue Kit (MP Biomedicals, Solon, Ohio, USA) following manufacturers instructions. Removal of DNA was performed by DNase digenstion for 1 hour at 37°C.

treatment_protocol: Artificial AI-2 precursor was added at two time points, after 5.5 h and 7 h of growth to gain a final concentration of 4.5 µM (with the first addtion) and 9 µM (with the second addition), respectively.

tag: strain background

tag: strain

value: SR ΔluxS

tag: genotype/variation

value: luxS-mutant

tag: artificial ai2 added

value: no


title: S.sanguinis_ΔluxS_sahH_2

description: This sample is of S. sanguinis SK36 ΔluxS/sahH.

source_name: 8 hours culture of S.sanguinis SR ΔluxS/sahH

value: SR ΔluxS/sahH

value: luxS-mutant, sahH complemented


title: S.sanguinis_ΔluxS_sahH_1


title: S.sanguinis_ΔluxS_2


title: S.sanguinis_ΔluxS_sahH_AI2_1

description: This sample is of S. sanguinis SK36 ΔluxS/sahH after the addition of artificial AI2.

source_name: 8 hours culture of S.sanguinis SR ΔluxS/sahH + AI2

value: yes


title: S.sanguinis_ΔluxS_sahH_3


title: S.sanguinis_ΔluxS_sahH_AI2_2


title: leukemia-45


title: S.sanguinis_ΔluxS_1


title: S.sanguinis_wt_3

description: This sample is of wild-type S. sanguinis SK36.

source_name: 8 hours culture of S.sanguinis SK36

value: wild type


title: leukemia-40

value: male


title: leukemia-37


title: leukemia-38


title: leukemia-34


title: leukemia-36


title: leukemia-35


title: leukemia-44


title: S.sanguinis_ΔluxS_sahH_AI2_3


title: S.sanguinis_wt_1


title: S.sanguinis_wt_2


title: leukemia-33


title: leukemia-31


title: leukemia-30


title: leukemia-39


title: leukemia-29


title: leukemia-32


title: leukemia-27


title: leukemia-26


title: leukemia-25


title: leukemia-24


title: leukemia-22


title: leukemia-20


title: leukemia-21


title: leukemia-23


title: leukemia-18


title: leukemia-19


title: leukemia-28


title: leukemia-66


title: Control-2-1

city: Beijing

first: Song

last: Wang

email: wscookie@163.com, chenjl@im.ac.cn

address: West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

description: This sample is A549 cells without WSN infection.

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

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. All mRNA level files were imported into Agilent GeneSpring Software (version 11.0) for further analysis. Differentially expressed lncRNAs and mRNAs were identified through Volcano Plot filtering.

source_name: Control A549 cells

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

growth_protocol: A549 cells were maintained in Dulbecco’s modified Eagle’s medium(DMEM) containing 10% fetal calf serum(FCS) supplemented with penicillin (100U/ml) and streptomycin (100μg /ml). They were grown in a humidified incubator at 37℃ and 5% CO2.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA).

tag: infection


title: Control-3-1


title: Treat-1-1

description: This sample is A549 cells with WSN infection.

source_name: WSN infected A549 cells

treatment_protocol: A549 cells were infected with WSN virus for 10 h.

value: WSN


title: Treat-2-1


title: Treat-3-1


title: -/-, Tbx1 mutant, biological replicate 2

city: Naples

first: Luna Simona

last: Pane

state: Italy

address: via Pietro Castellino, 111

country: Italy

institute: TIGEM

description: Gene expression data from a Tbx1 gene allelic series

hyb_protocol: Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome  Mouse430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s standard protocols.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

label: Biotin

source_name: -/-, Tbx1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the mouse mutant alleles used in this study have been previously reported: Tbx1- (Lindsay EA, et al.,2001,Nature 410(6824):97-10), Tbx1Neo (Xu H, et al.,2004, Development 131(13):3217-3227), Tbx1Neo2 (Zhang Z, Huynh T, & Baldini A., 2006, Development 133(18):3587-3595). Embryos were collected at  E9.5, considering the day of observation of a vaginal plug to be E0.5. Mice were genotyped by PCR as described in the original reports.

extract_protocol: Whole embryos were homogenized in 1 ml TRIzol (Invitrogen) and total RNA was extracted according to the manufacturer's instructions. RNA was then cleaned using the RNeasy cleanup Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Embryos were dissected in di-ethyl polycarbonate-treated phosphate-buffered saline and then quickly frozen in liquid nitrogen until total RNA extraction.

tag: developmental stage

tag: genotype

tag: genetic background

value: mixed 129SvEv and C57Bl/6

tag: tissue

value: whole embryo


title: -/-, Tbx1 mutant, biological replicate 1


title: Control-1-1

tag: cell line


title: leukemia-15

tag: gender


title: leukemia-17

tag: age (yrs)


title: leukemia-16

tag: tissue source


title: leukemia-13

tag: disease state


title: Rybp binding in Dnmt1-KO ESCs_Promoter [Agilent-014717]

type: genomic

city: Yokohama

first: Takaho

middle: A.

last: Endo

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Microarray 2 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)

tag: cell type

value: embryonic stem cells

value: Dnmt1 constitutive KO

tag: sample type

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: Rybp binding in Eed-KO ESCs_Promoter [Agilent-014717]

description: Microarray 2 of 2

source_name: Input from Eed-KO ESCs

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

tag: genotype/variation

value: Eed constitutive KO

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


title: Rybp binding in WT ESCs_Promoter [Agilent-014717]

description: Microarray 2 of 2

source_name: Input from WT ESCs

source_name: Immunoprecipitated DNA with anti-Rybp from WT ESCs


title: leukemia-14

value: peripheral blood (PB)

value: acute myeloid leukemia (AML)

tag: subtype

tag: abnormality


title: leukemia-12


title: leukemia-7

source_name: AML, Bi-Phenotypic

value: female

value: AML, Bi-Phenotypic

value: MLL-ENL


title: leukemia-6

value: bone marrow (BM)


title: leukemia-5


title: leukemia-8

value: male


title: leukemia-9


title: leukemia-10


title: leukemia-11


title: Neo/Neo, Tbx1 mutant, biological replicate 2

source_name: Neo/Neo, Tbx1 mutant

tag: developmental stage


title: leukemia-2


title: Neo2/Neo2, Tbx1 mutant, biological replicate 2

source_name: Neo2/Neo2, Tbx1 mutant

tag: genotype


title: leukemia-1


title: Neo2/-, Tbx1 mutant, biological replicate 1

source_name: Neo2/-, Tbx1 mutant

tag: genetic background


title: Neo2/Neo, Tbx1 mutant, biological replicate 2

source_name: Neo2/Neo, Tbx1 mutant

tag: tissue


title: Neo2/-, Tbx1 mutant, biological replicate 2


title: +/-, Tbx1 mutant, biological replicate 1

source_name: +/-, Tbx1 mutant


title: leukemia-4


title: Neo2/Neo, Tbx1 mutant, biological replicate 1


title: Neo/Neo, Tbx1 mutant, biological replicate 1


title: +/-, Tbx1 mutant, biological replicate 2


title: Neo/+, Tbx1 mutant, biological replicate 1

source_name: Neo/+, Tbx1 mutant


title: Neo/+, Tbx1 mutant, biological replicate 2


title: Neo2/+, Tbx1 mutant, biological replicate 2

source_name: Neo2/+, Tbx1 mutant


title: Neo2/+, Tbx1 mutant, biological replicate 1


title: WT, control, biological replicate 1

source_name: WT, control


title: C2_SA992

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

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

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.

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

value: F

value: Whole Blood

tag: illness

value: Bacteremia, osteo/?supp arth

value: yes

value: MRSA

value: IV

value: I

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

value: Invasive

value: Osteoarticular

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 (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

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)

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_SA985

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

tag: illness

value: Abscess/bacteremia

value: no

value: No Isolate

value: No Data

value: Tier 3

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: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

value: normal


title: WT, control, biological replicate 2

tag: developmental stage

tag: genotype

tag: genetic background

value: mixed 129SvEv and C57Bl/6

tag: tissue

value: whole embryo


title: C2_SA945

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: Whole Blood

tag: illness

value: Abscess

value: yes

value: MRSA

value: IV

value: I

tag: cluster

value: MQ

tag: mdth

value: Mild

value: Local

tag: treatment

value: Bactrimycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

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)

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: Neo2/Neo2, Tbx1 mutant, biological replicate 1

tag: developmental stage

tag: genotype

tag: genetic background

tag: tissue


title: Yaf2kd_(OHT-) rep1

description:
Yaf2 KD (I)
Gene expression data from clone#3086- (nontreated, Mut Yaf2 and wild type RYBP), biological duplicate 1

hyb_protocol: Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 16 hours.

scan_protocol: GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.

data_processing: The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.

label_protocol: The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.

growth_protocol: ES cells were cultivated 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: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Cell were treated with 0.8 µM of  4-hydroxytamoxifen for 24 hours to deplete Rybp.

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: yaf2 mutant


title: C2_SA906

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: illness

value: Disseminated:bacteremia, myositis, osteomyelitis L humerus with DVT, pulmonary

value: Quarter 2

value: Tier 1

tag: cluster

tag: mdth

value: Severe

value: Disseminated

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 (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

value: abnormal


title: C2_SA910

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Osteoarhritis

value: yes

value: MSSA

value: I

value: Quarter 3

value: Tier 3

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: meningitis

tag: emboli

tag: sepsis

tag: dvt

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

value: normal


title: Yaf2wt_(OHT-) rep1

description:
Wild tyep
Gene expression data from clone#3031- (nontreated, Wild type of Yaf2 and Wild type RYBP for control)

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: wild type


title: Yaf2kd_(OHT-) rep2

description:
Yaf2 KD (II)
Gene expression data from clone#3087- (nontreated, Mut Yaf2 and wild type RYBP), biological duplicate 2

value: yaf2 mutant


title: Yaf2wt_(OHT+) rep1

description:
RYBP KO
Gene expression data from clone#3031+ (tamoxifen treated, Wild type of Yaf2 and Mut RYBP)

value: wild type, Rybp-depleted


title: C2_SA897

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Abscess

value: MRSA

value: IV

tag: cluster

tag: mdth

value: Mild

value: Local

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

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: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

value: abnormal


title: C2_SA919

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

value: Abscess- L thigh req surgical i&d 9/16

value: no

value: No Isolate

value: No Data

value: Tier 3

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

value: Missing Data

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

value: normal


title: Yaf2kd_(OHT+) rep2

description:
Yaf2 KD RYBP KO (II)
Gene expression data from clone#3087+ (tamoxifen treated, Mut Yaf2 and Mut RYBP), biological duplicate 2

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: yaf2 mutant, Rybp-depleted


title: C2_SA890

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Abscess/bacteremia

value: MSSA

value: Quarter 1

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: endocarditis

tag: pericarditis

tag: cellulitis

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: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)


title: C2_SA891

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Abscess

value: no

value: No Isolate

value: No Data

value: Missing Data

tag: cluster

value: MQ

tag: mdth

value: Mild

value: Local

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: 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: Yaf2kd_(OHT+) rep1

description:
Yaf2 KD RYBP KO (I)
Gene expression data from clone#3086+ (tamoxifen treated, Mut Yaf2 and Mut RYBP), biological duplicate 1

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: yaf2 mutant, Rybp-depleted


title: Rybp#15 (OHT+)_12d_rep2

description:
15(+) 12d (II)
Gene expression data from clone#15 (12 days after tamoxifen treatment: Rybp-KO)

hyb_protocol: Heat the Hybridization Cocktail at 99C for 5 minutes. Cool to 45C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45C hybridization oven, at 60 rpm, and incubate for 16 hours.

growth_protocol: ES cells (#10, #15) 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: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: To deplete Rybp, ES cells (#10, #15) were treated with 4-hydoxytamoxifen (OHT) at a concentration of 800nM for 24 hours.

value: Rybp-KO


title: C2_SA862

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Abscess, s/p i&d x2

value: MRSA

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

value: Vancomycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

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: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

value: normal


title: Rybp#10 (OHT+)_12d_rep2

description:
10(+) 12d (II)
Gene expression data from clone#10 (12 days after tamoxifen treatment: Rybp-KO)

tag: strain background

tag: cell type

tag: genotype/variation


title: C2_SA864

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

tag: illness

value: Disseminated:bacteremia, suppurative arthritis, osteomyelitis LLE, myositis, L saphDVT

value: yes

value: IV

value: I

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Severe

value: Invasive

value: Osteoarticular

tag: treatment

value: Daptomycin/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)

value: Missing Data

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

value: abnormal


title: C2_SA858

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Osteomyelitis (pelvis), myositis, abscess

value: no

value: No Isolate

value: MSSA

value: No Data

value: Tier 3

tag: cluster

value: MQ

tag: mdth

value: Moderate

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)


title: C2_SA849

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

tag: illness

value: Pneumonia/empyema

value: yes

value: MRSA

value: IV

value: I

value: Quarter 3

tag: cluster

tag: mdth

value: Invasive

value: Pneumonia

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: 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: Rybp#15 (OHT-)_12d_rep2

description:
15(-) 12d (II)
Gene expression data from clone#15 (without tamoxifen treatment; Wild-type control)

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: wild-type control


title: C2_SA847

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Abscess

value: Tier 3

tag: cluster

tag: mdth

value: Mild

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: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

value: Missing Data

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

value: normal


title: C2_SA855

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: Osteomyelitis (radius), myositis, phlegmon forearm

value: yes

value: MRSA

value: IV

value: I

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Moderate

value: Osteoarticular

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: 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: C2_SA850

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: no

value: No Isolate

value: MSSA

value: No Data

tag: cluster

tag: mdth

value: Invasive

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)


title: Rybp#15 (OHT+)_4d_rep2

description:
15(+) 4d (II)
Gene expression data from clone#15 (4 days after tamoxifen treatment: Rybp-KO)

source_name: Rybp#15 (OHT+)_4d

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Rybp-KO


title: C2_SA859

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Abscess (thigh s/p I&D OR) / cellulitis

value: yes

value: MRSA

value: IV

value: I

value: Tier 3

tag: cluster

tag: mdth

value: Mild

value: Local

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)

value: Missing Data

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: C2_SA857

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

tag: illness

value: Abscess SST

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: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

tag: bands

tag: neutrophils (/ul)

tag: lymphocytes (/ul)

tag: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

value: normal


title: Rybp#10 (OHT+)_4d_rep2

description:
10(+) 4d (II)
Gene expression data from clone#10 (4 days after tamoxifen treatment: Rybp-KO)

source_name: Rybp#10 (OHT+)_4d

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Rybp-KO


title: Rybp#15 (OHT-)_12d_rep1

description:
15(-) 12d
Gene expression data from clone#15 (without tamoxifen treatment; Wild-type control)

value: wild-type control


title: Rybp#15 (OHT-)_4d_rep2

description:
15(-) 4d (II)
Gene expression data from clone#15 (without tamoxifen treatment; Wild-type control)

source_name: Rybp#15 (OHT-)_4d


title: C2_SA844

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Osteo (pelvic), SI joint, deep tissue abscess, no bacteremia

value: no

value: No Isolate

value: MSSA

value: No Data

value: Quarter 1

tag: cluster

tag: mdth

value: Moderate

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: 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: Rybp#15 (OHT+)_4d_rep1

description:
15(+) 4d
Gene expression data from clone#15 (4 days after tamoxifen treatment: Rybp-KO)

tag: strain background

tag: cell type

tag: genotype/variation


title: Rybp#10 (OHT+)_12d_rep1

description:
10(+) 12d
Gene expression data from clone#10 (12 days after tamoxifen treatment: Rybp-KO)


title: Rybp#15 (OHT-)_4d_rep1

description:
15(-) 4d
Gene expression data from clone#15 (without tamoxifen treatment; Wild-type control)


title: leukemia-3

tag: gender

value: female

tag: age (yrs)

tag: tissue source

value: bone marrow (BM)

tag: disease state

value: acute myeloid leukemia (AML)

tag: subtype

tag: abnormality


title: C2_SA807

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

value: M

tag: tissue

tag: illness

value: Disseminated:bacteremia, pneumonia, endocarditis, septic emboli kidneys

value: MRSA

value: Missing Data

value: Quarter 3

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Unknown

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: monocytes (/ul)

tag: eosinophils (/ul)

tag: basophils (/ul)

tag: hemoglobin (g/dl)

tag: hematocrit (%)

tag: mcv (um3)

tag: mch (pg)

value: abnormal


title: C2_SA811

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Septic arthritis

value: no

value: No Isolate

value: MSSA

value: No Data

value: Tier 2

tag: cluster

value: MQ

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: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology

value: normal


title: C2_SA815

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Disseminated:bacteremia, osteomyelitis, suppurative arthritis, pulmonary emboli, chest wall cellulitis

value: yes

value: MRSA

value: IV

value: I

value: Quarter 3

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Clindamycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: wbc (/ul)

value: Missing Data

tag: neutrophil (%)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

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: adpA regulon in liquid culture

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

hyb_protocol: Labelled cDNA hybridised using Hybstation. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1% SDS) at 42 °C ,  0.1x SSC (+0.05% SDS) and 0.1x SSC, each at 25 °C for 30 sec prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 6.1 software.

data_processing: Data analysis was carried out using Imagene, version 6.1 (Biodiscovery Inc). The mean values from each channel were normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from biological repeats with all replicates combined. data was compiled from his-adpA expressing and control delta adpA strains each with a dye-swap replicate, thus providing three biological repeats.

organism: Streptomyces griseus

source_name: his-adpA expressing delta adpA strain cultured in liquid YMPD for 18 h

label_protocol: Labelled with Cy3 and Cy5 after cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: his-adpA expressing and control delta adpA strains were cultivated in YMPD liquid medium for 18 h.

extract_protocol: Toral RNA was extracted using ISOGEN (Nippon Gene) and DNA was removed using Dnase I.

treatment_protocol: S. griseus strains were grown in a 500 ml Sakaguchi flask with recipropical shaking (120 rpm) and the temperature maintained at 30 °C.

tag: strain

value: his-adpA expressing delta adpA strain

source_name: control delta adpA strain cultured in liquid YMPD for 18 h

value: control delta adpA strain


title: Rybp#10 (OHT+)_4d_rep1

description:
10(+) 4d
Gene expression data from clone#10 (4 days after tamoxifen treatment: Rybp-KO)

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Rybp-KO


title: MH.S-miR127

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scaned by GenePix 4000B scanner

data_processing: Data were background subtracted and normalized within the array using the LOESS normalization by Genespring GX 11 software.

source_name: MH.S-miR127 cells

extract_protocol: mirVana isolation  kit

tag: cell line

value: MH-S

tag: transfection


title: C2_SA796

value: Test

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Disseminated:bacteremia, pneumonia, endocarditis, septic emboli kidneys

value: no

value: No Isolate

value: No Data

value: Quarter 2

value: Tier 1

tag: cluster

tag: mdth

tag: treatment

value: Vancomycin/Rifampin/Gentamycin

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: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology

value: abnormal


title: Rybp#15 (OHT+)_12d_rep1

description:
15(+) 12d
Gene expression data from clone#15 (12 days after tamoxifen treatment: Rybp-KO)

tag: strain background

value: 129/B6 hybrid

tag: cell type

tag: genotype/variation


title: Rybp#10 (OHT-)_4d_rep2

description:
10(-) 4d (II)
Gene expression data from clone#10 (without tamoxifen treatment; Wild-type control)

source_name: Rybp#10 (OHT-)_4d

value: embryonic stem cells

value: wild-type control


title: Rybp#10 (OHT-)_4d_rep1

description:
10(-) 4d
Gene expression data from clone#10 (without tamoxifen treatment; Wild-type control)


title: Untreated cells 1 vs Depsipeptide treated cells 1

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: biological replicate

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent whole genome array (G4112F) that was scanned using the Agilent G2505B scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: YB5 colon cancer cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: The YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum and 100 μg/mL Penicillin-Streptomycin solution.

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

tag: cell line

tag: treatment

treatment_protocol: Depsipeptide 20 nM for 24 hours

value: Depsipeptide


title: C2_SA756

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

tag: illness

value: Abscess

value: yes

value: MRSA

value: IV

value: I

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

value: Mild

value: Local

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 (%)

value: Missing Data

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)

value: normal


title: C2_SA824

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Pneumonia with empyema, skin/soft tissue pustule

value: no

value: No Isolate

value: MSSA

value: No Data

value: Tier 2

tag: cluster

tag: mdth

value: Severe

value: Invasive

value: Pneumonia

tag: treatment

value: Vancomycin/Oxacillin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: emboli

tag: lymphocyte (%)

tag: monocytes (%)

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_SA769

value: Test

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

tag: tissue

tag: illness

value: abscess/facial cellulitis

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

value: Mild

value: Local

tag: treatment

value: Oxacillin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

value: Missing Data

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: Untreated cells 2 vs Depsipeptide treated cells 2

description: biological replicate

label: Cy3 control

tag: treatment

value: Depsipeptide


title: MH.S-Sico

source_name: MH.S-Sico cells

tag: cell line

value: MH-S

tag: transfection

value: control non-targetting siCO


title: C2_SA657

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia, Osteomyelitis

value: yes

value: MRSA

value: IV

value: I

value: Quarter 1

tag: cluster

tag: mdth

value: Moderate

value: Osteoarticular

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: lymphocyte (%)

tag: monocytes (%)

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: normal


title: C2_SA704

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

tag: illness

value: Osteomyelitis, sepsis,

value: no

value: No Isolate

value: MSSA

value: No Data

value: Tier 3

tag: cluster

tag: mdth

value: Invasive

tag: treatment

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

value: Missing Data

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: C2_SA649

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia (x2d), Osteomyelitis (L femoral)

value: yes

value: III

value: Quarter 3

tag: cluster

tag: mdth

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: lymphocyte (%)

tag: monocytes (%)

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


title: C2_SA634

value: Test

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia, Osteomyelitis R tibia, myositis, cellulitis

value: MRSA

value: IV

value: I

tag: cluster

tag: mdth

value: Severe

value: Osteoarticular

tag: treatment

value: Clindamycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: intubation

tag: wbc (/ul)

tag: neutrophil (%)

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: Rybp#10 (OHT-)_12d_rep1

description:
10(-) 12d
Gene expression data from clone#10 (without tamoxifen treatment; Wild-type control)

tag: strain background

value: 129/B6 hybrid

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: wild-type control


title: adpA regulon in solid culture at 3 days

source_name: his-adpA expressing delta adpA strain cultured in solid YMPD for 3 days

growth_protocol: his-adpA expressing and control delta adpA strains were cultivated in YMPD solid medium for 1, 2 and 3 days.

treatment_protocol: S. griseus strains were grown on a YMPD plate and the temperature maintained at 28 °C.

tag: strain

value: his-adpA expressing delta adpA strain

source_name: control delta adpA strain cultured in solid YMPD for 3 days

value: control delta adpA strain


title: adpA regulon in solid culture at 1 day

source_name: his-adpA expressing delta adpA strain cultured in solid YMPD for 1 day

source_name: control delta adpA strain cultured in solid YMPD for 1 day


title: C2_SA626

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Empyema/bacteremia/pneumatocells

value: yes

value: Quarter 1

value: Tier 2

tag: cluster

tag: mdth

value: Disseminated

value: Pneumonia

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: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

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: adpA regulon in solid culture at 2 days

source_name: his-adpA expressing delta adpA strain cultured in solid YMPD for 2 days

tag: strain

source_name: control delta adpA strain cultured in solid YMPD for 2 days


title: C2_SA623

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

tag: illness

value: Osteomyelitis/bacteremiia/myosisitis

value: no

value: No Isolate

value: MSSA

value: No Data

value: Tier 3

tag: cluster

value: MQ

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: meningitis

tag: emboli

tag: wbc (/ul)

tag: neutrophil (%)

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: C2_SA614

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: O

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: yes

value: MRSA

value: IV

value: I

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Severe

tag: treatment

value: Vancomycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

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: normal


title: RAW264.7 cells, CAT overexpression, 0 hrs post-LPS, replicate 3

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

description: cSA8 - C - 0

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)

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: cell type

tag: construct

value: CAT

tag: lps exposure time


title: RAW264.7 cells, CAT overexpression, 3 hrs post-LPS, replicate 3

description: cSA8 - C - 3hr


title: RAW264.7 cells, CAT overexpression, 5 hrs post-LPS, replicate 2

description: cSA8 - B - 5 hr


title: C2_SA573

source_name: Human Whole Blood

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

tag: illness

value: Osteomyelitis/No bacteremia

value: Missing Data

value: Quarter 2

tag: cluster

value: MQ

tag: mdth

value: Moderate

tag: treatment

value: Unknown

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: wbc (/ul)

tag: neutrophil (%)

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: C2_SA1324

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/osteo

value: no

value: No Isolate

value: MRSA

value: No Data

value: Tier 2

tag: cluster

tag: mdth

value: Invasive

value: Osteoarticular

tag: treatment

value: Vancomyn/Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

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


title: C2_SA566

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

value: M

tag: tissue

tag: illness

value: Pneumonia

value: Quarter 1

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: wbc (/ul)

tag: neutrophil (%)

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_SA537

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: O

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia, suppurative arthritis, osteomyelitis

value: MSSA

value: Quarter 3

tag: cluster

value: MQ

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: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

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_SA1323

value: Test

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia/osteo

value: no

value: No Isolate

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: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: wbc (/ul)

tag: neutrophil (%)

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: RAW264.7 cells, CAT overexpression, 1 hrs post-LPS, replicate 2

description: cSA8 - B - 1hr

tag: cell type

tag: construct

value: CAT

tag: lps exposure time


title: RAW264.7 cells, CAT overexpression, 5 hrs post-LPS, replicate 1

description: cSA8 - A - 5 hr


title: RAW264.7 cells, CAT overexpression, 1 hrs post-LPS, replicate 3

description: cSA8 - C - 1hr


title: RAW264.7 cells, CAT overexpression, 3 hrs post-LPS, replicate 1

description: cSA8 - A - 3hr


title: RAW264.7 cells, CAT overexpression, 0 hrs post-LPS, replicate 2

description: cSA8 - B - 0


title: C2_SA1335

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: MRSA

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Disseminated

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: picu

tag: intubation

value: Missing Data

tag: lymphocyte (%)

tag: monocytes (%)

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


title: C2_SA598

value: Test

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

tag: illness

value: Abscess

value: yes

value: IV

value: I

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: dvt

tag: wbc (/ul)

tag: neutrophil (%)

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)

value: normal


title: RAW264.7 cells, CAT overexpression, 5 hrs post-LPS, replicate 3

description: cSA8 - C - 5 hr

tag: cell type

tag: construct

value: CAT

tag: lps exposure time


title: RAW264.7 cells, CAT overexpression, 0 hrs post-LPS, replicate 1

description: cSA8 - A - 0


title: C2_SA1351

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/osteo/UTI

value: no

value: No Isolate

value: MRSA

value: No Data

value: Quarter 1

tag: cluster

value: MQ

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: meningitis

tag: emboli

tag: sepsis

tag: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

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


title: RAW264.7 cells, CAT overexpression, 3 hrs post-LPS, replicate 2

description: cSA8 - B - 3hr

tag: cell type

tag: construct

tag: lps exposure time


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

description: cSA8 - A - 1hr


title: C2_SA493

value: Test

tag: disease

tag: age

tag: ethnicity

value: O

tag: gender

value: M

tag: tissue

tag: illness

value: Osteo/bacteremia

value: yes

value: MSSA

value: II

value: Tier 3

tag: cluster

tag: mdth

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: wbc (/ul)

tag: neutrophil (%)

value: Missing Data

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: C2_SA1309

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/osteo

value: no

value: No Isolate

value: MRSA

value: Quarter 2

value: Tier 2

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: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

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: normal


title: C2_SA1306

value: Test

tag: disease

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

tag: illness

value: No Data

value: Quarter 3

tag: cluster

value: MQ

tag: mdth

value: Moderate

value: Invasive

value: Osteoarticular

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: wbc (/ul)

tag: neutrophil (%)

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)

value: abnormal


title: C2_SA1313

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Abscess, Necrotizing fasciitis (severe)

value: no

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: picu

tag: intubation

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C2_SA1287

value: Test

tag: disease

tag: age

tag: ethnicity

tag: gender

tag: tissue

tag: illness

value: No Isolate

value: MRSA

value: No Data

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Severe

value: Disseminated

tag: treatment

value: Vancomycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: wbc (/ul)

tag: neutrophil (%)

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: RAW264.7 cells, Tbc1d23 overexpression, 5 hrs post-LPS, replicate 3

description: cSA2 - C - 5 hr

tag: cell type

tag: construct

tag: lps exposure time


title: Rybp#10 (OHT-)_12d_rep2

description:
10(-) 12d (II)
Gene expression data from clone#10 (without tamoxifen treatment; Wild-type control)

tag: strain background

value: 129/B6 hybrid

value: embryonic stem cells

tag: genotype/variation

value: wild-type control


title: C2_SA1232

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: O

tag: gender

value: M

tag: tissue

value: Whole Blood

tag: illness

value: Abscess

value: yes

value: IV

value: I

tag: cluster

value: MQ

tag: mdth

value: Mild

value: Local

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: 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_SA1184

value: Test

tag: disease

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

tag: illness

value: Pneumonia/efussion

value: MSSA

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Moderate

value: Invasive

value: Pneumonia

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: neutrophil (%)

value: Missing Data

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: C2_SA1137

tag: disease

value: S. aureus

tag: age

tag: ethnicity

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Abscess no bacteremia

value: no

value: No Isolate

value: MRSA

value: No Data

value: Quarter 3

value: Tier 3

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: sepsis

tag: dvt

tag: picu

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

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


title: RAW264.7 cells, Tbc1d23 overexpression, 5 hrs post-LPS, replicate 2

description: cSA2 - B - 5 hr

tag: cell type

tag: construct

tag: lps exposure time


title: RAW264.7 cells, Tbc1d23 overexpression, 1 hrs post-LPS, replicate 3

description: cSA2 - C - 1hr


title: RAW264.7 cells, Tbc1d23 overexpression, 0 hrs post-LPS, replicate 2

description: cSA2 - B - 0


title: RAW264.7 cells, Tbc1d23 overexpression, 3 hrs post-LPS, replicate 3

description: cSA2 - C - 3hr


title: RAW264.7 cells, Tbc1d23 overexpression, 3 hrs post-LPS, replicate 2

description: cSA2 - B - 3hr


title: RAW264.7 cells, Tbc1d23 overexpression, 3 hrs post-LPS, replicate 1

description: cSA2 - A - 3hr


title: RAW264.7 cells, Tbc1d23 overexpression, 0 hrs post-LPS, replicate 3

description: cSA2 - C - 0


title: RAW264.7 cells, Tbc1d23 overexpression, 5 hrs post-LPS, replicate 1

description: cSA2 - A - 5 hr


title: C2_SA1176

value: Test

tag: disease

tag: age

tag: ethnicity

value: AA

tag: gender

value: M

tag: tissue

tag: illness

value: Osteo-no bacteremia

value: yes

value: IV

value: I

value: Quarter 2

value: Tier 2

tag: cluster

tag: mdth

value: Severe

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: neutrophil (%)

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)

value: normal


title: C2_SA1189

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

value: F

tag: tissue

value: Whole Blood

tag: illness

value: Osteomyelitis-no bacteremia

value: no

value: No Isolate

value: MSSA

tag: cluster

tag: mdth

value: Moderate

value: Invasive

tag: treatment

value: Cephalexin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: intubation

tag: wbc (/ul)

value: Missing Data

tag: lymphocyte (%)

tag: monocytes (%)

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


title: C2_SA1030

value: Test

tag: disease

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: tissue

tag: illness

value: Bacteremia, osteomyelitis

value: yes

value: MRSA

value: IV

value: I

value: Quarter 1

tag: cluster

tag: mdth

tag: treatment

value: Clindamycin/Rifampin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: meningitis

tag: emboli

tag: sepsis

tag: dvt

tag: picu

tag: neutrophil (%)

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)

value: abnormal


title: pNZ8900 vs pNZ-ykrK rep3

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) {A}

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

tag: sample type

value: control

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

value: test

value: YkrK Overexpression Mutant

value: pNZ-ykrK


title: C2_SA1083_A

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: H

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: Bacteremia/Pyomyositis

value: MSSA

value: No Data

value: Quarter 3

value: Tier 2

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: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

tag: eosinophils (%)

tag: basophils (%)

value: Missing Data

tag: mchc (g/dl)

tag: rdw (%)

tag: platelets (103/mm3)

tag: mpv (um3)

tag: esr

tag: crp (mg/dl)

tag: rbc morphology


title: C2_SA1009

value: Test

tag: disease

tag: age

tag: ethnicity

tag: gender

value: M

tag: tissue

tag: illness

value: Myositis/bacteremia/Pericarditis

value: yes

value: MRSA

value: IV

value: I

value: Quarter 1

value: Tier 1

tag: cluster

tag: mdth

value: Disseminated

tag: treatment

value: Vancomycin/Clindamycin

tag: bacteremia

tag: osteomyelitis

tag: pyomyositis

tag: pneumonia

tag: empyema

tag: endocarditis

tag: pericarditis

tag: cellulitis

tag: meningitis

tag: picu

tag: neutrophil (%)

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)

value: abnormal


title: RAW264.7 cells, Tbc1d23 overexpression, 0 hrs post-LPS, replicate 1

description: cSA2 - A - 0

tag: cell type

tag: construct

tag: lps exposure time


title: C2_SA1006

tag: disease

value: S. aureus

tag: age

tag: ethnicity

value: AA

tag: gender

tag: tissue

value: Whole Blood

tag: illness

value: L orbital abscess, cellulitis

value: Tier 3

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: emboli

tag: sepsis

tag: dvt

tag: intubation

tag: wbc (/ul)

tag: lymphocyte (%)

tag: monocytes (%)

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: normal


title: pNZ8900 vs pNZ-ykrK rep4

tag: genotype

value: Wild Type

tag: strain

tag: plasmid

tag: sample type

value: control

value: test

value: YkrK Overexpression Mutant

value: pNZ-ykrK


title: RAW264.7 cells, Tbc1d23 overexpression, 1 hrs post-LPS, replicate 2

description: cSA2 - B - 1hr

tag: cell type

tag: construct

tag: lps exposure time