title: Calvarial_OB_5

status: Public on Nov 15 2008

city: London

first: Simon

last: Rawlinson

address: 4 Newark Street

country: United Kingdom

institute: Bart's and The London School of Medicine and Dentistry

hyb_protocol: According to protocol provided by Illumina

scan_protocol: Scanning procedures were carried out as described by Illumina

data_processing: The data were normalised using quantile normalisation with Illumina GUI

source_name: RAT_5; calvarial osteoblasts

label_protocol: Illumina protocol

growth_protocol: 95% confluent , P3 osteoblasts

extract_protocol: RNA was extracted using QIAGEN Rneasy mini kit

tag: Normal


title: Ulnar_Ob_1

type: RNA

middle: Charles

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: RAT_1; ulnar osteoblasts


title: Calvarial_OB_4

source_name: RAT_4; calvarial osteoblasts


title: Calvarial_OB_2

source_name: RAT_2; calvarial osteoblasts


title: Ulnar_Ob_2

source_name: RAT_2; ulnar osteoblasts


title: Ulnar_Ob_5

source_name: RAT_5; ulnar osteoblasts


title: Ulnar_Ob_3

source_name: RAT_3; ulnar osteoblasts


title: GBM Cell B vs Exosome B

status: Public on Nov 16 2008

city: Charlestown

first: Johan

last: Skog

state: MA

address: 149 13th street

department: Molecular Neurogenetics

country: USA

institute: Massachusetts General Hospital

description: The Agilent Feature Extraction Software (FES) determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). The Rosetta Resolverâ software offers – among other features – the possibility to visualize the results of the data analysis in a double-log scatter plot.

hyb_protocol: The Agilent array data was performed by Miltenyi Biotech. The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent FES was used to read out and process the microarray image files. The VALUE columns are based on the Agilent ProcessedSignal values that have gone through the Agilent Feature Extraction steps. For determination of differential gene expression, FES-derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). Data was analyzed using the GeneSifter software.

organism: Homo sapiens

source_name: Primary glioblastoma cells

label_protocol: For the linear T7-based amplification step, 1 μg of each total RNA and 0.5 μg of each exosome RNA sample was used as starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Glioblastoma cells at passage 1–15 were grown for 48 hrs in DMEM with exosome-depleted 5% FBS. After 48 hrs, the supernatant was collected for exosome purification, and in parallel, the cells were harvested for RNA extraction.

extract_protocol: The cells were washed in PBS and then subjected to total RNA extraction with the MirVana RNA isolation kit according to manufacturer's recommendation.

tag: Primary human glioblastoma cells cultured in vitro.

source_name: Exosomes shed from primary human glioblastoma cells

growth_protocol: Glioblastoma cells at passage 1–15 were cultured in microvesicle-free medium (DMEM containing 5% dFBS) and conditioned medium was collected after 48 h. Microvesicles were purified by differential centrifugation. In brief, glioblastoma-conditioned medium was centrifuged for 10 min at 300g to eliminate cell contamination. Supernatants were further centrifuged for 20 min at 16,500g and filtered through a 0.22 μm filter. Microvesicles were pelleted by ultracentrifugation at 110,000g for 70 min. The microvesicle pellets were washed in 13 ml PBS, pelleted again and resuspended in PBS before RNA extraction.

extract_protocol: The exosomes were washed in PBS and then subjected to total RNA extraction with the MirVana RNA isolation kit according to manufacturer's recommendation.

tag: Exosomes were isolated from the glioblastoma cells analyzed in channel 1.


title: Ulnar_Ob_4

source_name: RAT_4; ulnar osteoblasts


title: Calvarial_OB_1

source_name: RAT_1; calvarial osteoblasts


title: ES MC1 Actinomycin D Lif+ RA 8hours rep #2 (251508710458A4)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Mus musculus

source_name: ES MC1 Actinomycin D Lif+ RA 8hours

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50ul of DEPC dH2O.

tag: Embryonic stem cells

tag: Strain

tag: Gender

value: male

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: ES MC1 Actinomycin D Lif+ RA 2hours rep #2 (251508710456A4)

source_name: ES MC1 Actinomycin D Lif+ RA 2hours


title: ES MC1 Actinomycin D Lif+ RA 4hours rep #2 (251508710458A2)

source_name: ES MC1 Actinomycin D Lif+ RA 4hours


title: GBM Cell A vs Exosome A


title: ES MC1 Actinomycin D Lif+ RA 8hours rep #1 (251508710458A3)


title: ES MC1 Actinomycin D Lif+ RA 1hour rep #1 (251508710456A1)

source_name: ES MC1 Actinomycin D Lif+ RA 1hour


title: ES MC1 Actinomycin D Lif+ RA 4hours rep #1 (251508710458A1)


title: ES MC1 Actinomycin D Lif+ RA 2hours rep #1 (251508710456A3)


title: ES MC1 Intact Lif+ RA rep #2 (251508710455A4)

source_name: ES MC1 Intact Lif+ RA


title: ES MC1 ActinomycinD Lif- 8hours rep #2 (251508710455A2)

source_name: ES MC1 ActinomycinD Lif- 8hours

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30ul of DEPC dH2O.


title: ES MC1 Intact Lif+ RA rep #1 (251508710455A3)


title: ES MC1 ActinomycinD Lif- 4hours rep #2 (251508710454A4)

source_name: ES MC1 ActinomycinD Lif- 4hours

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 60ul of DEPC dH2O.


title: ES MC1 ActinomycinD Lif- 2hours rep #2 (251508710454A2)

source_name: ES MC1 ActinomycinD Lif- 2hours


title: ES MC1 ActinomycinD Lif- 4hours rep #1 (251508710454A3)


title: ES MC1 ActinomycinD Lif- 8hours rep #1 (251508710455A1)


title: ES MC1 ActinomycinD Lif- 1hour rep #1 (251508710453A3)

source_name: ES MC1 ActinomycinD Lif- 1hour


title: ES MC1 Intact Lif- rep #2 (251508710453A2)

source_name: ES MC1 Intact Lif-

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 70ul of DEPC dH2O.


title: F1c_Seedling_78h_gDNA_rep4

status: Public on Nov 18 2008

type: genomic

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description: F1c whole seedling at 78 hour

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor package Affy

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: F1c whole seedling at 78 hour

label_protocol: Invitrogen  Bioprime random labeling

extract_protocol: Qiagen DNeasy Plant Mini Kit

tag: accession

value: Col female x Van male

tag: tissue

value: whole seedling

tag: stage

value: 78 hour on MS plate

tag: growth condition

value: Percival chamber, 12h light/12h dark, 20 degree


title: ES MC1 Actinomycin D Lif+ RA 1hour rep #2 (251508710456A2)


title: ES MC1 Intact Lif- rep #1 (251508710453A1)

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 70 ul of DEPC dH2O.


title: ES MC2-B6 Actinomycin D Lif+ 1hour rep #2 (251508710451A4)

source_name: ES MC2-B6 Actinomycin D Lif+ 1hour

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 55 ul of DEPC dH2O.


title: ES MC2-B6 Actinomycin D Lif+ 8hours rep #1 (251508710452A3)

source_name: ES MC2-B6 Actinomycin D Lif+ 8hours


title: ES MC1 ActinomycinD Lif- 1hour rep #2 (251508710453A4)


title: F1c_Seedling_78h_gDNA_rep2

description: F1c whole seedling at 78 hour


title: ES MC1 Actinomycin D Lif+ 8hours rep #1 (251508710451A2)

source_name: ES MC1 Actinomycin D Lif+ 8hours

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.


title: ES MC2-B6 Actinomycin D Lif+ 4hours rep #1 (251508710452A2)

source_name: ES MC2-B6 Actinomycin D Lif+ 4hours

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 55ul of DEPC dH2O.


title: F1v_Seedling_78h_gDNA_rep3

description: F1v whole seedling at 78 hour

source_name: F1v whole seedling at 78 hour

value: Van female x Col male


title: F1c_Seedling_78h_gDNA_rep1

description: F1c whole seedling at 78 hour


title: Calvarial_OB_3

source_name: RAT_3; calvarial osteoblasts


title: ES MC1 ActinomycinD Lif- 2hours rep #1 (251508710454A1)

source_name: Universal Mouse Reference Cell Line Pool


title: ES MC1 Actinomycin D Lif+ 4hours rep #2 (251508710451A1)

source_name: ES MC1 Actinomycin D Lif+ 4hours


title: F1v_Seedling_78h_gDNA_rep4

description: F1v whole seedling at 78 hour


title: Col_Seedling_78h_gDNA_rep4

description: Col whole seedling at 78 hour

source_name: Col whole seedling at 78 hour

value: Col


title: ES MC1 Actinomycin D Lif+ 1hour rep #2 (251508710450A3)

source_name: ES MC1 Actinomycin D Lif+ 1hour

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 65 ul of DEPC dH2O.


title: ES MC1 Actinomycin D Lif+ 2hours rep #2 (251508710450A4)

source_name: ES MC1 Actinomycin D Lif+ 2hours


title: ES MC2-B6 Actinomycin D Lif+ 8hours rep #2 (251508710452A4)


title: ES MC2-B6 Actinomycin D Lif+ 2hours rep #1 (251508710445A3)

source_name: ES MC2-B6 Actinomycin D Lif+ 2hours


title: ES MC2-B6 Actinomycin D Lif+ 4hours rep #2 (251508710445A4)


title: Col_Seedling_78h_gDNA_rep3

description: Col whole seedling at 78 hour


title: ES MC2-B6 Intact rep #1 (251508710444A3)

source_name: ES MC2-B6 Intact


title: ES MC1 Actinomycin D Lif+ 2hours rep #1 (251508710444A1)


title: ES MC2-B6 Intact rep #2 (251508710444A4)


title: F1v_Seedling_78h_gDNA_rep2

description: F1v whole seedling at 78 hour


title: ES MC2-B6 Actinomycin D Lif+ 1hour rep #1 (251508710445A2)

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 35 ul of DEPC dH2O.


title: ES MC1 Actinomycin D Lif+ 8hours rep #2 (251508710451A3)


title: ES MC2-B6 Actinomycin D Lif+ 2hours rep #2 (251508710452A1)


title: ES MC1 Actinomycin D Lif+ 1hour rep #1 (251508710443A4)


title: ES MC1 Intact rep #1 (251508710443A1)

source_name: ES MC1 Intact


title: ES MC1 Intact rep #2 (251508710443A2)


title: ES MC1 Actinomycin D Lif+ 4hours rep #1 (251508710444A2)

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 40 ul of DEPC dH2O.


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse91_Pro/Pro_Chow_Male_Liver

city: Seattle

first: eric

middle: e

last: schadt

state: WA

address: 401 Terry Ave N

department: Genetics

institute: Merck

description: Samples from liver, adipose (epididymal fat pads) and muscle (gastrocnemius) were acquired from 10 male wildtype mice and 10 male pro12ala knock-in mice. All mice were fed a chow diet for eight weeks then half were switched to high fat (R&D, D12907B, 41% milk fat, 43% carbohydrate) diet for an additional 12 weeks while the remaining mice stayed on chow. Individuals from each strain were compared to a common pool created from equal portions of RNA from 10 wildtype samples

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model

source_name: Liver

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: Diet as specified

tag: HFD, WT, Liver N=10 (virtual pool)


title: Van_Seedling_78h_gDNA_rep3

description: Van whole seedling at 78 hour

source_name: Van whole seedling at 78 hour

value: Van


title: Van_Seedling_78h_gDNA_rep2

description: Van whole seedling at 78 hour


title: F1c_Seedling_78h_gDNA_rep3

description: F1c whole seedling at 78 hour

source_name: F1c whole seedling at 78 hour


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse94_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse77_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse88_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse95_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse80_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse74_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse85_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse84_Pro/Pro_Chow_Male_Liver


title: F1v_Seedling_78h_gDNA_rep1

description: F1v whole seedling at 78 hour


title: Van_Seedling_78h_gDNA_rep1

description: Van whole seedling at 78 hour


title: Van_Seedling_78h_gDNA_rep4

description: Van whole seedling at 78 hour


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse149_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse152_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse154_Ala/Ala_Chow_Male_Liver


title: Col_Seedling_78h_gDNA_rep2

description: Col whole seedling at 78 hour


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse73_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse137_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse131_Pro/Pro_HFD_Male_Liver


title: Col_Seedling_78h_gDNA_rep1

description: Col whole seedling at 78 hour


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse127_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse141_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse128_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse99_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse72_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse143_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse147_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse122_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse155_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse125_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse123_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse120_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse119_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse116_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse99_Ala/Ala_HFD_Male_Gastroc

source_name: Gastrocnemius

tag: HFD, WT, Gastroc N=10 (virtual pool)


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse110_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse118_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse105_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse117_Ala/Ala_HFD_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse113_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse106_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse114_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse95_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse101_Pro/Pro_Chow_Male_Liver


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse109_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse94_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse80_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse73_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse88_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse91_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse84_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse155_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse85_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse147_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse152_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse149_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse154_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse141_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse143_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse131_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse137_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse123_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse120_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse125_Pro/Pro_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse118_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse119_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse111_Pro/Pro_HFD_Male_Liver


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse122_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse121_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse127_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse113_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse117_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse128_Ala/Ala_HFD_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse109_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse114_Ala/Ala_Chow_Male_Gastroc


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse99_Ala/Ala_HFD_Male_eWAT

source_name: epididymal fat pad

tag: HFD, WT, eWAT n=10 (virtual pool)


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse106_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, Liver N=10 (virtual pool) vs. Mouse121_Ala/Ala_Chow_Male_Liver


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse105_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse85_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse88_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse101_Pro/Pro_Chow_Male_Gastroc


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse80_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse77_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse94_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse74_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse91_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse73_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse95_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse72_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse143_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse155_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse84_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse154_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse152_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse141_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse89_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse147_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse137_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse149_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse131_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse128_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse125_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse123_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse122_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse120_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse116_Ala/Ala_HFD_Male_eWAT


title: Rat ulna_1

description: Samples underwent 1 round of amplification prior to labeling using the Affymetrix GeneChip® One-Cycle cDNA Synthesis Kit.

hyb_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.

data_processing: MAS5 algorithm

label: biotin

source_name: Rat ulnar bone

extract_protocol: Tissue dissected and ground to a paste in liquid nitrogen in pestle and mortar. Immediate immersion/homogenization in QIAzol. Aqueous phase transferred to QIAgen RNeasy (Fibrous tissue) Mini column for RNA prep.

treatment_protocol: Bone samples taken from different skeletal sites

tag: RAT

value: CD

value: Male

tag: Weight

tag: Tissue

value: Calvarial bone – attendant soft tissue removed


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse117_Ala/Ala_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse121_Ala/Ala_Chow_Male_eWAT


title: ChIP-CHIP of Mcm1-TAP in hyphal state-2

city: Montreal

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

country: Canada

institute: CNRC-IRB

description: Arrays are organized in 48 sub-arrays containing 280 spots each.

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: ChIP of Mcm1-TAP expressing hyphal cells

label_protocol:
Linkers were added to the extracted genomic DNA by ligation-mediated PCR (LM-PCR) as described elsewhere:
http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html
B. Guillemette, A. R. Bataille, N. Gevry et al., PLoS biology 3 (12), e384 (2005)

growth_protocol: Cells were grown in YPD + uridine to an OD600 of 1.0. They were then transfered to YPD + uridine +10% FBS (Fetal Bovine Serum) at 37°C for 1 hour.

extract_protocol:
ChIP with IgG-sepharose beads (GE Healthcare). The rest of the extraction protocol was as described:
http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html
B. Guillemette, A. R. Bataille, N. Gevry et al., PLoS biology 3 (12), e384 (2005)

value: BWP17 containing a TAP-tag integrated at the Mcm1 locus and selected with a URA3 marker.

source_name: ChIP of Mock hyphal cells


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse113_Ala/Ala_Chow_Male_eWAT


title: Rat ulna_2

label_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.


title: Rat ulna_4

tag: Treatment protocol

value: Bone samples taken from different skeletal sites


title: Rat ulna_3


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse114_Ala/Ala_Chow_Male_eWAT


title: HFD, WT, Gastroc N=10 (virtual pool) vs. Mouse77_Ala/Ala_HFD_Male_Gastroc


title: ChIP-CHIP of Mcm1-TAP in hyphal state


title: ChIP-CHIP of Mcm1-TAP in yeast state

source_name: ChIP of Mcm1-TAP expressing yeast cells

growth_protocol: Cells were grown in YPD + uridine to an OD600 of 1.0

source_name: ChIP of Mock yeast cells


title: Rat calvaria_3

source_name: Rat calvarial bone


title: Rat calvaria_4


title: Rat ulna_5

value: Limb bone – attendant soft tissue removed


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse109_Ala/Ala_Chow_Male_eWAT


title: ChIP-CHIP of Mcm1-TAP in yeast state-2


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse110_Pro/Pro_HFD_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse111_Pro/Pro_HFD_Male_eWAT


title: Rat calvaria_2


status: Public on Nov 14 2008

city: Frederick

first: Richard

middle: A

last: Lempicki

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Post-Vacination, Media

hyb_protocol: Labeled cRNA was fragmented and hybridized to the GeneChips, which were then washed and stained with streptavidin-conjugated PE by using the Affymetrix GeneChip Fluid Station 400 (Affymetrix, Inc.).

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the first normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.  Values were log2 transformed and normalized a second time using the Loess method.
All results from a donor were excluded if one of the conditions (media and VLP cultures for the pre- and post-vaccination specimens) did not fulfill one of the previously mentioned quality control filters used to ensure that all chips were of comparable quality. These quality control procedures resulted in exclusion of two of the vaccine recipients and one placebo.  One additional vaccine recipient was excluded due to a high degree of granulocyte contamination (61% versus 0.2-13.6% granulocytes for remaining samples), possibly due to poor PBMC Ficoll isolation, and because neutralizing antibodies against HPV-16 were detectable before vaccination. Two additional placebos were excluded because they had detectable antibodies in the course of our study. After all exclusions, 17 vaccine and 4 placebo recipients were used in subsequent analysis.
Data from probesets that were not reliably detected with a mean intensity> log2 =5 in at least one experimental condition (media and VLP cultures for the pre- and post-vaccination specimens) were excluded before further analysis. A total of 7145 probesets remained after applying this criterion.

source_name: Human PBMCs cultured for 3 days

label_protocol: Total RNA preparation and labeled cRNA synthesis and hybridization were performed according to the manufacturer's recommended protocol (Affymetrix, Inc.). In short, 10 µg of total RNA were used for double-stranded cDNA (ds-cDNA) synthesis with the SuperScript™ II Reverse Transcriptase Kit (Invitrogen) and an oligo (dT) primer containing a T7 RNA polymerase promoter to prime the first-strand synthesis. Biotin-labeled cRNA was obtained by in vitro transcription after addition of T7 RNA polymerase and biotinylated nucleotides (Enzo Biochem) to the ds-cDNA.

growth_protocol:
Participants were selected from a double-blind, randomized, placebo-controlled phase II trial of the HPV-16 L1 VLP vaccine without adjuvant, which was conducted in a sample of 220 healthy, HIV seronegative adult female volunteers 18-25 years of age, as described previously (17). Briefly, subjects were enrolled at The Johns Hopkins University Center for Immunization Research (Baltimore). Women were randomly assigned to receive three intramuscular doses of either 50 µg of HPV-16 L1 VLP vaccine without adjuvant, or placebo (0.5 mL saline). Blood specimens were collected before the initial dose (month 0), and 1 month after each of the subsequent vaccinations (months 2 and 7). The Johns Hopkins University Institutional Review Board approved the protocol for this study. Blood specimens were shipped to the HPV Immunology Laboratory (Frederick, MD), where PBMCs were cryopreserved.
Twenty-seven subjects (20 vaccine and 7 placebo recipients) were randomly selected for microarray measurements. Only month 0 and month 2 samples were selected for this study because earlier findings indicated that the largest increases in cytokine responses were typically observed at month 2 (17).
HPV-16 L1 VLPs were expressed in baculovirus-infected Sf9 insect cells (Novavax, Rockville, MD). Production of clinical lots of recombinant HPV-16 L1 VLP vaccines was performed in accordance with GMP guidelines as previously reported (37). VLPs were provided at 1 mg/mL, stored at -80ºC and thawed immediately preceding in vitro stimulation, as previously described (16).

extract_protocol: When harvesting, cultures were centrifuged and cell-free supernatants were aliquoted and frozen at -80ºC. Total RNA extracts were performed using an RNeasy Total RNA isolation Kit (Qiagen). RLT lysis buffer was quickly added to the culture well and then to the cell pellet, in order to include both adherent and suspension cells. RNA purity and integrity were tested by microcapillary electrophoresis using the Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol:
Cryopreserved PBMCs were thawed and cultured (2.0x106 cells/mL) as previously described (17). 10x106 PBMCs were plated in each well of a 6-well plate (Costar) in RPMI-1640 supplemented with penicillin-streptomycin (100 µg/mL-100 U/mL; Gibco), L-glutamine (2mM), HEPES buffer (10 mM) and 10% heat-inactivated fetal calf serum (HyClone). Cells were cultured for 72 hours at 37ºC with: media; HPV-16 L1 VLP (2.5 µg/mL); or Sf9/baculovirus insect cell lysate (0.1 µg/mL, Novavax) all diluted in cell culture media. Media was used as a background measurement for untreated cells. The Sf9/baculovirus insect cell lysate was used as a control antigen for the L1 VLP production system.
A total of eight incubations were setup on the same day for each subject. Incubations for two subjects were setup on the same day. The order of sample preparation was randomly defined from the list of selected subjects.

tag: Donor ID

tag: Donor Grouping

value: Vaccinee

tag: Time

value: Post-Vacination

tag: Treatment

value: Media

tag: Experiment Date

tag: Hybridization Date

tag: Array Lot


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse106_Pro/Pro_Chow_Male_eWAT


title: HFD, WT, eWAT n=10 (virtual pool) vs. Mouse105_Pro/Pro_Chow_Male_eWAT


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP

value: Pre-Vacination

value: 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae

value: 0.1 ug/ml Sf9/baculovirus Lystae


title: ChIP-CHIP of Tbf1-TAP

source_name: ChIP of Tbf1-TAP expressing cells

tag: Strain

value: BWP17 containing a TAP-tag integrated at the Tbf1 locus and selected with a URA3 marker.

source_name: ChIP of Mock cells


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Pre-Vacination, Media


title: ChIP-CHIP of Cbf1-TAP

source_name: ChIP of Cbf1-TAP expressing cells

value: BWP17 containing a TAP-tag integrated at the Cbf1 locus and selected with a URA3 marker.


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt177, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP

value: Placebo


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt135, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt143, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt134, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt133, Placebo, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt120, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt127, Placebo, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt078, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt082, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt078, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt082, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


title: Rat calvaria_1

description: Samples underwent 1 round of amplification prior to labeling using the Affymetrix GeneChip® One-Cycle cDNA Synthesis Kit.

tag: Gender


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt082, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Post-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt082, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt078, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt078, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Post-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt078, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt060, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt062, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt059, Placebo, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt056, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt049, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt061, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt048, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt052, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt020, Vaccinee, Pre-Vacination, 2.5 ug/ml HPV-16 L1 VLP


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt018, Vaccinee, Pre-Vacination, Media


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt024, Vaccinee, Pre-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt082, Vaccinee, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae


title: Teratoma, human embryonic stem cells injected to the testis of SCID-NOD mouse, 30 days, sample 0227, U133A

city: Jerusalem

first: Nissim

last: Benvenisty

address: Givat-Ram

country: Israel

institute: Hebrew University

description: Gene expression data of teratoma form human embryonic stem cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data was analyzed using MAS5 probe set condensation algorithm

source_name: Teratoma from human embryonic stem cells H9 line passage 42-47 made for 30 days in the testis of SCID-NOD mouse

label_protocol: Affymetrix protocol

growth_protocol: For teratoma induction, approximately 2Ð3 x 106 undifferentiated HESCS were trypsinized, washed with phosphate-buffered saline (PBS), and suspended in 100 µl of PBS. Cells were transplanted into the testis of SCID-NOD mice.

extract_protocol: Guanidium thiocyanate


title: PBMCs_Control_paired_rep7 (HG-U133A)

first: Alan

middle: E.

last: Berger

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description: PBMC's were isolated from 7 healthy NIH blood bank donors.

hyb_protocol: cRNA was hybridized to Affymetrix Human Genome-U133A and HG-U133B microarray chips according to the manufacturer’s instructions.  GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station Model 400.

scan_protocol: GeneChips were scanned by the HP-Affymetrix GeneArray Scanner using the manufacturer's protocol.

data_processing: The data were analyzed with Microarray Suite version 5 (MAS5) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean (2% trim at bottom and at top) target intensity of each array was arbitrarily set to 500.

source_name: PBMCs, Control, Sample 1775

label_protocol: Biotin-labeled cRNA was synthesized using the BioArray High Yield RNA transcript labeling kit (Enzo Life Sciences, Inc., Farmingdale, NY) Affymetrix).

growth_protocol: as described in Wendy T. Watford, et al., Tpl2 kinase regulates T cell interferon gamma production and host resistance to Toxoplasma gondii. Journal of Experimental Medicine.

extract_protocol: Cytokine-stimulated cells were lysed in RNeasy lysis buffer (Qiagen, Valencia, CA) and total RNA was isolated with the Qiagen RNeasy Midi kit using the standard protocol. RNA was purified using Trizol (Invitrogen Life Technologies, Carlsbad, CA) and chloroform, followed by ethanol precipitation.

value: female, Race:Caucasian


title: PBMCs_Control_paired_rep6 (HG-U133A)

source_name: PBMCs, Control, Sample 1769

treatment_protocol: as described in Wendy T. Watford, et al., Tpl2 kinase regulates T cell interferon gamma production and host resistance to Toxoplasma gondii. Journal of Experimental Medicine.

value: male, Race:Black


title: Teratoma, human embryonic stem cells injected under the kidney capsule of SCID-NOD mouse, 30 days, sample 0229, U133A

source_name: Teratoma from human embryonic stem cells H9 line passage 42-47 made for 30 days under the kidney capsule of SCID-NOD mouse

growth_protocol: For teratoma induction, approximately 2Ð3 x 106 undifferentiated HESCS were trypsinized, washed with phosphate-buffered saline (PBS), and suspended in 100 µl of PBS. Cells were transplanted under the kidney capsule of male SCID-NOD mice.


title: PBMCs_IL12_paired_rep4 (HG-U133A)

source_name: PBMCs, IL12, Sample 2115

value: male, Race:Caucasian


title: PBMCs_IL12_paired_rep5 (HG-U133A)

source_name: PBMCs, IL12, Sample 635


title: PBMCs_Control_paired_rep4 (HG-U133A)

source_name: PBMCs, Control, Sample 2115


title: CD36_RHE30min_vs_0min_Rep3

city: Rockville

first: Martin

last: Spiering

address: 9600 Gudelsky Dr

department: UMBI

institute: University of Maryland

description: Biological replicate 3 of 3.

hyb_protocol: About 5 μl of Cy-labelled aaRNA (1 μg of each treatment) was incubated at 70°C for 5 min, chilled on ice for 1 min, added to 55 μl DIG EasyHyb solution (Roche Diagnostics), and immediately added to a microarray slide, placed in a hybridization chamber. The slide was covered with a HybriSlip (Schleicher & Schuell), and incubated stationary at 42°C for 16-18 h in a hybridization oven. Slides were washed in 50-ml washing solutions at room temperature. Washes were for 10 min with 1×SSC, 0.2% SDS; 10 min with 0.1×SSC, 0.2% SDS; and 5 min with 0.1×SSC. Slides were dipped in 0.1×SSC and in sterile MilliQ water, quickly dried by centrifugation at 500g, and scanned immediately.

scan_protocol: Microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments, Sunnyvale, CA, USA) at a resolution of 10 μm, using the auto PMT setting. Fluorescent intensity data were extracted using GenePix Pro 6.1 software (Axon Instruments).

data_processing: GenePix result (gpr) files were uploaded into ArrayPipe (http://www.pathogenomics.ca /arraypipe/). Data were background subtracted with the normexp algorithm and normalized by loess normalization on each subgrid. Log2-transformed ratios of experimental/control intensities were calculated for each detected feature.

organism: Candida dubliniensis

source_name: CD36 on RHE 30 min postinoculation

label_protocol:
The Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) was used for RNA
amplification and labelling, following the manufacturer’s protocol. One μg of total RNA was used for reverse transcription, and amino-allyl-labelled RNA (aaRNA) amplified by T7-based in vitro transcription. The aaRNA obtained was Cy labelled, using N-hydroxysuccinimide esters of Cy3 and Cy5 dyes (GE Healthcare, Bucks, UK) as per the manufacturer’s instructions. Labelling efficiency was routinely assessed by measuring spectrophotometric absorbance at 550 nm (Cy3), 650 nm (Cy5), and 260 nm (DNA).

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS, and adjusted to a density of 4 × 10^7 cells/mL in PBS. Reconstituted human oral epithelium (RHE) tissues (4 cm^2) were inoculated with 200 μl of Candida cell suspension in PBS, and incubated on maintenance medium (MCDB153) at 37°C, 5% CO2, and 100% humidity.

extract_protocol: Cell suspensions containing RHE membranes in RNAlater solution (Ambion) were thawed at room temperature, vortexed for 5-10 sec, and centrifuged at 3200g for 5 min. The membranes were removed with clean forceps, the tubes again centrifuged, and the supernatant removed by slow aspiration. The cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 μl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

treatment_protocol: Fungal cells were incubated on RHE for 30 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–RHE culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.

tag: Strain CD36 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 30 min at 37C, 5% CO2.

source_name: CD36 incoculum (0 min)

extract_protocol: Cell suspensions were centrifuged (6000g, 5 min) and the cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 μl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

treatment_protocol: Fungal cells were in stationary phase after growth in yeast-extract peptone broth for 14 h at 37°C with shaking (200 rpm).

tag: Strain CD36 overnight YPD culture 37C, 200 rpm.


title: PBMCs_IL12_paired_rep6 (HG-U133A)

source_name: PBMCs, IL12, Sample 1769


title: CD36_RHE30min_vs_0min_Rep1

description: Biological replicate 1 of 3.

source_name: CD36 inoculum (0 min)

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS, and adjusted to a density of 4 × 10^7 cells/mL in PBS.

extract_protocol: Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.


title: PBMCs_Control_paired_rep1 (HG-U133A)

source_name: PBMCs, Control, Sample 541

value: male, Race:Asian


title: PBMCs_IL12_paired_rep7 (HG-U133A)

source_name: PBMCs, IL12, Sample 1775


title: PBMCs_Control_paired_rep2 (HG-U133A)

source_name: PBMCs, Control, Sample 546


title: PBMCs_Control_paired_rep5 (HG-U133A)

source_name: PBMCs, Control, Sample 635


title: Teratoma, human embryonic stem cells injected to the testis of SCID-NOD mouse, 30 days, sample 0225, U133A

tag: Teratoma from human embryonic stem cells


title: Donor 3 Control

city: Brisbane

first: Katharine

last: Irvine

address: 306 Carmody Rd

country: Australia

institute: Institute for Molecular Bioscience

description: Donor 3 Control

data_processing: Raw Bead Summary data exported from BeadStudio was background corrected and normalized using the GC-RMA algorithm provided by the BeadExplorer package in R.

source_name: CSF-1 starved monocyte derived macrophage

label_protocol: Biotin labeled cRNA.   Refer to the Illumina Gene Expression System Manual

growth_protocol: CD14+ monocytes were isolated from peripheral blood mononuclear cells by positive selection, and differentiated into HMDM in vitro for 6 days in the presence of recombinant CSF-1 in IMDM with 10% FCS and 10e4 U/ml recombinant human CSF-1, experiments were

extract_protocol: Qiagen Rneasy column with on-column Dnase treament

treatment_protocol: HMDM were starved of CSF-1 overnight followed by acute CSF-1 stimulation for 6h.


title: Donor 1 CSF-1

description: Donor 1 CSF-1

hyb_protocol: Refer to the Illumina Gene Expression System Manual

source_name: CSF-1 stimulated (6h) monocyte derived macrophage


title: CD36_RHE30min_vs_0min_Rep2

description: Biological replicate 2 of 3.


title: Donor 2 CSF-1

description: Donor 2 CSF-1

scan_protocol: Refer to the Illumina Gene Expression System Manual

tag: CSF-1 stimulated (6h) monocyte derived macrophage


title: PBMCs_Control_paired_rep3 (HG-U133A)

source_name: PBMCs, Control, Sample 1193


title: PBMCs_IL12_paired_rep3 (HG-U133A)

source_name: PBMCs, IL12, Sample 1193


title: PBMCs_IL12_paired_rep2 (HG-U133A)

source_name: PBMCs, IL12, Sample 546


title: SC5314_RHE30min_vs_0min_Rep3

description: Biological replicate 3 of 3.

hyb_protocol: About 5 µl of Cy-labelled aaRNA (1 µg of each treatment) was incubated at 70°C for 5 min, chilled on ice for 1 min, added to 55 µl DIG EasyHyb solution (Roche Diagnostics), and immediately added to a microarray slide, placed in a hybridization chamber. The slide was covered with a HybriSlip (Schleicher & Schuell), and incubated stationary at 42°C for 16-18 h in a hybridization oven. Slides were washed in 50-ml washing solutions at room temperature. Washes were for 10 min with 1×SSC, 0.2% SDS; 10 min with 0.1×SSC, 0.2% SDS; and 5 min with 0.1×SSC. Slides were dipped in 0.1×SSC and in sterile MilliQ water, quickly dried by centrifugation at 500g, and scanned immediately.

scan_protocol: Microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments, Sunnyvale, CA, USA) at a resolution of 10 µm, using the auto PMT setting. Fluorescent intensity data were extracted using GenePix Pro 6.1 software (Axon Instruments).

data_processing: GenePix result (gpr) files were uploaded into ArrayPipe (http://www.pathogenomics.ca/arraypipe/). Data were background subtracted with the normexp algorithm and normalized by loess normalization on each subgrid. Log2-transformed ratios of experimental/control intensities were calculated for each detected feature.

source_name: SC5314 on RHE 30 min postinoculation

label_protocol: The Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) was used for RNA amplification and labelling, following the manufacturer’s protocol. One µg of total RNA was used for reverse transcription, and amino-allyl-labelled RNA (aaRNA) amplified by T7-based in vitro transcription. The aaRNA obtained was Cy labelled, using N-hydroxysuccinimide esters of Cy3 and Cy5 dyes (GE Healthcare, Bucks, UK) as per the manufacturer’s instructions. Labelling efficiency was routinely assessed by measuring spectrophotometric absorbance at 550 nm (Cy3), 650 nm (Cy5), and 260 nm (DNA).

extract_protocol:
Cell suspensions containing RHE membranes in RNAlater solution (Ambion) were thawed at room temperature, vortexed for 5-10 sec, and centrifuged at 3200g for 5 min. The membranes were removed with clean forceps, the tubes again centrifuged, and the supernatant removed by slow aspiration. The cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 μl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000
rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy
manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

tag: Strain SC5314 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 30 min at 37C, 5% CO2.

source_name: SC5314 inoculum (0 min)

tag: Strain SC5314 overnight YPD culture 37C, 200 rpm.


title: SC5314_RHE30min_vs_0min_Rep1

description: Biological replicate 1 of 3.

extract_protocol: Cell suspensions were centrifuged (6000g, 5 min) and the cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 µl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 µl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS, and adjusted to a density of 4 × 10^7 cells/mL in PBS. Reconstituted human oral epithelium (RHE) tissues (4 cm^2) were inoculated with 200 µl of Candida cell suspension in PBS, and incubated on maintenance medium (MCDB153) at 37°C, 5% CO2, and 100% humidity.

extract_protocol: Cell suspensions containing RHE membranes in RNAlater solution (Ambion) were thawed at room temperature, vortexed for 5-10 sec, and centrifuged at 3200g for 5 min. The membranes were removed with clean forceps, the tubes again centrifuged, and the supernatant removed by slow aspiration. The cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 µl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 µl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

treatment_protocol: Fungal cells were incubated on RHE  for 30 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–RHE culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.


title: Donor 3 CSF-1

description: Donor 3 CSF-1


title: PBMCs_IL12_paired_rep1 (HG-U133A)

source_name: PBMCs, IL12, Sample 541


title: Donor 2 Control

description: Donor 2 Control

tag: CSF-1 starved monocyte derived macrophage


title: SC5314_RHE30min_vs_0min_Rep2

description: Biological replicate 2 of 3.

tag: Strain SC5314 overnight YPD culture 37C, 200 rpm


title: Donor 1 Control

description: Donor 1 Control


title: SC5314_vs_CD36_PCF_30min_Rep1F

description: Biological replicate 1 of 2.

source_name: CD36 on PCF 30 min postinoculation

label_protocol: The Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) was used for RNA amplification and labelling, following the manufacturer’s protocol. One μg of total RNA was used for reverse transcription, and amino-allyl-labelled RNA (aaRNA) amplified by T7-based in vitro transcription. The aaRNA obtained was Cy labelled, using N-hydroxysuccinimide esters of Cy3 and Cy5 dyes (GE Healthcare, Bucks, UK) as per the manufacturer’s instructions. Labelling efficiency was routinely assessed by measuring spectrophotometric absorbance at 550 nm (Cy3), 650 nm (Cy5), and 260 nm (DNA).

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS, and adjusted to a density of 4 × 10^7 cells/mL in PBS. PCF (4 cm^2) were inoculated with 200 μl of Candida cell suspension in PBS, and incubated on maintenance medium (MCDB153) at 37°C, 5% CO2, and 100% humidity.

extract_protocol: Cell suspensions containing PCF membranes in RNAlater solution (Ambion) were thawed at room temperature, vortexed for 5-10 sec, and centrifuged at 3200g for 5 min. The membranes were removed with clean forceps, the tubes again centrifuged, and the supernatant removed by slow aspiration. The cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The cell pellet was suspended in 300 μl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

treatment_protocol: Fungal cells were incubated on PCF for 30 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–PCF culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.

tag: Strain CD36 incubated on polycarbonate filter (PCF; Skinethic, France) for 30 min at 37C, 5% CO2.

source_name: SC5314 on PCF 30 min postinoculation

tag: Strain SC5314 incubated on polycarbonate filter (PCF; Skinethic, France) for 30 min at 37C, 5% CO2.


title: SC5314_vs_CD36_PCF_30min_Rep2F

description: Biological replicate 2 of 2.


title: SC5314_vs_CD36_PCF_90min_Rep1R

description: Biological replicate 1 of 2.

source_name: SC5314 on PCF 90 min postinoculation

treatment_protocol: Fungal cells were incubated on PCF for 90 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–PCF culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.

tag: Strain SC5314 incubated on polycarbonate filter (PCF; Skinethic, France) for 90 min at 37C, 5% CO2.

source_name: CD36 on PCF 90 min postinoculation

tag: Strain CD36 incubated on polycarbonate filter (PCF; Skinethic, France) for 90 min at 37C, 5% CO2.


title: SC5314_vs_CD36_RHE_90min_Rep2R

description: Biological replicate 2 of 3.

source_name: SC5314 on RHE 90 min postinoculation

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS, and adjusted to a density of 4 × 10^7 cells/mL in PBS. RHE (4 cm^2) were inoculated with 200 μl of Candida cell suspension in PBS, and incubated on maintenance medium (MCDB153) at 37°C, 5% CO2, and 100% humidity.

treatment_protocol: Fungal cells were incubated on RHE for 90 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–RHE culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.

tag: Strain SC5314 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 90 min at 37C, 5% CO2.

source_name: CD36 on RHE 90 min postinoculation

tag: Strain CD36 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 90 min at 37C, 5% CO2.


title: SC5314_vs_CD36_PCF_90min_Rep1F

description: Biological replicate 1 of 2.


title: SC5314_vs_CD36_RHE_30min_Rep1R

description: Biological replicate 1 of 3.

source_name: CD36 on RHE 30 min postinoculation


title: SC5314_vs_CD36_PCF_90min_Rep2F

description: Biological replicate 2 of 2.


title: SC5314_vs_CD36_RHE_90min_Rep3F

description: Biological replicate 3 of 3.


title: SC5314_vs_CD36_RHE_30min_Rep2R

description: Biological replicate 2 of 3.


title: SC5314_vs_CD36_RHE_90min_Rep1R

description: Biological replicate 1 of 3.


title: SC5314_vs_CD36_PCF_30min_Rep2R

description: Biological replicate 2 of 2.


title: SC5314_vs_CD36_PCF_90min_Rep2R

description: Biological replicate 2 of 2.


title: SC5314_vs_CD36_RHE_90min_Rep2F

description: Biological replicate 2 of 3.


title: SC5314_vs_CD36_RHE_30min_Rep3F

description: Biological replicate 3 of 3.


description: Gene expression data for human PBMCs cultured 3 days with the following donor, time and treatment characteristics:  DonorPt086, Placebo, Post-Vacination, 0.1 ug/ml Sf9/baculovirus Lystae

source_name: Human PBMCs cultured for 3 days

tag: Donor ID

tag: Donor Grouping

tag: Time

tag: Treatment

tag: Experiment Date

tag: Hybridization Date

tag: Array Lot


title: SC5314_vs_CD36_RHE_30min_Rep3R

description: Biological replicate 3 of 3.

tag: Strain SC5314 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 30 min at 37C, 5% CO2.

tag: Strain CD36 incubated on reconstituted human oral epithelium (RHE; Skinethic, France) for 30 min at 37C, 5% CO2.


title: SC5314_vs_CD36_RHE_90min_Rep1F

description: Biological replicate 1 of 3.


title: SC5314_vs_CD36_RHE_30min_Rep1F

description: Biological replicate 1 of 3.


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep3R

description: Biological replicate 3 of 3.

source_name: SC5314 inoculum

growth_protocol: Candida cells from -80°C stocks were streaked on YPD agar, and grown for 20 h at 37°C or 64 h at 22°C. About 5 fungal colonies were resuspended and washed thrice in phosphate-buffered saline (PBS) and used to inoculate 10 mL filter-sterilized YPD to a density of 2 × 10^5 cells/mL. Cells were grown for 16-20 h at 22-25°C with shaking (200 rpm) and used to inoculate 10 mL filter-sterilized YPD to a density of 4 × 10^6 cells/mL. Cells were grown for 14 h at 37°C with shaking (200 rpm), harvested by centrifugation, washed thrice in PBS before final collection and storage.

extract_protocol: The cell pellet was used in RNA extraction with the RNeasy Mini Kit (Qiagen). Cell disruption was performed with a Mikro-Dismembrator S system (Sartorius Stedim Biotech, Göttingen, Germany). The pellet was suspended in 300 μl of buffer RLT (Qiagen), and the suspension transferred to a Teflon vessel with a tungsten-carbide bead (7 mm), pre-chilled with liquid N2, and shaken for 2 min at 2000 rpm in the dismembrator. The tungsten bead was quickly removed, another 400 μl RLT buffer added, and the homogenate used in RNA extraction following the RNeasy manufacturer's protocol. Total RNA was taken up in nuclease-free water and DNase I treated with DNAfree Turbo Kit (Ambion), quantified and purity assessed by 260/280 spectrophotometer measurements, and integrity checked on 1.2% TBE gels. Absence of contaminating DNA after DNase treatment was checked by PCR using RNA samples as template.

treatment_protocol: Inoculum cultures (~8 ml) were harvested by centrifugation (3200g, 5 min) and taken up in 2 ml RNAlater solution for storage at  -20°C; RNA was extracted from cell pellets obtained from 300 µl of cell suspension.

tag: SC5314 inoculum culture

source_name: CD36 inoculum

tag: CD36 inoculum culture


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep2F

description: Biological replicate 2 of 3.


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep1R

description: Biological replicate 1 of 3.


title: SC5314_vs_CD36_RHE_30min_Rep2F

description: Biological replicate 2 of 3.


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep3F

description: Biological replicate 3 of 3.


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep1F

description: Biological replicate 1 of 3.


title: SC5314_vs_CD36_RHE/PCF_inocula_Rep2R

description: Biological replicate 2 of 3.


title: CD36_RHE_90min_vs_PCF_90min_Rep2R

description: Biological replicate 2 of 2.


title: CD36_RHE_90min_vs_PCF_90min_Rep2F

description: Biological replicate 2 of 2.


title: CD36_RHE_90min_vs_PCF_90min_Rep1R

description: Biological replicate 1 of 2.

treatment_protocol: Fungal cells were incubated on PCF for 90 min. Two mL of a solution containing two parts (v/v) of RNAlater solution (Ambion) and one part of filter-sterilized 10% (w/v) saponin (Sigma-Aldrich) in PBS was added to a 4-cm^2 Candida–RHE culture. To dislodge fungal cells, membranes were rinsed 3-4 times with the RNAlater-saponin solution, and the cell suspension was transferred to a 50-ml screw-cap tube along with the cut filter membranes, and immediately frozen and stored at -20°C.


title: CD36_RHE_90min_vs_PCF_90min_Rep1F

description: Biological replicate 1 of 2.


title: SC5314_vs_CD36_RHE_90min_Rep3R

description: Biological replicate 3 of 3.


title: SC5314_RHE_90min_vs_PCF_90min_Rep1F

description: Biological replicate 1 of 2.


title: spt16 versus wild type, replicate 2

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive, N.W.

department: Biological Sciences

institute: University of Calgary

description: 30°C to 37°C for 80 minutes

hyb_protocol: Hyb procedure was carried out in Hegde et al. (2000) Biotechniques 29: 548-556

scan_protocol: Microarrays were scanned on an Axon 4000B instrument with GenePix 3.0 software

data_processing: Spatial detrending and variance stabilization normalization of raw microarray data was performed as previously described in Zhang et al. (2004) 3:21

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: wild-type strain

label_protocol: Two micrograms of poly(A)+ mRNA was reverse transcribed for cDNA synthesis and labeled with Cy3 and Cy5 dyes as described by Hughes et a., (2000) Cell 102:109-126

growth_protocol: Wild-type and mutant cells were grown in YPD medium at 30°C to mid-log phase (1-3 x 107 cells/mL), and then shifted to 37°C for 80 minutes

extract_protocol: RNA was extracted by hot phenol followed by ethanol precipitation and mRNA was purified on oligo(dT) cellulose

treatment_protocol: Cells were harvested by 2 min of centrifugation at 3,000 rpm in a tabletop centrifuge at room temperature and immediately frozen in liquid N2

tag: Genetic background S288c, parent strain BY4741

source_name: spt16-197 strain


title: SC5314_RHE_90min_vs_PCF_90min_Rep2F

description: Biological replicate 2 of 2.


title: SC5314_RHE_90min_vs_PCF_90min_Rep2R

description: Biological replicate 2 of 2.


title: SC5314_RHE_90min_vs_PCF_90min_Rep1R

description: Biological replicate 1 of 2.


title: spt6 versus wild type, replicate 3

description: 30°C to 37°C for 80 minutes

source_name: spt6-1004 strain


title: spt6 versus wild type, replicate 1

description: 30°C to 37°C for 80 minutes


title: spt6 versus wild type, replicate 2

description: 30°C to 37°C for 80 minutes


title: spt6 versus wild type, replicate 4

description: 30°C to 37°C for 80 minutes


title: spt16 versus wild type, replicate 1

description: 30°C to 37°C for 80 minutes


title: Teratoma, human embryonic stem cells injected under the kidney capsule of SCID-NOD mouse, 30 days, sample 0229, U133B

source_name: Teratoma from human embryonic stem cells H9 line passage 42-47 made for 30 days under the kidney capsule of SCID-NOD mouse


title: Teratoma, human embryonic stem cells injected to the testis of SCID-NOD mouse, 30 days, sample 0227, U133B

source_name: Teratoma from human embryonic stem cells H9 line passage 42-47 made for 30 days in the testis of SCID-NOD mouse


title: Teratoma, human embryonic stem cells injected to the testis of SCID-NOD mouse, 30 days, sample 0225, U133B

tag: Teratoma from human embryonic stem cells


title: seedlings, heat stress, 1h after treatment, replicate C

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: Replicate: C

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: Data were quantile normalized and repetitive probes were deleted (see Laubinger et al., 2008, for details)

source_name: seedling, 7d

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: 1h after transfer to liquid MS at 30°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days

tag: Arabidopsis (Col)


title: seedlings, heat stress, 12h after treatment, replicate B

description: Replicate: B

treatment_protocol: 12h after transfer to liquid MS at 30°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, heat stress, 12h after treatment, replicate A

description: Replicate: A


title: PBMCs_Control_paired_rep7 (HG-U133B)

source_name: PBMCs, Control, Sample 1775

tag: Gender


title: seedlings, cold stress, 12h after treatment, replicate A

description: Replicate: A

treatment_protocol: 12h after transfer to liquid MS at 10°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, cold stress, 1h after treatment, replicate B

description: Replicate: B

treatment_protocol: 1h after transfer to liquid MS at 10°C, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, heat stress, 1h after treatment, replicate B

description: Replicate: B


title: seedlings, ABA treatment, 12h after treatment, replicate B

description: Replicate: B

treatment_protocol: 12h after transfer to liquid MS with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, osmotic stress, 1h after treatment, replicate A

description: Replicate: A

treatment_protocol: 1h after transfer to liquid MS with 300mM Mannitol, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: PBMCs_IL12_paired_rep7 (HG-U133B)

source_name: PBMCs, IL12, Sample 1775

treatment_protocol: as described in Wendy T. Watford, et al., Tpl2 kinase regulates T cell interferon gamma production and host resistance to Toxoplasma gondii. Journal of Experimental Medicine.


title: seedlings, salt stress, 12h after treatment, replicate A

description: Replicate: A

treatment_protocol: 12h after transfer to liquid MS with 150mM NaCl, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, heat stress, 1h after treatment, replicate A

description: Replicate: A


title: seedlings, heat stress, 12h after treatment, replicate C

description: Replicate: C


title: PBMCs_IL12_paired_rep6 (HG-U133B)

source_name: PBMCs, IL12, Sample 1769


title: seedlings, osmotic stress, 1h after treatment, replicate C

description: Replicate: C


title: seedlings, cold stress, 12h after treatment, replicate B

description: Replicate: B


title: seedlings, osmotic stress, 12h after treatment, replicate B

description: Replicate: B

treatment_protocol: 12h after transfer to liquid MS with 300mM Mannitol, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, osmotic stress, 1h after treatment, replicate B

description: Replicate: B


title: seedlings, cold stress, 1h after treatment, replicate C

description: Replicate: C


title: seedlings, ABA treatment, 12h after treatment, replicate C

description: Replicate: C


title: seedlings, salt stress, 12h after treatment, replicate C

description: Replicate: C


title: seedlings, ABA treatment, 1h after treatment, replicate C

description: Replicate: C

treatment_protocol: 1h after transfer to liquid MS with 100µM ABA, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, cold stress, 12h after treatment, replicate C

description: Replicate: C


title: seedlings, osmotic stress, 12h after treatment, replicate C

description: Replicate: C


title: seedlings, ABA treatment, 1h after treatment, replicate B

description: Replicate: B


title: seedlings, osmotic stress, 12h after treatment, replicate A

description: Replicate: A


title: seedlings, salt stress, 1h after treatment, replicate B

description: Replicate: B

treatment_protocol: 1h after transfer to liquid MS with 150mM NaCl, LL, 0.5MS + 1% sucrose, 23°C, 7 days


title: seedlings, cold stress, 1h after treatment, replicate A

description: Replicate: A


title: seedlings, salt stress, 12h after treatment, replicate B

description: Replicate: B