title: Healthy03-HRV

city: Chicago

first: Peter

last: McErlean

state: Illinois

address: 240 E. Huron, McGaw M-530h

department: Allergy Immunology

institute: Northwestern University

description:
Healthy infected
H03-HRV

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

scan_protocol: BeadStudio software v3.2

data_processing: For microarray analysis, log2 ratios of the methylated and unmethylated probes (i.e. M values) were quantile normalized and then subject to linear modeling using Empirical Bayes variance correction. Tests of contrast on linear model parameters were used to evaluate pairwise comparisons of interest (Asthma x Healthy pre-HRV, A x H post-HRV, HRV changes in A, HRV changes in H, A x H HRV changes). Statistical analyses of microarray data were performed in R (v2.15.2) using packages from the Bioconductor.

label: Cy3, Cy5

source_name: Nasal Epithelial cell

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

growth_protocol: Nasal epithelial cells (NECs) were plated in 12-well dishes pre-coated with 0.2 mg/mL Type I purified collagen (Vitrogen 100, Advanced Biomatrix Corp.) in complete Bronchial Epithelial Cell Media (BEGM, Lonza) and incubated at 37°C with 5% CO2 until 80-90% confluence was achieved. Cells were then trypsinized (0.25% Trypsin EDTA), harvested, split and sub cultured onto collagen coated 24-well plates and maintained in BEGM (passage 1).

extract_protocol: Total nucleic acids were isolated from nasal cell cultures using TRI reagent (Life Technologies), phenol/chloroform extraction and ethanol precipitation.

treatment_protocol: When NEC cultures reached 80-90% confluence, cells were infected either with HRV-16 (multiplicity of infection=2) or phosphate buffered saline (PBS, Mock) in a final volume of 100µL Bronchial Epithelial Basal Medium (Lonza) for 1hr at 33°C with mild shaking. Infection media was then removed and cells washed twice with warm PBS then 500µL of fresh BEGM was added and cultures returned to 37°C for 48hrs.

value: Non-Asthmatic

tag: culture condition

value: Infected

tag: gender

tag: ethnicity

value: White/caucasian

tag: atopy

value: No

tag: asthma medication


title: cartilage_RAAK_17_Healthy

status: Public on Jul 28 2014

type: RNA

city: Leiden

first: Yolande

middle: F. M.

last: Ramos

address: Einthovenweg 20

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit

scan_protocol: Slides were scanned with the Illumina Beadscanner 500GX

data_processing: Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization or background substraction and with imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: articular cartilage

label_protocol: To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).

tag: Sex

value: Female

tag: age (yrs)

tag: tissue

value: cartilage

tag: disease state

value: Healthy


title: cartilage_RAAK_19_OA

value: Male

value: OA


title: Healthy02-HRV

type: genomic

country: USA

description:
Healthy infected
H02-HRV

molecule: genomic DNA


title: cartilage_RAAK_18_OA


title: cartilage_RAAK_18_Preserved

value: Preserved


title: cartilage_RAAK_16_Preserved


title: cartilage_RAAK_15_Preserved


title: cartilage_RAAK_15_OA


title: cartilage_RAAK_13_OA


title: Healthy03-Mock

description:
Healthy mock
H03-M

value: Mock


title: cartilage_RAAK_14_OA


title: cartilage_RAAK_16_OA


title: Healthy01-Mock

description:
Healthy mock
H01-M


title: cartilage_RAAK_13_Preserved


title: cartilage_RAAK_14_Preserved


title: cartilage_RAAK_11_Preserved


title: Healthy01-HRV

description:
Healthy infected
H01-HRV


title: cartilage_RAAK_12_Preserved


title: Healthy02-Mock

description:
Healthy mock
H02-M


title: Asthma06-HRV

description:
Asthmatic infected
A06-RV

value: Asthmatic

value: Asian/oriental


title: cartilage_RAAK_11_OA


title: cartilage_RAAK_10_Preserved


title: cartilage_RAAK_9_Preserved


title: cartilage_RAAK_7_Preserved


title: Asthma05-Mock

description:
Asthmatic mock
A05-M

value: Yes


title: cartilage_RAAK_10_OA


title: cartilage_RAAK_7_OA


title: Asthma05-HRV

description:
Asthmatic infected
A05-RV


title: cartilage_RAAK_5_OA


title: cartilage_RAAK_9_OA


title: Asthma06-Mock

description:
Asthmatic mock
A06-M


title: Asthma04-HRV

description:
Asthmatic infected
A04-RV


title: cartilage_RAAK_4_OA


title: cartilage_RAAK_8_Preserved


title: cartilage_RAAK_5_Preserved


title: cartilage_RAAK_6_OA


title: Asthma03-Mock

description:
Asthmatic mock
A03-M


title: Asthma03-HRV

description:
Asthmatic infected
A03-RV


title: cartilage_RAAK_3_OA


title: cartilage_RAAK_6_Preserved


title: Asthma04-Mock

description:
Asthmatic mock
A04-M


title: cartilage_RAAK_12_OA


title: cartilage_RAAK_4_Preserved


title: cartilage_RAAK_22_Preserved


title: Asthma02-Mock

description:
Asthmatic mock
A02-M


title: cartilage_RAAK_8_OA


title: Asthma02-HRV

description:
Asthmatic infected
A02-RV


title: Donor JJ - HIN1 - 4 HAU/ml - mAdbID:111342

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 111342

hyb_protocol: Hybrization Protocol Other: Hybridization was carried out in a water bath at 42C for 18 hours.

scan_protocol: Scan_MicronsPerPixelX: 10 Scan_MicronsPerPixelY: 10 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-NonAT_95_Feb07 (Read Only)

source_name: Pooled PBMC Reference

label_protocol:
Cy3 Sample Labeling
Other: Samples were directly labeled with the Kreatech (Durham, NC) ULS aRNA fluorescent labeling kit.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated from virus-stimulated samples and untreated controls with Qiagen RNeasy Plus microkits (Qiagen, Valencia, CA).

value: blood

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: other

value: Sample Pooling Protocol:A pool of total RNA derived from independent human PBMCs served as a common reference.

source_name: Donor JJ - H1N1 - 4 HAU/ml

label_protocol:
Cy5 Sample Labeling
Other: Samples were directly labeled with the Kreatech (Durham, NC) ULS aRNA fluorescent labeling kit.

treatment_protocol:
Treatment dose: 4 HAU/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 4 HAU/ml.

value: Plasmacytoid dendritic cells (pDCs)

tag: individual

value: Donor JJ


title: Asthma01-Mock

description:
Asthmatic mock
A01-M

value: Black/african american


title: Donor II - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111335

description: mAdb experiment ID: 111335

treatment_protocol:
Treatment dose: 1.00x10^5 TCID50/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HIV-1 BaL (Advanced Biotechnologies) at 1.00x10^5 50% tissue culture infective doses (TCID50)/ml.

value: Donor II


title: Asthma01-HRV

description:
Asthmatic infected
A01-RV

value: Infected

value: Female


title: Donor JJ - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111340

description: mAdb experiment ID: 111340


title: Donor JJ - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111341

description: mAdb experiment ID: 111341

treatment_protocol:
Treatment dose: 1.00x10^5 TCID50/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HIV-1 IIIB (Advanced Biotechnologies) at 1.00x10^5 50% tissue culture infective doses (TCID50)/ml.


title: Donor II - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111336

description: mAdb experiment ID: 111336


title: Donor II - HIN1 - 4 HAU/ml - mAdbID:111337

description: mAdb experiment ID: 111337

source_name: Donor II - H1N1 - 4 HAU/ml


title: Donor JJ - PBS Control - mAdbID:111338

description: mAdb experiment ID: 111338

source_name: Donor JJ - PBS Control

treatment_protocol:
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were treated for 6 hours with PBS (control).


title: Donor HH - HIN1 - 4 HAU/ml - mAdbID:111332

description: mAdb experiment ID: 111332

source_name: Donor HH - H1N1 - 4 HAU/ml

value: Donor HH


title: cartilage_RAAK_3_Preserved

value: cartilage


title: Donor II - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111334

description: mAdb experiment ID: 111334

treatment_protocol:
Treatment dose: 1.00x10^6 RNA copies/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HCV JFH-1 at 1.00x10^6 RNA copies/ml.


title: Donor II - PBS Control - mAdbID:111333

description: mAdb experiment ID: 111333

source_name: Donor II - PBS Control


title: Donor HH - PBS Control - mAdbID:111328

description: mAdb experiment ID: 111328

source_name: Donor HH - PBS Control


title: Donor HH - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111329

description: mAdb experiment ID: 111329


title: Donor HH - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111331

description: mAdb experiment ID: 111331


title: Donor GG - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111326

description: mAdb experiment ID: 111326

value: Donor GG


title: Donor GG - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111325

description: mAdb experiment ID: 111325


title: Donor GG - HIN1 - 4 HAU/ml - mAdbID:111327

description: mAdb experiment ID: 111327

source_name: Donor GG - H1N1 - 4 HAU/ml


title: Donor GG - PBS Control - mAdbID:111323

description: mAdb experiment ID: 111323

source_name: Donor GG - PBS Control


title: Donor FF - HIN1 - 4 HAU/ml - mAdbID:111322

description: mAdb experiment ID: 111322

source_name: Donor FF - H1N1 - 4 HAU/ml

value: Donor FF


title: Donor GG - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111324

description: mAdb experiment ID: 111324


title: Donor HH - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111330

description: mAdb experiment ID: 111330


title: Donor FF - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111319

description: mAdb experiment ID: 111319


title: Donor FF - PBS Control - mAdbID:111318

description: mAdb experiment ID: 111318

source_name: Donor FF - PBS Control


title: Donor FF - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111320

description: mAdb experiment ID: 111320


title: Donor FF - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111321

description: mAdb experiment ID: 111321


title: Donor EE - HIN1 - 4 HAU/ml - mAdbID:111317

description: mAdb experiment ID: 111317

source_name: Donor EE - H1N1 - 4 HAU/ml

value: Donor EE


title: Donor DD - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111310

description: mAdb experiment ID: 111310

value: Donor DD


title: Donor EE - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111316

description: mAdb experiment ID: 111316


title: Donor EE - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111315

description: mAdb experiment ID: 111315


title: Donor JJ - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111339

description: mAdb experiment ID: 111339


title: Donor EE - PBS Control - mAdbID:111313

description: mAdb experiment ID: 111313

source_name: Donor EE - PBS Control


title: Donor DD - PBS Control - mAdbID:111343

description: mAdb experiment ID: 111343

source_name: Donor DD - PBS Control


title: Donor DD - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111311

description: mAdb experiment ID: 111311


title: Donor EE - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111314

description: mAdb experiment ID: 111314


title: Donor CC - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111305

description: mAdb experiment ID: 111305

value: Donor CC


title: Donor CC - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111303

description: mAdb experiment ID: 111303


title: Donor BB - HIN1 - 4 HAU/ml - mAdbID:111301

description: mAdb experiment ID: 111301

source_name: Donor BB - H1N1 - 4 HAU/ml

value: Donor BB


title: Donor CC - HIN1 - 4 HAU/ml - mAdbID:111306

description: mAdb experiment ID: 111306

value: blood

source_name: Donor CC - H1N1 - 4 HAU/ml


title: Donor BB - PBS Control - mAdbID:111297

description: mAdb experiment ID: 111297

value: peripheral blood mononuclear cells (PBMCs)

source_name: Donor BB - PBS Control


title: Donor CC - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111304

description: mAdb experiment ID: 111304

source_name: Pooled PBMC Reference

value: Sample Pooling Protocol:A pool of total RNA derived from independent human PBMCs served as a common reference.


title: Donor BB - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111299

description: mAdb experiment ID: 111299

value: Plasmacytoid dendritic cells (pDCs)


title: ONFH Patient 98

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4).  Genotypes were assigned using Affymetrix Power Tools software (version 1.14.4.1) with Birdseed v2 models and a confidence score cutoff of 0.1.

label: Biotin

source_name: ONFH_whole blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted and purified from the whole blood of all the participants using a kit (QIAamp DNA Blood Midi Kit; Qiagen, Hilden, Germany). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: subject status

value: osteonecrosis of the femoral head (ONFH) patient

tag: patient id

value: patient 98

value: Chinese


title: Donor CC - PBS Control - mAdbID:111302

description: mAdb experiment ID: 111302

source_name: Donor CC - PBS Control


title: Donor BB - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111298

description: mAdb experiment ID: 111298


title: Donor DD - HIN1 - 4 HAU/ml - mAdbID:111312

description: mAdb experiment ID: 111312

source_name: Donor DD - H1N1 - 4 HAU/ml


title: ONFH Patient 97

value: patient 97


title: Donor BB - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111300

description: mAdb experiment ID: 111300


title: Donor AA - HIV-IIIB - 1.00x10^5 TCID50/ml - mAdbID:111295

description: mAdb experiment ID: 111295

value: Donor AA


title: ONFH Patient A10

value: patient A10


title: Donor AA - HIN1 - 4 HAU/ml - mAdbID:111296

description: mAdb experiment ID: 111296

source_name: Donor AA - H1N1 - 4 HAU/ml


title: ONFH Patient A9

value: patient A9


title: Donor AA - HIV-BaL - 1.00x10^5 TCID50/ml - mAdbID:111294

description: mAdb experiment ID: 111294


title: ONFH Patient 135

value: patient 135


title: HCV - Donor X - 1.00x10^6 RNA copies/ml - mAdbID:109009

description: mAdb experiment ID: 109009

source_name: HCV - Donor X - 1.00x10^6 RNA copies/ml

value: Donor X


title: HCV - Donor Z - 1.00x10^4 RNA copies/ml - mAdbID:109010

description: mAdb experiment ID: 109010

source_name: HCV - Donor Z - 1.00x10^4 RNA copies/ml

treatment_protocol:
Treatment dose: 1.00x10^4 RNA copies/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HCV JFH-1 at 1.00x10^4 RNA copies/ml.

value: Donor Z


title: HCV - Donor Z - 1.00x10^6 RNA copies/ml - mAdbID:109011

description: mAdb experiment ID: 109011

source_name: HCV - Donor Z - 1.00x10^6 RNA copies/ml


title: HCV - Donor X - Conditioned Medium Control - mAdbID:109006

description: mAdb experiment ID: 109006

treatment_protocol:
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with conditioned medium (control 2).


title: ONFH Patient 134

value: patient 134


title: Donor DD - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111309

description: mAdb experiment ID: 111309

value: Donor DD


title: ONFH Patient 138

value: patient 138


title: HCV - Donor X - 1.00x10^5 RNA copies/ml - mAdbID:109008

description: mAdb experiment ID: 109008

value: blood

source_name: HCV - Donor X - 1.00x10^5 RNA copies/ml

treatment_protocol:
Treatment dose: 1.00x10^5 RNA copies/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HCV JFH-1 at 1.00x10^5 RNA copies/ml.


title: Donor AA - PBS Control - mAdbID:111292

description: mAdb experiment ID: 111292

value: peripheral blood mononuclear cells (PBMCs)

source_name: Donor AA - PBS Control


title: ONFH Patient 132

value: patient 132


title: ONFH Patient 150

value: patient 150


title: ONFH Patient A3

value: osteonecrosis of the femoral head (ONFH) patient

value: patient A3


title: Donor AA - HCV - 1.00x10^6 RNA copies/ml - mAdbID:111293

description: mAdb experiment ID: 111293

value: Sample Pooling Protocol:A pool of total RNA derived from independent human PBMCs served as a common reference.

value: Plasmacytoid dendritic cells (pDCs)


title: HCV - Donor Z - Conditioned Medium Control - mAdbID:108888

description: mAdb experiment ID: 108888


title: HCV - Donor X - PBS Control - mAdbID:109005

description: mAdb experiment ID: 109005

source_name: HCV - Donor X - PBS Control


title: HCV - Donor Z - 1.00x10^5 RNA copies/ml - mAdbID:108890

description: mAdb experiment ID: 108890

source_name: HCV - Donor Z - 1.00x10^5 RNA copies/ml


title: HCV - Donor X - 1.00x10^4 RNA copies/ml - mAdbID:109007

description: mAdb experiment ID: 109007

source_name: HCV - Donor X - 1.00x10^4 RNA copies/ml


title: ONFH Patient A8

value: patient A8

value: Chinese


title: ONFH Patient 93

value: patient 93


title: ONFH Patient A5

value: patient A5


title: ONFH Patient 85

value: patient 85


title: frontal cortices_female infection_6 month_rep4

city: Baltimore

first: JC

last: xiao

state: MD

address: 600 N. Wolfe Street, Blalock 1109

institute: Johns Hopkins University

description: Mm CTX Female Treated #19

hyb_protocol: Biotinylated cRNAs were purified, fragmented, and subsequently hybridized to Illumina Mouse Ref-8 v2.0 Expression BeadChips.  Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy.

scan_protocol: The arrays were scanned using an Illumina BeadStation 500X Genetic Analysis Systems scanner and the image data extracted using Illumina GenomeStudio software, version 3.0.

data_processing: Data were analyzed using GeneSpring software v. 11.0.2. Raw data were imported into GeneSpring and normalized using global normalization.

organism: Mus musculus

source_name: female infection_frontal cortices

label_protocol: Total RNA was used to generate biotin labeled cRNA using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was harvested using the RNeasy reagent .  The RNA concentration and integrity was determined using Agilent BioAnalyzer.

treatment_protocol: Mice of each gender were either mock-infected with sterile DPBS or infected with 400 tachyzoites (2 parasites/μl) intraperitoneally.

tag: strain

value: BALB/c

value: female

value: Frontal Cortex

tag: infection

value: 400 tachyzoites of Toxoplasma pru strain


title: frontal cortices_female infection_6 month_rep2

description: Mm CTX Female Treated #17


title: frontal cortices_female infection_6 month_rep3

description: Mm CTX Female Treated #18


title: HCV - Donor Z - PBS Control - mAdbID:108887

description: mAdb experiment ID: 108887

value: blood

source_name: HCV - Donor Z - PBS Control

value: Donor Z


title: HCV - Donor W - 1.00x10^4 RNA copies/ml - mAdbID:108884

description: mAdb experiment ID: 108884

value: peripheral blood mononuclear cells (PBMCs)

source_name: HCV - Donor W - 1.00x10^4 RNA copies/ml

value: Donor W


title: HCV - Donor W - PBS Control - mAdbID:108882

description: mAdb experiment ID: 108882

source_name: HCV - Donor W - PBS Control


title: HCV - Donor W - 1.00x10^5 RNA copies/ml - mAdbID:108885

description: mAdb experiment ID: 108885

source_name: Pooled PBMC Reference

source_name: HCV - Donor W - 1.00x10^5 RNA copies/ml

value: p


title: frontal cortices_female infection_6 month_rep1

description: Mm CTX Female Treated #16


title: ONFH Patient 70

source_name: ONFH_whole blood

value: osteonecrosis of the femoral head (ONFH) patient

value: patient 70


title: ONFH Patient 101

value: patient 101


title: frontal cortices_female infection_6 month_rep5

description: Mm CTX Female Treated #20


title: HIV - Donor S - PBS Control - mAdbID:108716

description: mAdb experiment ID: 108716

value: Sample Pooling Protocol:A pool of total RNA derived from independent human PBMCs served as a common reference.

source_name: HIV - Donor S - PBS Control

value: Plasmacytoid dendritic cells (pDCs)

value: Donor S


title: HIV - Donor S - 1.00x10^4 TCID50/ml - mAdbID:108853

description: mAdb experiment ID: 108853

source_name: HIV - Donor S - 1.00x10^4 TCID50/ml

treatment_protocol:
Treatment dose: 1.00x10^4 TCID50/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HIV-1 IIIB (Advanced Biotechnologies) at 1.00x10^4 50% tissue culture infective doses (TCID50)/ml.


title: ONFH Patient 84

value: patient 84

value: Chinese


title: frontal cortices_female control_6 month_rep4

description: Mm CTX Female Control #14

source_name: female control_frontal cortices

value: BALB/c

value: none (control)


title: HIV - Donor S - 1.00x10^5 TCID50/ml - mAdbID:108854

description: mAdb experiment ID: 108854

source_name: HIV - Donor S - 1.00x10^5 TCID50/ml


title: HCV - Donor W - 1.00x10^6 RNA copies/ml - mAdbID:108886

description: mAdb experiment ID: 108886

source_name: HCV - Donor W - 1.00x10^6 RNA copies/ml


title: frontal cortices_female control_6 month_rep5

description: Mm CTX Female Control #15

value: female

value: Frontal Cortex


title: HIV - Donor S - 1.00x10^3 TCID50/ml - mAdbID:108718

description: mAdb experiment ID: 108718

value: blood

source_name: HIV - Donor S - 1.00x10^3 TCID50/ml

treatment_protocol:
Treatment dose: 1.00x10^3 TCID50/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HIV-1 IIIB (Advanced Biotechnologies) at 1.00x10^3 50% tissue culture infective doses (TCID50)/ml.


title: HCV - Donor W - Conditioned Medium Control - mAdbID:108883

description: mAdb experiment ID: 108883


title: HIV - Donor Q - 1.00x10^5 TCID50/ml - mAdbID:108715

description: mAdb experiment ID: 108715

source_name: HIV - Donor Q - 1.00x10^5 TCID50/ml

value: Donor Q


title: HIV - Donor S - 1.00x10^2 TCID50/ml - mAdbID:108717

description: mAdb experiment ID: 108717

value: peripheral blood mononuclear cells (PBMCs)

source_name: HIV - Donor S - 1.00x10^2 TCID50/ml

treatment_protocol:
Treatment dose: 1.00x10^2 TCID50/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with HIV-1 IIIB (Advanced Biotechnologies) at 1.00x10^2 50% tissue culture infective doses (TCID50)/ml.


title: ONFH Patient 125

value: patient 125


title: ONFH Patient 46

value: patient 46


title: ONFH Patient 13

value: osteonecrosis of the femoral head (ONFH) patient

value: patient 13


title: frontal cortices_female control_6 month_rep3

description: Mm CTX Female Control #13


title: frontal cortices_female control_6 month_rep2

description: Mm CTX Female Control #12


title: HIV - Donor Q - 1.00x10^2 TCID50/ml - mAdbID:108712

description: mAdb experiment ID: 108712

source_name: HIV - Donor Q - 1.00x10^2 TCID50/ml


title: ONFH Patient 3

value: patient 3


title: frontal cortices_male infection_6 month_rep4

description: Mm CTX Male Treated #9

source_name: male infection_frontal cortices

value: Male

value: 400 tachyzoites of Toxoplasma pru strain


title: frontal cortices_male infection_6 month_rep5

description: Mm CTX Male Treated #10


title: frontal cortices_female control_6 month_rep1

description: Mm CTX Female Control #11


title: HIV - Donor P - 1.00x10^5 TCID50/ml - mAdbID:108710

description: mAdb experiment ID: 108710

value: Sample Pooling Protocol:A pool of total RNA derived from independent human PBMCs served as a common reference.

source_name: HIV - Donor P - 1.00x10^5 TCID50/ml

value: Plasmacytoid dendritic cells (pDCs)

value: Donor P


title: HIV - Donor P - 1.00x10^3 TCID50/ml - mAdbID:108708

description: mAdb experiment ID: 108708

source_name: HIV - Donor P - 1.00x10^3 TCID50/ml


title: HIV - Donor Q - 1.00x10^4 TCID50/ml - mAdbID:108714

description: mAdb experiment ID: 108714

source_name: HIV - Donor Q - 1.00x10^4 TCID50/ml


title: HIV - Donor Q - 1.00x10^3 TCID50/ml - mAdbID:108713

description: mAdb experiment ID: 108713

source_name: HIV - Donor Q - 1.00x10^3 TCID50/ml


title: HIV - Donor P - 1.00x10^4 TCID50/ml - mAdbID:108709

description: mAdb experiment ID: 108709

source_name: Pooled PBMC Reference

source_name: HIV - Donor P - 1.00x10^4 TCID50/ml


title: HIV - Donor P - 1.00x10^2 TCID50/ml - mAdbID:108707

description: mAdb experiment ID: 108707

source_name: HIV - Donor P - 1.00x10^2 TCID50/ml


title: HIV - Donor P - PBS Control - mAdbID:108706

description: mAdb experiment ID: 108706

source_name: HIV - Donor P - PBS Control


title: HIV - Donor Q - PBS Control - mAdbID:108711

description: mAdb experiment ID: 108711

source_name: HIV - Donor Q - PBS Control


title: frontal cortices_male infection_6 month_rep2

description: Mm CTX Male Treated #7

value: BALB/c


title: frontal cortices_male infection_6 month_rep3

description: Mm CTX Male Treated #8


title: H1N1 - Donor X - 32 HAU/ml - mAdbID:107553

description: mAdb experiment ID: 107553

source_name: H1N1 - Donor X - 32 HAU/ml

treatment_protocol:
Treatment dose: 32 HAU/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 32 HAU/ml.

value: Donor X


title: H1N1 - Donor X - 256 HAU/ml - mAdbID:107554

description: mAdb experiment ID: 107554

source_name: H1N1 - Donor X - 256 HAU/ml

treatment_protocol:
Treatment dose: 256 HAU/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 256 HAU/ml.


title: H1N1 - Donor C - 32 HAU/ml - mAdbID:107172

description: mAdb experiment ID: 107172

source_name: H1N1 - Donor C - 32 HAU/ml

value: Donor C


title: H1N1 - Donor X - 2048 HAU/ml - mAdbID:107560

description: mAdb experiment ID: 107560

source_name: H1N1 - Donor X - 2048 HAU/ml

treatment_protocol:
Treatment dose: 2048 HAU/ml
Treatment time: 6 hours
In-vitro treatment: Human plasmacytoid dendritic cells (pDCs) were isolated by negative selection from PBMCs of healthy blood donors and cultured for 18 hours prior to infection. pDCs were stimulated for 6 hours with influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 2048 HAU/ml.


title: H1N1 - Donor C - 256 HAU/ml - mAdbID:107173

description: mAdb experiment ID: 107173

source_name: H1N1 - Donor C - 256 HAU/ml


title: frontal cortices_male infection_6 month_rep1

description: Mm CTX Male Treated #6

value: Frontal Cortex


title: H1N1 - Donor C - 2048 HAU/ml - mAdbID:107174

description: mAdb experiment ID: 107174

value: blood

source_name: H1N1 - Donor C - 2048 HAU/ml


title: frontal cortices_male control_6 month_rep4

description: Mm CTX Male Control #4

source_name: male control_frontal cortices

value: none (control)


title: H1N1 - Donor B - 2048 HAU/ml - mAdbID:107169

description: mAdb experiment ID: 107169

value: peripheral blood mononuclear cells (PBMCs)

source_name: H1N1 - Donor B - 2048 HAU/ml

value: Donor B


title: H1N1 - Donor C - 4 HAU/ml - mAdbID:107171

description: mAdb experiment ID: 107171

source_name: H1N1 - Donor C - 4 HAU/ml


title: H1N1 - Donor B - 32 HAU/ml - mAdbID:107167

description: mAdb experiment ID: 107167

source_name: H1N1 - Donor B - 32 HAU/ml


title: Cerevisiae_rad53_342min_rep2

status: Public on Jul 27 2014

city: Durham

first: Steven

last: Haase

state: NC

department: Biology

institute: Duke University

description: Cell cycle gene expression data from DNA replication checkpoint arrested without Rad53 activity and CDK on yeast synchronized by elutration

hyb_protocol: DNA microarray hybridization was performed according to standard Affymetrix protocols by the Duke Micorarray Core Facility.

scan_protocol: Array scanning was carried by the Duke Micorarray Core Facility using standard Affymetrix protocols.

data_processing: Data from all chips and data from Orlando et al 2008 was normalized together using the dChip implementation with default parameters from the affy package (1.32.1) within R/Bioconductor. S. pombe probes are removed before analysis.

organism: Saccharomyces cerevisiae

source_name: Cerevisiae culture, rad53, 342 min, rep2

label_protocol: Amplification and labeling using the GeneChip One-Cycle target Labeling (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted using standard yeast methods.

treatment_protocol: synchronous G1 populations collected by elutration.


title: frontal cortices_male control_6 month_rep2

description: Mm CTX Male Control #2


title: frontal cortices_male control_6 month_rep3

description: Mm CTX Male Control #3


title: Cerevisiae_rad53_360min_rep2

source_name: Cerevisiae culture, rad53, 360 min, rep2


title: frontal cortices_male control_6 month_rep1

description: Mm CTX Male Control #1


title: Cerevisiae_rad53_288min_rep2

source_name: Cerevisiae culture, rad53, 288 min, rep2


title: H1N1 - Donor B - 4 HAU/ml - mAdbID:107166

description: mAdb experiment ID: 107166

source_name: Pooled PBMC Reference

source_name: H1N1 - Donor B - 4 HAU/ml


title: H1N1 - Donor C - PBS Control - mAdbID:107170

description: mAdb experiment ID: 107170

source_name: H1N1 - Donor C - PBS Control


title: Cerevisiae_rad53_306min_rep2

source_name: Cerevisiae culture, rad53, 306 min, rep2


title: Cerevisiae_rad53_324min_rep2

source_name: Cerevisiae culture, rad53, 324 min, rep2


title: Cerevisiae_rad53_198min_rep2

source_name: Cerevisiae culture, rad53, 198 min, rep2


title: Cerevisiae_rad53_216min_rep2

source_name: Cerevisiae culture, rad53, 216 min, rep2


title: Cerevisiae_rad53_234min_rep2

source_name: Cerevisiae culture, rad53, 234 min, rep2


title: Cerevisiae_rad53_252min_rep2

source_name: Cerevisiae culture, rad53, 252 min, rep2


title: H1N1 - Donor X - 4 HAU/ml - mAdbID:107161

description: mAdb experiment ID: 107161

source_name: H1N1 - Donor X - 4 HAU/ml


title: Cerevisiae_rad53_162min_rep2

source_name: Cerevisiae culture, rad53, 162 min, rep2


title: H1N1 - Donor B - 256 HAU/ml - mAdbID:107168

description: mAdb experiment ID: 107168

source_name: H1N1 - Donor B - 256 HAU/ml


title: Cerevisiae_rad53_126min_rep2

source_name: Cerevisiae culture, rad53, 126 min, rep2


title: Cerevisiae_rad53_144min_rep2

source_name: Cerevisiae culture, rad53, 144 min, rep2


title: Cerevisiae_rad53_180min_rep2

source_name: Cerevisiae culture, rad53, 180 min, rep2


title: H1N1 - Donor B - PBS Control - mAdbID:107165

description: mAdb experiment ID: 107165

source_name: H1N1 - Donor B - PBS Control


title: Cerevisiae_rad53_270min_rep2

source_name: Cerevisiae culture, rad53, 270 min, rep2


title: H1N1 - Donor X - PBS Control - mAdbID:107160

description: mAdb experiment ID: 107160

source_name: Pooled PBMC Reference

source_name: H1N1 - Donor X - PBS Control


title: Cerevisiae_rad53_108min_rep2

source_name: Cerevisiae culture, rad53, 108 min, rep2


title: Cerevisiae_rad53_90min_rep2

source_name: Cerevisiae culture, rad53, 90 min, rep2


title: ONFH Patient 90

source_name: ONFH_whole blood

value: patient 90

value: Chinese


title: Cerevisiae_rad53_72min_rep2

source_name: Cerevisiae culture, rad53, 72 min, rep2


title: Cerevisiae_rad53_54min_rep2

source_name: Cerevisiae culture, rad53, 54 min, rep2


title: Cerevisiae_rad53_36min_rep2

source_name: Cerevisiae culture, rad53, 36 min, rep2


title: Cerevisiae_rad53_306min_rep1

source_name: Cerevisiae culture, rad53, 306 min, rep1


title: Cerevisiae_rad53_324min_rep1

source_name: Cerevisiae culture, rad53, 324 min, rep1


title: Cerevisiae_rad53_180min_rep1

source_name: Cerevisiae culture, rad53, 180 min, rep1


title: Cerevisiae_rad53_198min_rep1

source_name: Cerevisiae culture, rad53, 198 min, rep1


title: Cerevisiae_rad53_216min_rep1

source_name: Cerevisiae culture, rad53, 216 min, rep1


title: Cerevisiae_rad53_360min_rep1

source_name: Cerevisiae culture, rad53, 360 min, rep1


title: Cerevisiae_rad53_162min_rep1

source_name: Cerevisiae culture, rad53, 162 min, rep1


title: Cerevisiae_rad53_234min_rep1

source_name: Cerevisiae culture, rad53, 234 min, rep1


title: Cerevisiae_rad53_288min_rep1

source_name: Cerevisiae culture, rad53, 288 min, rep1


title: Cerevisiae_rad53_90min_rep1

source_name: Cerevisiae culture, rad53, 90 min, rep1


title: Cerevisiae_rad53_342min_rep1

source_name: Cerevisiae culture, rad53, 342 min, rep1


title: Cerevisiae_rad53_72min_rep1

source_name: Cerevisiae culture, rad53, 72 min, rep1


title: Cerevisiae_rad53_270min_rep1

source_name: Cerevisiae culture, rad53, 270 min, rep1


title: Cerevisiae_rad53_252min_rep1

source_name: Cerevisiae culture, rad53, 252 min, rep1


title: Cerevisiae_rad53_126min_rep1

source_name: Cerevisiae culture, rad53, 126 min, rep1


title: Cerevisiae_rad53_108min_rep1

source_name: Cerevisiae culture, rad53, 108 min, rep1


title: Cerevisiae_cdc8cdc20_342min_rep1

description: Cell cycle gene expression data from DNA replication checkpoint arrested in CDK on  yeast synchronized by elutration

source_name: Cerevisiae culture, cdc8cdc20, 342 min, rep1


title: Cerevisiae_cdc8cdc20_324min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 324 min, rep1


title: Cerevisiae_rad53_18min_rep1

source_name: Cerevisiae culture,rad53, 18 min, rep1


title: Cerevisiae_cdc8cdc20_360min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 360 min, rep1


title: Cerevisiae_rad53_36min_rep1

source_name: Cerevisiae culture, rad53, 36 min, rep1


title: Cerevisiae_cdc8cdc20_306min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 306 min, rep1


title: Cerevisiae_rad53_18min_rep2

source_name: Cerevisiae culture,rad53, 18 min, rep2


title: Cerevisiae_cdc8cdc20_288min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 288 min, rep1


title: Cerevisiae_rad53_144min_rep1

source_name: Cerevisiae culture, rad53, 144 min, rep1


title: Cerevisiae_rad53_54min_rep1

source_name: Cerevisiae culture, rad53, 54 min, rep1


title: Cerevisiae_cdc8cdc20_252min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 252 min, rep1


title: Cerevisiae_cdc8cdc20_234min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 234 min, rep1


title: Cerevisiae_cdc8cdc20_216min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 216 min, rep1


title: Cerevisiae_cdc8cdc20_270min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 270 min, rep1


title: Cerevisiae_cdc8cdc20_198min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 198 min, rep1


title: Cerevisiae_cdc8cdc20_180min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 180 min, rep1


title: Cerevisiae_cdc8cdc20_162min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 162 min, rep1


title: Cerevisiae_cdc8cdc20_144min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 144 min, rep1


title: Cerevisiae_cse4_315min_rep2

description: Cell cycle gene expression data from spindle assembly checkpoint arrested yeast synchronized by elutration

source_name: Cerevisiae culture, cse4, 315 min, rep2

growth_protocol: YEPGalactose/1M sorbitol at 30c


title: Cerevisiae_cse4_300min_rep2

source_name: Cerevisiae culture, cse4, 300 min, rep2


title: Cerevisiae_cdc8cdc20_54min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 54 min, rep1


title: Cerevisiae_cse4_330min_rep2

source_name: Cerevisiae culture, cse4, 330 min, rep2


title: Cerevisiae_cse4_245min_rep2

source_name: Cerevisiae culture, cse4, 345 min, rep2


title: Cerevisiae_cdc8cdc20_18min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 18 min, rep1


title: Cerevisiae_cdc8cdc20_36min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 36 min, rep1


title: Cerevisiae_cdc8cdc20_72min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 72 min, rep1


title: Cerevisiae_cse4_285min_rep2

source_name: Cerevisiae culture, cse4, 285 min, rep2


title: Cerevisiae_cdc8cdc20_90min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 90 min, rep1


title: Cerevisiae_cse4_165min_rep2

source_name: Cerevisiae culture, cse4, 165 min, rep2


title: Cerevisiae_cse4_255min_rep2

source_name: Cerevisiae culture, cse4, 255 min, rep2


title: Cerevisiae_cse4_270min_rep2

source_name: Cerevisiae culture, cse4, 270 min, rep2


title: Cerevisiae_cdc8cdc20_126min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 126 min, rep1


title: Cerevisiae_cdc8cdc20_108min_rep1

source_name: Cerevisiae culture, cdc8cdc20, 108 min, rep1


title: Cerevisiae_cse4_180min_rep2

source_name: Cerevisiae culture, cse4, 180 min, rep2


title: Cerevisiae_cse4_210min_rep2

source_name: Cerevisiae culture, cse4, 210 min, rep2


title: Cerevisiae_cse4_225min_rep2

source_name: Cerevisiae culture, cse4, 225 min, rep2


title: Cerevisiae_cse4_135min_rep2

source_name: Cerevisiae culture, cse4, 135 min, rep2


title: Cerevisiae_cse4_195min_rep2

source_name: Cerevisiae culture, cse4, 195 min, rep2


title: Cerevisiae_cse4_150min_rep2

source_name: Cerevisiae culture, cse4, 150 min, rep2


title: Cerevisiae_cse4_240min_rep2

source_name: Cerevisiae culture, cse4, 240 min, rep2


title: Cerevisiae_cse4_105min_rep2

source_name: Cerevisiae culture, cse4, 105 min, rep2


title: Cerevisiae_cse4_90min_rep2

source_name: Cerevisiae culture, cse4, 90 min, rep2


title: Cerevisiae_cse4_245min_rep1

source_name: Cerevisiae culture, cse4, 345 min, rep1


title: Cerevisiae_cse4_330min_rep1

source_name: Cerevisiae culture, cse4, 330 min, rep1


title: Cerevisiae_cse4_120min_rep2

source_name: Cerevisiae culture, cse4, 120 min, rep2


title: Cerevisiae_cse4_315min_rep1

source_name: Cerevisiae culture, cse4, 315 min, rep1


title: Cerevisiae_cse4_300min_rep1

source_name: Cerevisiae culture, cse4, 300 min, rep1


title: Cerevisiae_cse4_270min_rep1

source_name: Cerevisiae culture, cse4, 270 min, rep1


title: Cerevisiae_cse4_285min_rep1

source_name: Cerevisiae culture, cse4, 285 min, rep1


title: Cerevisiae_cse4_255min_rep1

source_name: Cerevisiae culture, cse4, 255 min, rep1


title: Cerevisiae_cse4_90min_rep1

source_name: Cerevisiae culture, cse4, 90 min, rep1


title: Cerevisiae_cdc8_260min_rep2

description: Cell cycle gene expression data from replication checkpoint arrested yeast synchronized by elutration

source_name: Cerevisiae culture, cdc8, 260 min, rep2

growth_protocol: YEPDextrose/1M sorbitol at 30c

value: BF264-15DU MATa; cdc8-ts


title: Cerevisiae_cdc8_180min_rep2

source_name: Cerevisiae culture, cdc8, 180 min, rep2


title: Cerevisiae_cdc8_140min_rep2

source_name: Cerevisiae culture, cdc8, 140 min, rep2


title: Cerevisiae_cse4_195min_rep1

source_name: Cerevisiae culture, cse4, 195 min, rep1


title: Cerevisiae_cdc8_160min_rep2

source_name: Cerevisiae culture, cdc8, 160 min, rep2


title: Cerevisiae_cse4_240min_rep1

source_name: Cerevisiae culture, cse4, 240 min, rep1


title: Cerevisiae_cse4_225min_rep1

source_name: Cerevisiae culture, cse4, 225 min, rep1


title: Cerevisiae_cdc8_240min_rep2

source_name: Cerevisiae culture, cdc8, 240 min, rep2


title: Cerevisiae_cdc8_220min_rep2

source_name: Cerevisiae culture, cdc8, 220 min, rep2


title: Cerevisiae_cdc8_110min_rep2

source_name: Cerevisiae culture, cdc8, 110 min, rep2


title: Cerevisiae_cdc8_100min_rep2

source_name: Cerevisiae culture, cdc8, 100 min, rep2


title: Cerevisiae_cse4_180min_rep1

source_name: Cerevisiae culture, cse4, 180 min, rep1


title: Cerevisiae_cse4_165min_rep1

source_name: Cerevisiae culture, cse4, 165 min, rep1


title: Cerevisiae_cdc8_90min_rep2

source_name: Cerevisiae culture, cdc8, 90 min, rep2


title: Cerevisiae_cdc8_80min_rep2

source_name: Cerevisiae culture, cdc8, 80 min, rep2


title: Cerevisiae_cdc8_120min_rep2

source_name: Cerevisiae culture, cdc8, 120 min, rep2


title: Cerevisiae_cse4_135min_rep1

source_name: Cerevisiae culture, cse4, 135 min, rep1


title: Cerevisiae_cse4_120min_rep1

source_name: Cerevisiae culture, cse4, 120 min, rep1


title: Cerevisiae_cse4_210min_rep1

source_name: Cerevisiae culture, cse4, 210 min, rep1


title: Cerevisiae_cdc8_200min_rep2

source_name: Cerevisiae culture, cdc8, 200 min, rep2


title: Cerevisiae_cse4_150min_rep1

source_name: Cerevisiae culture, cse4, 150 min, rep1


title: Cerevisiae_cse4_105min_rep1

source_name: Cerevisiae culture, cse4, 105 min, rep1


title: Cerevisiae_cdc8_70min_rep2

source_name: Cerevisiae culture, cdc8, 70 min, rep2


title: Cerevisiae_cdc8_30min_rep2

source_name: Cerevisiae culture, cdc8, 30 min, rep2


title: Cerevisiae_cdc8_260min_rep1

source_name: Cerevisiae culture, cdc8, 260 min, rep1


title: Cerevisiae_cdc8_50min_rep2

source_name: Cerevisiae culture, cdc8, 50 min, rep2


title: Cerevisiae_cdc8_220min_rep1

source_name: Cerevisiae culture, cdc8, 220 min, rep1


title: Cerevisiae_cdc8_240min_rep1

source_name: Cerevisiae culture, cdc8, 240 min, rep1


title: Cerevisiae_cdc8_60min_rep2

source_name: Cerevisiae culture, cdc8, 60 min, rep2


title: Cerevisiae_cdc8_200min_rep1

source_name: Cerevisiae culture, cdc8, 200 min, rep1


title: Cerevisiae_cdc8_180min_rep1

source_name: Cerevisiae culture, cdc8, 180 min, rep1


title: Cerevisiae_cdc8_110min_rep1

source_name: Cerevisiae culture, cdc8, 110 min, rep1


title: Cerevisiae_cdc8_160min_rep1

source_name: Cerevisiae culture, cdc8, 160 min, rep1


title: Cerevisiae_cdc8_140min_rep1

source_name: Cerevisiae culture, cdc8, 140 min, rep1


title: Cerevisiae_cdc8_80min_rep1

source_name: Cerevisiae culture, cdc8, 80 min, rep1


title: Cerevisiae_cdc8_60min_rep1

source_name: Cerevisiae culture, cdc8, 60 min, rep1


title: Cerevisiae_cdc8_70min_rep1

source_name: Cerevisiae culture, cdc8, 70 min, rep1


title: Cerevisiae_cdc8_30min_rep1

source_name: Cerevisiae culture, cdc8, 30 min, rep1


title: Cerevisiae_cdc8_90min_rep1

source_name: Cerevisiae culture, cdc8, 90 min, rep1


title: Cerevisiae_cdc8_100min_rep1

source_name: Cerevisiae culture, cdc8, 100 min, rep1


title: BY4742, 7G vs. 1G

city: Nagahama

first: Yukio

last: Mukai

state: Shiga

address: 1266 Tamura-cho

department: Department of Bioscience

country: Japan

institute: Nagahama Institute of Bio-Science and Technology

description: 7th gener

hyb_protocol: Hybridization was performed for 16 h at 37°C with rotary shake (250 rpm).

scan_protocol: The hybridized array was scanned with a 3D-Gene Scanner 3000 (Toray).

data_processing: The average intensity of the background was subtracted from the detected signals, then the sample values were determined by the global normalization method (Cy3/Cy5 ratio median=1).

source_name: 7th generation cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, #1753). CyDye labeling was performed using Cy3 Mono-Reactive Dye (GE, #PA23001) and Cy5 Mono-Reactive Dye (GE, #PA25001). Antisense RNA was synthesized and labeled with Cy3 for the 4th, 7th, and 11th generation and with Cy5 for the 1st generation.

growth_protocol: Cells of yeast strain BY4742 were cultivated in YPD medium at 30°C after labeling with biotin.

extract_protocol: Total RNAs were isolated from yeast cells using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: generation

source_name: 1st generation cells


title: BY4742, 11G vs. 1G

description: 11th gener

source_name: 11th generation cells


title: H441_siTTF-1_TGF-beta_24h

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al, Genomics 68:136-143, 2000).

source_name: siTTF-1 transfected H441 cells treated with TGF-beta for 24h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: H441 cells were maintained in RPMI 1640 (#11875; Life Technologies) supplemented with 10% FBS, 100 U/ml penicillin G, and 100 ug/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using RNeasy mini kit (QIAGEN).

treatment_protocol: Cells were transfected with siRNAs and stimulated with 3 ng/ml of TGF-beta for the indicated times.

tag: cell line

value: human lung adenocarcinoma


title: BY4742, 4G vs. 1G

description: 4th gener

source_name: 4th generation cells


title: H441_siTTF-1_0h

source_name: siTTF-1 transfected H441 cells without TGF-beta stimulation


title: Cerevisiae_cdc8_50min_rep1

source_name: Cerevisiae culture, cdc8, 50 min, rep1


title: H441_siTTF-1_TGF-beta_1p5h

source_name: siTTF-1 transfected H441 cells treated with TGF-beta for 1.5h


title: Cerevisiae_cdc8_120min_rep1

source_name: Cerevisiae culture, cdc8, 120 min, rep1


title: H441_siControl_TGF-beta_24h

source_name: siControl transfected H441 cells treated with TGF-beta for 24h


title: H441_siControl_0h

source_name: siControl transfected H441 cells without TGF-beta stimulation


title: fer-1_120h S. enterica SL1344_rep2

status: Public on Jul 26 2014

first: Brian

middle: P

last: Head

address: Box 3580 DUMC

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

hyb_protocol: Hybridization was performed in the Agilent Rotisserie Hybridization Oven (Agilent) for 17 hours.

scan_protocol: Agilent B scanner according to standard Agilent protocols (Agilent).

data_processing: Log2 transformation and quantile normalization using Partek Genomics Suite (Partek).

organism: Caenorhabditis elegans

source_name: fer-1, infected, 120h

label_protocol: 100ng of total RNA was converted to 1.65ug Cy-3-labeled, linearly amplified cRNA using the Low Input Quick Amp (LIQA) One-Color Microarray-Based Gene Expression Analysis Kit (Agilent)

growth_protocol: Synchronized L1 fer-1(b232ts) C. elegans animals grown on E. coli OP50 for 36 hours or S. enterica SL1344 for 36, 72, 96, and 120 hours. Synchronized L1 fer-1(b232ts) C. elegans animals grown on S. enterica SL1344 for 72 hours and then shifted to E. coli HT115 plus Tetracycline plates. Synchronized L1 fer-1(b232ts) C. elegans animals grown on S. enterica SL1344 for 96 hours and then shifted to E. coli HT115 plus Tetracycline plates. All animals grown at 25dC.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) and the RNeasy Plus Universal Kit (Qiagen).

treatment_protocol: For recovery, tetracycline was included in the plate at 50ug/ml.

tag: allele

tag: hours

tag: diet

value: S. enterica SL1344

tag: condition

value: infected


title: fer-1_72h S. enterica SL1344_rep2

source_name: fer-1, infected, 72h


title: fer-1_36h S. enterica SL1344_rep2

source_name: fer-1, infected, 36h


title: fer-1_120h E. coli HT115 plus Tet_rep1

source_name: fer-1, treated, 120h

value: S. enterica SL1344 then E. coli HT115 plus Tetracycline

value: recovered


title: fer-1_120h S. enterica SL1344_rep1


title: fer-1_72h S. enterica SL1344_rep1


title: fer-1_36h E. coli OP50_rep2

source_name: fer-1, uninfected, 36h

value: E. coli OP50

value: uninfected


title: fer-1_36h E. coli OP50_rep1


title: H441_siControl_TGF-beta_1p5h

source_name: siControl transfected H441 cells treated with TGF-beta for 1.5h


title: fer-1_120h E. coli HT115 plus Tet_rep2


title: fer-1_96h E. coli HT115 plus Tet_rep1

source_name: fer-1, treated, 96h


title: fer-1_36h S. enterica SL1344_rep1


title: fer-1_96h E. coli HT115 plus Tet_rep2


title: fer-1_96h S. enterica SL1344_rep1

source_name: fer-1, infected, 96h


title: VV000854_dn

city: Seoul

first: Jin Hwan

last: Park

address: Gwanak-ro 599

country: South Korea

institute: Seoul National University

hyb_protocol: 1) Activate slide in pre-Hybridization buffer for 30-60 min at 42°C.  2) Wash the slide with D.W..  3) Dry the slide with centrifugation (700 rpm) for 5 min.  4) Add the 35 µl of hybridization buffer into the dried labeled sample tube.  5) Denaturation (95°C, 5min).  6) Centrifuge for 2 min at 11,000 rpm.  7) Mix two labeled samples well.  8) Attach the MAUI lid (heating 65°C).  9) Inject the labeled samples.   10) Sealing.   11) Mix in Lid + slide MAUI Hybridization system (42°C, 16 hrs).

scan_protocol: After hybridization, the arrays were washed, dried and scanned using GenePix 4000B (Axon Instruments, Foster City, CA).

data_processing: Data from three independent experiments were normalized and then analyzed using the GenePix Pro 3.0 software (Axon Instruments).

organism: Vibrio vulnificus

source_name: Total cellular RNA from the biofilm cells of V. vulnificus

label_protocol: To synthesize aminoallyl-cDNA, reactions were performed with an Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX) according to the manufacturer’s procedures with 50 µg of total RNA. The aminoallyl-cDNA from the biofilm cells and the plaktonic cells were respectively labeled with Cy3 or Cy5 (Ambion).

growth_protocol: The V. vulnificus were grown in Center for Disease Control (CDC) reactor containing AB (autoinducer bioassay) medium.

extract_protocol: Total cellular RNAs from the planktonic cells and biofilm cells were isolated using an RNeasy® Mini Kit (Qiagen, Valencia, CA) and any residual DNA was removed using DNase I (NEB, Ipswich, MA).

value: biofilm cells

source_name: Total cellular RNA from the planktonic cells of V. vulnificus

value: planktonic cells


title: VV000854_up


title: A. tumefaciens_exoR_WT_Rep2

city: Bloomington

first: Aaron

last: Buechlein

state: IN

address: 1001 E 3rd St

department: Center for Genomics and Bioinformatics

institute: Indiana University

description:
Biological replicate 2 of 4.
adt array 10B

hyb_protocol: Hybridization reactions were performed using Agilent in situ Hybridization Kit Plus, boiled 5 min 95 C, applied to Agilent custom arrays for A. tumefaciens C58, and hybridized overnight at 65 C.  Hybridized arrays were washed with Agilent Wash Solutions 1 and 2, rinsed with acetonitrile, and incubated in Agilent Stabilization and Drying Solution immediately prior to scanning the arrays

scan_protocol: Scanned on an GenePix 4200A 01 scanner. Images were quantified using GenePix Pro (version 6.0.1.25.)

data_processing:
Limma Software (v.3.6.9) from Bioconductor (v.2.7) was used for background subtraction, Loess within arrays normalization  and Quantile between arrays normalization.
Please note that the *0311_PlusAnnot.xls file contains the final LIMMA results describing fold-change for the experiment merged with the annotation for the ID’s and the data processing details are provided in the readme.txt.

organism: Agrobacterium tumefaciens

source_name: Whole cell_lab culture, Wild type

label_protocol: Labeled cDNA with Invitrogen SuperScript Indirect Labeling Kit, cDNA was purified on QIAgen QIAQuick columns.  cDNA was labeled with AlexaFluor 542 and 655 dyes using Invitrogen SuperScript cDNA Labeling Kit

growth_protocol: Grown w/shaking in AT minimal medium w/ Succinate (0.4% w/v) as carbon source, 28 C, mid-log phase cultures

extract_protocol: 11 ml of cultures at OD600~0.6. Cells lysed with lysozyme, and RNA extracts with QIA-Gen RNEasy Kit

tag: strain background

tag: genotype/variation

value: wild type

source_name: Whole cell_lab culture, exoR

value: ExoR mutant


title: A. tumefaciens_exoR_WT_Rep1

description:
Biological replicate 1 of 4.
adt array 10A


title: VV000852_dn


title: fer-1_96h S. enterica SL1344_rep2


title: VV000853_up


title: VV000853_dn


title: A. tumefaciens_exoR_WT_Rep3

description:
Biological replicate 3 of 4.
adt array 16A


title: A. tumefaciens_exoR_WT_Rep4

description:
Biological replicate 4 of 4.
adt array 16B


title: A. tumefaciens_exoRA_exoA_Rep3

description:
Biological replicate 3 of 3.
adt array 18B

source_name: Whole cell_lab culture, exoRA

value: exoRexoA double mutant

source_name: Whole cell_lab culture, exoA

value: exoA mutant


title: Patient 6 Exosomes

status: Public on Jul 25 2014

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

country: United Kingdom

institute: University of Leicester

description: SAMPLE 14

hyb_protocol: Microtitre plates were read in a 7900HT Real Time PCR system; Human microRNA Array (A) plates (containing assays for 377 miRNA) were used (Applied Biosystems, #4398972)

data_processing: Data were not normalised because different sample types i.e. cells and exosomes were compared. Comparisons of miRNA expression levels (Ct values) on individual cell or exosomal miRNA plates showed that within each type there were very similar rank orders suggesting that within this small dataset comparisons were valid.

label: FAM/TAMRA

source_name: miRNA from exosomes

label_protocol: Taqman probes were utilised as provided by the manufacturer

growth_protocol: Patient samples were layered on Ficoll and centrifuged for 20 minutes at 2500 rpm following which the interface layer conatining mononuclear cells was removed. The cells were washed in PBS and cultured on a feeder layer of mouse fibroblasts transfected with human CD154 in the presence of IL-4 (10 ng/ml) for 24 hours

extract_protocol: Exosomes were harvested at 4 ˚C by differential centrifugation of culture supernatant. Supernatants were spun at 250 g for 5 minutes followed by 2000 g for 10 minutes to pellet cells and debris; and 10 000 g for 30 minutes to pellet debris and larger membrane bound particles. Exosomes were pelleted by centrifugation at 100 000 g for 110 minutes, washed in PBS then re-pelleted, and finally resuspended in culture media

treatment_protocol: Leukaemic cells in culture were incubated with recombinant human CD40 ligand (sCD154) (1 ug/ml) (R&D Systems, Lexington, MA, USA) and IL-4 (20 ng/ml) (R&D Systems); and anti-CD40 antibody (clone EA-5) at 1 µg/ml (Santa Cruz Biotechnology, Santa Cruz, CA, USA; sc65264) for 36 hours.

value: chronic lymphocytic leukaemia patient

tag: subject id

value: Patient 6

tag: gender

value: female

tag: vh mutation status

value: unmutated VH

value: Exosomes purified from stimulated leukaemic cells

tag: molecule subtype

value: small RNAs


title: Patient 7 Exosomes

description: SAMPLE 15

value: Patient 7

tag: cell type


title: Patient 8 Exosomes

description: SAMPLE 16

tag: subject status

value: Patient 8

value: male


title: A. tumefaciens_exoRA_exoA_Rep1

description:
Biological replicate 1 of 3.
adt array 17A


title: imDC

city: Seongnam

first: Dae-seog

last: Lim

institute: CHA medical science University

description: replicate 1

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Mouse Ref-8 expression v.2 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Array probes transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using Fold change and LPE(Local Pooled Error) test in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For a DEG set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp)

source_name: Mouse Bone-marrow

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: DCs were generated from bone marrow progenitors of 6-week-old DBA mice, as described previously[15, 20]. Briefly, bone marrow single-cell suspensions were prepared, the cells were washed, and the washed cells were cultured in RPMI 1640 supplemented with 10% FBS (Life Technologies, Grand Island, NY, USA), 20 ng/mL recombinant mouse GM-CSF (JW CreaGene, Gyeonggi, Korea), and 2 ng/mL rmIL-4 (JW CreaGene) at 37°C with 5% CO2. On Day 3, non-adherent cells were washed and re-fed using the same culture conditions. On Day 6, 50% of the culture medium was replaced with fresh medium containing the same concentrations of GM-CSF and IL-4.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: After 8 days of culture, tDCs and mature DCs (mDCs) were generated by additional incubation with 10 ng/mL rmTNF-α (BD Biosciences, Mountain View, CA, USA) and 50 µg/mL type II collagen (Sigma-Aldrich) for 4 h, and with 1 µg/mL lipopolysaccharide (Sigma-Aldrich) and 50 µg/mL type II collagen for 24 h, respectively.

value: DBA

tag: age

value: 6 week

value: immature DC


title: Patient 7 Cells

description: SAMPLE 7

source_name: miRNA from CLL cells

value: Leukaemic cells stimulated with soluble CD154/anti-CD40 antibody and IL-4


title: Patient 6 Cells

description: SAMPLE 6


title: Patient 4 Exosomes

description: SAMPLE 12

value: Patient 4

value: mutated VH


title: Patient 5 Exosomes

description: SAMPLE 13

value: Patient 5


title: Patient 2 Exosomes

description: SAMPLE 10

value: Patient 2


title: Patient 5 Cells

description: SAMPLE 5

value: chronic lymphocytic leukaemia patient


title: tDC

description: replicate 1

tag: strain

value: semi-mature or tolerogenic DC


title: Patient 4 Cells

description: SAMPLE 4


title: VV000852_up

value: biofilm cells

value: planktonic cells


title: Patient 8 Cells

description: SAMPLE 8

value: unmutated VH


title: mDC

description: replicate 1

value: Fully mature DC


title: Patient 3 Cells

description: SAMPLE 3

value: Patient 3

value: small RNAs


title: Patient 1 Cells

description: SAMPLE 1

value: Patient 1

value: male


title: Patient 2 Cells

description: SAMPLE 2

value: female


title: Patient 3 Exosomes

description: SAMPLE 11

value: Exosomes purified from stimulated leukaemic cells


title: Patient 1 Exosomes

description: SAMPLE 9


title: CCCP-1, biological rep1

city: Gary

first: Roman

last: Dziarski

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

description:
Aerobic conditions
irs_DZ_8328_BS_32311.mas5-Signal

hyb_protocol: Hybridization to the custom whole genome Affymetrix 900513 GeneChip B. subtilis Genome Array was done using Affymetrix Hybridization Oven 640 and Affymetrix GeneChip® Fluidics Station 450 and the protocols provided by Affymetrix GeneChip® Technical Manual at the Genomic and RNA Profiling Core facility, Baylor College of Medicine, Houston, TX 77030.

scan_protocol: Scanning, and data extraction was done using Affymetrix GeneChip® Scanner 3000 and the protocols provided by Affymetrix GeneChip® Technical Manual at the Genomic and RNA Profiling Core facility, Baylor College of Medicine, Houston, TX 77030.

data_processing:
The hybridization intensity data signals were analyzed, normalized, and corrected for batch effect using Affymetrix GeneChip® Command Console® Software (AGCC v.3.0). Signal average, noise average, scaling factor, % present, and % absent were calculated for each probe, from which the signal intensity of >78 was calculated as reliable expression. Using this cutoff, 3355 probes were classified as present out of total 5039 probes on the array.
Signal intensities with all probes are shown in sample data table. The 'expressed_present_probes.txt (available on Series records) contains Signal intensities with present probes. Average signal intensities from 3 experiments were used to calculate fold increases in gene expression between treated and control groups, with signal intensity of 78 used as a minimum intensity, using the formula: average intensity in treated group/average intensity in control group (the 'Avg' columns). Transformed Ln (signal intensity) values, shown in columns 'Ln', were used for direct statistical comparisons of expression signals between treated and control groups by t-test (columns 't-test' ). The probes in the expressed_present_probes.txt are arranged in descending order from the highest to the lowest ratio of gene induction in PGRP/control (column 'Ratio' in 'expressed_present_probes.txt').

organism: Bacillus subtilis

source_name: B. subtilis_CCCP_15 min

label_protocol: The cDNA was synthesized with random hexamer primers, fragmented, and labeled with terminal transferase and biotin at the Genomic and RNA Profiling Core facility, Baylor College of Medicine, Houston, TX 77030, using the protocols provided by Affymetrix GeneChip® Technical Manual.

growth_protocol: B. subtilis (OD660 nm = 0.1) was incubated with control protein or antibacterial preparations in TRIS-Schaeffer medium with 0.05% NH4Cl, 10 µM ZnSO4, 0.2% glucose, and 2% LB, at 37oC aerobically with shaking.

extract_protocol: Total RNA was obtained from B. subtilis using Ambion RiboPureTM-bacteria RNA extraction kit after disrupting the cells by shaking with Zirconia beads according to the manufacturer’s instructions.

treatment_protocol: B. subtilis was treated at 37C aerobically with shaking with BSA (control, 100 µg/ml), or PGRP (human recombinant PGLYRP4, 100 µg/ml), or gentamicin (5 µg/ml) for 30 min, or with CCCP (carbonyl cyanide 3-chlorophenylhydrazone, 50 µM) for 15 min. Each experiment was repeated 3 times.

value: strain 168

tag: tissue

value: entire bacterial cell

tag: growth phase

value: logarithmic growth

tag: treated with

value: 50 µM CCCP for 15min


title: CCCP-2, biological rep2

description:
Aerobic conditions
irs_DZ_8772_BS_34106.mas5-Signal


title: CCCP-3, biological rep3

description:
Aerobic conditions
irs_DZ_8772_BS_34110.mas5-Signal


title: Gentamicin-3, biological rep3

description:
Aerobic conditions
irs_DZ_8772_BS_34109.mas5-Signal

source_name: B. subtilis_gentamicin_30 min

value: 5 µg/ml gentamicin for 30 min


title: Gentamicin-2, biological rep2

description:
Aerobic conditions
irs_DZ_8772_BS_34105.mas5-Signal


title: PGRP-3, biological rep3

description:
Aerobic conditions
irs_DZ_8772_BS_34108.mas5-Signal

source_name: B. subtilis_PGRP_30 min

value: 100 µg/ml PGRP for 30min


title: PGRP-2, biological rep2

description:
Aerobic conditions
irs_DZ_8772_BS_34104.mas5-Signal


title: Gentamicin-1, biological rep1

description:
Aerobic conditions
irs_DZ_8328_BS_31760.mas5-Signal


title: PGRP-1, biological rep1

description:
Aerobic conditions
irs_DZ_8328_BS_31759.mas5-Signal


title: Control-2, biological rep2

description:
Aerobic conditions
irs_DZ_8772_BS_34103.mas5-Signal

source_name: B. subtilis_control_30 min

value: 100 µg/ml BSA for 30min (control)


title: Control-1, biological rep1

description:
Aerobic conditions
irs_DZ_8328_BS_31758.mas5-Signal


title: Control-3, biological rep3

description:
Aerobic conditions
irs_DZ_8772_BS_34302.mas5-Signal


title: NFF, biological rep2

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

country: Spain

institute: UNIVERSITY OF GRANADA

description: Gene expression data from WHJSC cultures

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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 normalization method

source_name: Normal forehand fascia (NFF)

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

extract_protocol: TRIZOL extraction and QIAgen RNAeasy purification, following manufacturer's recommendations

value: fascia


title: DDC, biological rep1

source_name: Dupuytren's diseased contracture cords (DDC)


title: NFF, biological rep1


title: DDC, biological rep2


title: NPF, biological rep2

source_name: Palmar fascia clinically unaffected by Dupuytren's disease contracture (NPF)


title: NPF, biological rep1


title: normal sample rp42

city: Oslo

first: Jovana

last: Klajic

address: Ullernchauseen 70

department: Genetics

country: Norway

institute: OUS/Radium Hospital

description: genomic DNA from normal breast

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

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

data_processing: Data processing was performed using BeadStudio.  All targets that contained a “zero” value in one sample for methylated and unmethylated signals were removed (n=10). Second, intra-sample normalization, which consists of colour bias and background level correction, was performed using the lumi R package. Subsequently, quantile normalization was performed for between sample normalization. After preprocessing, seven paired samples treated with doxorubicin were excluded due to low methylation levels, resulting in 26 paired tumor samples that were further analyzed. Beta values were used for further analysis.

label: Cy5 and Cy3

source_name: genomic DNA from normal breast

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using standard phenol/chloroform procedure

value: Female

tag: tissue type

value: normal breast

tag: responder (1


title: normal sample rp40

description: genomic DNA from normal breast


title: tumor sample Fumi37a

description: genomic DNA from breast tumors

source_name: tumor sample after treatment with 5-fluorouracil

value: breast tumor


title: normal sample rp36

description: genomic DNA from normal breast


title: tumor sample Fumi49b

description: genomic DNA from breast tumors

source_name: tumor sample before treatment with 5-fluorouracil


title: normal sample rp38

description: genomic DNA from normal breast


title: tumor sample Fumi29a

description: genomic DNA from breast tumors


title: tumor sample Fumi29b

description: genomic DNA from breast tumors


title: tumor sample Fumi31b

description: genomic DNA from breast tumors


title: tumor sample Fumi20b

description: genomic DNA from breast tumors


title: normal sample rp59

description: genomic DNA from normal breast


title: tumor sample Fumi31a

description: genomic DNA from breast tumors


title: normal sample rp73

description: genomic DNA from normal breast


title: tumor sample Fumi23b

description: genomic DNA from breast tumors


title: tumor sample Fumi23a

description: genomic DNA from breast tumors


title: tumor sample Fumi49a

description: genomic DNA from breast tumors


title: normal sample rp71

description: genomic DNA from normal breast


title: tumor sample Fumi43a

description: genomic DNA from breast tumors


title: normal sample rp68

description: genomic DNA from normal breast


title: tumor sample Fumi43b

description: genomic DNA from breast tumors


title: normal sample rp37

description: genomic DNA from normal breast


title: tumor sample Fumi37b

description: genomic DNA from breast tumors


title: tumor sample Fumi20a

description: genomic DNA from breast tumors


title: tumor sample Fumi16a

description: genomic DNA from breast tumors


title: tumor sample Fumi16b

description: genomic DNA from breast tumors


title: tumor sample Fumi07a

description: genomic DNA from breast tumors


title: tumor sample Fumi06a

description: genomic DNA from breast tumors


title: A. tumefaciens_exoRA_exoA_Rep2

description:
Biological replicate 2 of 3.
adt array 18A

value: exoRexoA double mutant

value: exoA mutant


title: tumor sample Fumi06b

description: genomic DNA from breast tumors


title: tumor sample Fumi02b

description: genomic DNA from breast tumors


title: tumor sample Fumi07b

description: genomic DNA from breast tumors


title: tumor sample Fumi04b

description: genomic DNA from breast tumors


title: tumor sample Fumi05b

description: genomic DNA from breast tumors


title: tumor sample Fumi05a

description: genomic DNA from breast tumors


title: tumor sample Fumi01a

description: genomic DNA from breast tumors


title: tumor sample Doxo308a

description: genomic DNA from breast tumors

source_name: tumor sample after treatment with doxorubicin


title: tumor sample Doxo305b(after)

description: genomic DNA from breast tumors


title: tumor sample Fumi04a

description: genomic DNA from breast tumors


title: tumor sample Doxo214a

description: genomic DNA from breast tumors


title: tumor sample Doxo711a

description: genomic DNA from breast tumors


title: tumor sample Fumi02a

description: genomic DNA from breast tumors


title: tumor sample Doxo305a(before)

description: genomic DNA from breast tumors

source_name: tumor sample before treatment with doxorubicin


title: tumor sample Fumi01b

description: genomic DNA from breast tumors


title: tumor sample Doxo123b

description: genomic DNA from breast tumors


title: tumor sample Doxo115b

description: genomic DNA from breast tumors


title: tumor sample Doxo711b

description: genomic DNA from breast tumors


title: tumor sample Doxo123a

description: genomic DNA from breast tumors


title: tumor sample Doxo208b(after)

description: genomic DNA from breast tumors


title: tumor sample Doxo214b

description: genomic DNA from breast tumors


title: tumor sample Doxo115a

description: genomic DNA from breast tumors


title: tumor sample Doxo114a(before)

description: genomic DNA from breast tumors


title: tumor sample Doxo208a(before)

description: genomic DNA from breast tumors


title: tumor sample Doxo118a

description: genomic DNA from breast tumors


title: tumor sample Doxo114b(after)

description: genomic DNA from breast tumors


title: tumor sample Doxo308b

description: genomic DNA from breast tumors


title: tumor sample Doxo112b

description: genomic DNA from breast tumors


title: WT_+ARS317_3hr Re-rep Fig S2

city: San Francisco

first: Stacey

middle: L

last: Hanlon

state: California

address: 600 16th Street Genentech Hall S376

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: Used for re-replication analysis on Chromosome V in Hanlon and Li, 2014

hyb_protocol: Hybridization was performed in 3X SSC + 25mM HEPES pH7.0 + 0.25% SDS at 63C for 18-48 hours.

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePixPro6.0.

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy3/Cy5 median of ratios values were normalized such that the average ratio was equal to 1. VALUE is the log2 of the normalized ratio of Cy3 to Cy5; note that to convert to usable copy number profiles raise two to the indicated value.

source_name: Post-re-replication strain

label_protocol: Amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.

extract_protocol: Clean Genomic Prep

tag: strain parent

tag: position in cell cycle prepratory to dna extraction

value: Mitosis (nocodazole arrest)

tag: induction time

value: 3 hours

tag: colony number

tag: sector color

source_name: Non-re-replicating strain arrested in mitosis


title: WT_+ARS317_No arrest_Sector sample 39

description: Used for chromosome copy number analysis in Hanlon and Li, 2014

source_name: Red sector of a red/pink sectored colony

extract_protocol: Small DNA prep

value: G0 (stationary phase)

value: Red


title: tumor sample Doxo112a

description: genomic DNA from breast tumors

tag: gender


title: WT_+ARS317_No arrest_Sector sample 38

source_name: Pink sector of a red/pink sectored colony

value: Pink


title: tumor sample Doxo101b(after)

description: genomic DNA from breast tumors


title: WT_+ARS317_No arrest_Sector sample 40


title: tumor sample Doxo118b

description: genomic DNA from breast tumors


title: WT_+ARS317_No arrest_Sector sample 37


title: tumor sample Doxo101a(before)

description: genomic DNA from breast tumors


title: tumor sample Doxo109a

description: genomic DNA from breast tumors


title: tumor sample Doxo109b

description: genomic DNA from breast tumors


title: WT_+ARS317_No arrest_Sector sample 33


title: WT_+ARS317_No arrest_Sector sample 34


title: WT_+ARS317_No arrest_Sector sample 35


title: WT_+ARS317_No arrest_Sector sample 30


title: WT_+ARS317_No arrest_Sector sample 32


title: WT_+ARS317_No arrest_Sector sample 36


title: WT_+ARS317_No arrest_Sector sample 28


title: WT_+ARS317_No arrest_Sector sample 31


title: WT_+ARS317_No arrest_Sector sample 26


title: WT_+ARS317_No arrest_Sector sample 29


title: WT_+ARS317_No arrest_Sector sample 27


title: WT_+ARS317_No arrest_Sector sample 25


title: WT_–ARS317_No arrest_Sector sample 19


title: WT_–ARS317_No arrest_Sector sample 18


title: WT_+ARS317_No arrest_Sector sample 22


title: WT_–ARS317_No arrest_Sector sample 17


title: WT_–ARS317_No arrest_Sector sample 13


title: WT_–ARS317_No arrest_Sector sample 21


title: WT_+ARS317_No arrest_Sector sample 21


title: WT_–ARS317_No arrest_Sector sample 12


title: WT_+ARS317_No arrest_Sector sample 23


title: WT_–ARS317_No arrest_Sector sample 20


title: WT_–ARS317_No arrest_Sector sample 9


title: WT_+ARS317_No arrest_Sector sample 24


title: WT_–ARS317_No arrest_Sector sample 15


title: WT_–ARS317_No arrest_Sector sample 10


title: WT_–ARS317_No arrest_Sector sample 22


title: WT_–ARS317_No arrest_Sector sample 8


title: WT_–ARS317_No arrest_Sector sample 11


title: WT_–ARS317_No arrest_Sector sample 6


title: WT_+ARS317_No arrest_Sector sample 20

source_name: White sector of a red/white sectored colony

value: White


title: WT_–ARS317_No arrest_Sector sample 5


title: WT_–ARS317_No arrest_Sector sample 16


title: WT_–ARS317_No arrest_Sector sample 3


title: WT_–ARS317_No arrest_Sector sample 4


title: WT_+ARS317_No arrest_Sector sample 19

source_name: Red sector of a red/white sectored colony


title: WT_+ARS317_No arrest_Sector sample 17


title: WT_–ARS317_No arrest_Sector sample 14


title: WT_+ARS317_No arrest_Sector sample 18


title: WT_+ARS317_No arrest_Sector sample 16


title: WT_+ARS317_No arrest_Sector sample 15


title: WT_–ARS317_No arrest_Sector sample 7


title: WT_+ARS317_No arrest_Sector sample 12


title: WT_+ARS317_No arrest_Sector sample 11


title: WT_+ARS317_No arrest_Sector sample 8


title: WT_+ARS317_No arrest_Sector sample 6


title: WT_+ARS317_No arrest_Sector sample 7


title: WT_+ARS317_No arrest_Sector sample 9


title: WT_+ARS317_No arrest_Sector sample 13


title: WT_–ARS317_No arrest_Sector sample 2


title: WT_+ARS317_No arrest_Sector sample 14


title: WT_+ARS317_No arrest_Sector sample 3


title: ∆rad52∆dnl4_+ARS317_Sector sample 20


title: WT_+ARS317_No arrest_Sector sample 10


title: WT_+ARS317_No arrest_Sector sample 2


title: WT_+ARS317_No arrest_Sector sample 5


title: ∆rad52∆dnl4_+ARS317_Sector sample 18


title: WT_+ARS317_No arrest_Sector sample 1


title: ∆rad52∆dnl4_+ARS317_Sector sample 16


title: ∆rad52∆dnl4_+ARS317_Sector sample 14


title: WT_–ARS317_No arrest_Sector sample 1


title: ∆rad52∆dnl4_+ARS317_Sector sample 17


title: ∆rad52∆dnl4_+ARS317_Sector sample 19


title: ∆rad52∆dnl4_+ARS317_Sector sample 11


title: WT_+ARS317_No arrest_Sector sample 4


title: ∆rad52∆dnl4_+ARS317_Sector sample 15


title: ∆rad52∆dnl4_+ARS317_Sector sample 7


title: ∆rad52∆dnl4_+ARS317_Sector sample 9


title: ∆rad52∆dnl4_+ARS317_Sector sample 6


title: ∆rad52∆dnl4_+ARS317_Sector sample 10


title: ∆rad52∆dnl4_+ARS317_Sector sample 8


title: ∆rad52∆dnl4_+ARS317_Sector sample 13


title: ∆rad52∆dnl4_+ARS317_Sector sample 5


title: ∆rad52∆dnl4_+ARS317_Sector sample 12


title: ∆rad52∆dnl4_+ARS317_Sector sample 1


title: ∆rad52∆dnl4_+ARS317_Sector sample 2


title: ∆rad52∆dnl4_+ARS317_Sector sample 3


title: ∆dnl4_+ARS317_Sector sample 17


title: ∆rad52∆dnl4_+ARS317_Sector sample 4


title: ∆dnl4_+ARS317_Sector sample 19


title: ∆dnl4_+ARS317_Sector sample 12


title: ∆dnl4_+ARS317_Sector sample 13


title: ∆dnl4_+ARS317_Sector sample 18


title: ∆dnl4_+ARS317_Sector sample 14


title: ∆dnl4_+ARS317_Sector sample 20


title: ∆dnl4_+ARS317_Sector sample 15


title: Pre_unstim_2

city: La Jolla

first: Gerhard

last: Wingender

state: CA

address: 9420 Athena Circle

department: Developmental Immunology

institute: La Jolla Institute for Allergy and Immunology

description: Splenocytes

hyb_protocol: Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).

data_processing: The data were analyzed withPLIER using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples 1 and 2 and samples 3 and 4 were generated using VAMPIRE software (Subramanian lab, UCSD).

source_name: sorted splenic Va14i NKT cells from 12 unstimulated C57BL/6 mice pretreated 4weeks earlier with 4ug aGalCer i.v.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen).  In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).

treatment_protocol: NKT cells were enriched by magnetic depletion of CD8a+, CD11b+, CD11c+, CD19+, CD24+, CD45RA+, CD62L+, F4/80+, Ly6C/G+ and TER119+ cells with LS columns and supplied reagents and protocols from Miltenyi, then stained with aGalCer-loaded CD1d-Streptavidin tetramers, anti-TCRb and anti-CD44 antibodies, and sorted using a FACS ARIA. 0.4 to 2 million Va14i NKT cells were collected.

value: C57Bl/6 background

value: 12 weeks

value: female

value: sorted splenic Va14i NKT cells

tag: treatment


title: ∆dnl4_+ARS317_Sector sample 16


title: Ctr_stim_2

description: Splenocytes

source_name: sorted splenic Va14i NKT cells from 12 stimulated (1ug aGalCer i.v. for 1h) C57BL/6 mice


title: ∆dnl4_+ARS317_Sector sample 11


title: Pre_stim_1

description: Splenocytes

source_name: sorted splenic Va14i NKT cells from 18 stimulated (1ug aGalCer i.v. for 1h) C57BL/6 mice pretreated 4weeks earlier with 4ug aGalCer i.v.


title: Pre_stim_2

description: Splenocytes

source_name: sorted splenic Va14i NKT cells from 19 stimulated (1ug aGalCer i.v. for 1h) C57BL/6 mice pretreated 4weeks earlier with 4ug aGalCer i.v.


title: Ctr_stim_1

description: Splenocytes

value: 12 stimulated (1ug aGalCer i.v. for 1h) C57BL/6 mice


title: ∆dnl4_+ARS317_Sector sample 10


title: ∆dnl4_+ARS317_Sector sample 9


title: SnTox3, 48 hpi, triplicate II

city: Canberra

first: Britta

last: Winterberg

state: ACT

address: Linnaeus Way, Bldg.134

department: Plant Sciences

country: Australia

institute: The Australian National University

description: Leave sample infiltrated with purified SnTox3

hyb_protocol: 12.5 mg of fragmented, biotin labelled aRNA was hybridized to each array, Arrays were hybridized for 16 h at 45°at 60rom using an Affymetrix hybridization oven. The arrays were washed according to manyfacturer's instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays wre scanned on an Affymetrix Scanner GC3000 7

data_processing: CEL files were analysed with the Partek Genomics Suite Version 6.3 using the following parameters: Adjust for GC Content; Background Correction: RMA Background Correction; Quantile Normalization: Quantile Normalization; Log Probes using Base: 2; Probeset Summarization: Mean.

organism: Triticum aestivum

source_name: SnTox3, 48 hpi, triplicate II

label_protocol: 100 ng of total Rna was amplified, labelled with biotin and fragmented following the Affymetrix GeneChip 3' IVT Kit user manual

growth_protocol: T. aestivum variety BG220 was grown as described in Solomon et al. (2006), Mol. Micro., 62:367-381

extract_protocol:
P. pastoris strain x33 was transformed with pGAP2A (empty vector) or pGAP2A containing the coding sequence of SnTox3. Resulting strains were inoculated into YPD medium and incubated for 4 days at 30°C with shaking. Culture supernatans were collected by centrifugation and frozen in liquid nitrogen before lyophyliasation. The lyophiliised material was resuspended in a minimal amount of water and dialysed against water over night before hurther purified usiding a PD-10 desalting column.
13 day-old seedlings were syringe-infiltrated with SnTox3 or mepty vector-control.
Infiltrated leave areas were harvested 6, 12, 24 amd 48 hpi, snap frozen in liquid nitrogen
Total RNA was isolated using the Sigma Spectrum Plant Total RNA kit

tag: protocol


title: Ctr_unstim_2

description: Splenocytes

source_name: sorted splenic Va14i NKT cells from 8 unstimulated C57BL/6 mice

tag: cell type

value: 8 unstimulated C57BL/6 mice


title: CC-129A

city: Madison

first: Christian

last: Capitini

state: WI

address: 1111 Highland Ave, WIMR 4137

institute: University of Wisconsin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix genechip mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.FS450-0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Affymetrix array data were analyzed with Affymetrix Power Tools software package. The Robust Multi-array Analysis (RMA) algorithm was used for gene intensity analysis.

source_name: pDCs reconstituted from STAT1+/+ bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix)

extract_protocol: pDCs isolated from bone marrow were snap frozen on dry ice. RNA was extracted using Trizol (Sigma) and cleaned up using Rneasy kit (Qiagen)

treatment_protocol: On Day +0 donor 129 bone marrow was transplanted into 12 B6 x C3H.SW recipients. On Day +14, pDCs were extracted and pooled from all recipients for analysis.

tag: recipient strain

value: B6 x C3H.SW

tag: donor strain

tag: transplanted with

value: STAT1+/+ bone marrow

value: spleen

value: Plasmacytoid dendritic cells (pDC)


title: Ctr_unstim_1

description: Splenocytes

tag: strain

tag: age


title: ∆dnl4_+ARS317_Sector sample 8


title: SnTox3, 24 hpi, triplicate III

source_name: SnTox3, 24 hpi, triplicate III


title: CC-STAT1

source_name: pDCs reconstituted from STAT1-/- bone marrow

treatment_protocol: On Day +0 donor STAT1-/- bone marrow was transplanted into 12 B6 x C3H.SW recipients. On Day +14, pDCs were extracted and pooled from all recipients for analysis.

value: STAT1-/- bone marrow

tag: tissue


title: ∆dnl4_+ARS317_Sector sample 7

value: Mitosis (nocodazole arrest)


title: SnTox3, 24 hpi, triplicate I

source_name: SnTox3, 24 hpi, triplicate I


title: SnTox3, 24 hpi, triplicate II

source_name: SnTox3, 24 hpi, triplicate II


title: ∆dnl4_+ARS317_Sector sample 4

value: 3 hours


title: ∆dnl4_+ARS317_Sector sample 3

value: G0 (stationary phase)


title: ∆dnl4_+ARS317_Sector sample 2


title: SnTox3, 12 hpi, triplicate II

source_name: SnTox3, 12 hpi, triplicate II


title: ∆rad52_+ARS317_Sector sample 19

value: Red

source_name: Non-re-replicating strain arrested in mitosis


title: ∆dnl4_+ARS317_Sector sample 6

value: Pink


title: SnTox3, 12 hpi, triplicate I

source_name: SnTox3, 12 hpi, triplicate I


title: ∆rad52_+ARS317_Sector sample 20

source_name: Pink sector of a red/pink sectored colony


title: SnTox3, 12 hpi, triplicate III

source_name: SnTox3, 12 hpi, triplicate III


title: ∆dnl4_+ARS317_Sector sample 1

source_name: Red sector of a red/pink sectored colony


title: SnTox3, 6 hpi, triplicate I

source_name: SnTox3, 6 hpi, triplicate I


title: ∆dnl4_+ARS317_Sector sample 5


title: SnTox3, 6 hpi, triplicate III

source_name: SnTox3, 6 hpi, triplicate III


title: empty vector, 48 hpi, triplicate III

description: Leave sample infiltrated with empty vector control

source_name: empty vector, 48 hpi, triplicate III

value: empty vector


title: SnTox3, 6 hpi, triplicate II

source_name: SnTox3, 6 hpi, triplicate II


title: empty vector, 48 hpi, triplicate II

source_name: empty vector, 48 hpi, triplicate II


title: ∆rad52_+ARS317_Sector sample 16


title: empty vector, 48 hpi, triplicate I

source_name: empty vector, 48 hpi, triplicate I


title: ∆rad52_+ARS317_Sector sample 17


title: ∆rad52_+ARS317_Sector sample 15


title: ∆rad52_+ARS317_Sector sample 18


title: empty vector, 24 hpi, triplicate II

source_name: empty vector, 24 hpi, triplicate II


title: ∆rad52_+ARS317_Sector sample 14


title: ∆rad52_+ARS317_Sector sample 13


title: CCCP-3, biological rep3

description:
Aerobic conditions
irs_DZ_8749_EC_34102.mas5-Signal

hyb_protocol: Hybridization to whole genome Affymetrix E. coli Genome 2.0 Array GPL3154 was done using Affymetrix Hybridization Oven 640 and Affymetrix GeneChip® Fluidics Station 450 and the protocols provided by Affymetrix GeneChip® Technical Manual at the Genomic and RNA Profiling Core facility, Baylor College of Medicine, Houston, TX 77030.

data_processing:
The hybridization intensity data signals were analyzed, normalized, and corrected for batch effect using Affymetrix GeneChip® Command Console® Software (AGCC v.3.0). Signal average, noise average, scaling factor, % present, and % absent were calculated for each probe, from which the signal intensity of >39 was calculated as reliable expression. Using this cutoff, 5531 probes were classified as present out of total 10208 probes on the array (full_expressed_data.txt).
Signal intensities with all probes are shown in Sample data table. The 'expressed_present_probes.txt (available on Series records) contains Signal intensities with present probes.  Average signal intensities from 3 experiments were used to calculate fold increases in gene expression between treated and control groups, with signal intensity of 39 used as a minimum intensity, using the formula: average intensity in treated group/average intensity in control group (the 'Avg' columns). Transformed Ln (signal intensity) values, shown in columns 'Ln', were used for direct statistical comparisons of expression signals between treated and control groups by t-test (columns 't-test' ). The probes in the expressed_present_probes.txt are arranged in descending order from the highest to the lowest ratio of gene induction in PGRP/control (column 'Ratio' in 'expressed_present_probes.txt').

organism: Escherichia coli

source_name: E. coli_CCCP_15 min

growth_protocol: E. coli (OD660 nm = 0.3) was incubated with control protein or antibacterial preparations in 5 mM TRIS (pH 7.6) with 150 mM NaCl, 10 µM ZnSO4, and 2% LB, at 37oC aerobically with shaking.

extract_protocol: RNA was obtained from each culture using Ambion RiboPureTM-bacteria RNA extraction kit according to the manufacturer’s instructions.

treatment_protocol: E. coli was treated at 37C aerobically with shaking with BSA (control, 100 µg/ml), PGRP (human recombinant PGLYRP4, 100 µg/ml), or gentamicin (5 µg/ml) for 30 min, or with CCCP (carbonyl cyanide 3-chlorophenylhydrazone, 800 µM) for 15 min. Each experiment was repeated 3 times.

value: K-12 substrain MG1655

value: entire bacterial cell

tag: growth phase

value: logarithmic growth

tag: treated with

value: 800 µM CCCP for 15min


title: empty vector, 24 hpi, triplicate I

source_name: empty vector, 24 hpi, triplicate I


title: CCCP-2, biological rep2

description:
Aerobic conditions
irs_DZ_8749_EC_34098.mas5-Signal


title: ∆rad52_+ARS317_Sector sample 12

tag: strain parent


title: ∆rad52_+ARS317_Sector sample 11

tag: position in cell cycle prepratory to dna extraction


title: ∆rad52_+ARS317_Sector sample 10

tag: induction time


title: empty vector, 12 hpi, triplicate III

source_name: empty vector, 12 hpi, triplicate III


title: empty vector, 12 hpi, triplicate I

source_name: empty vector, 12 hpi, triplicate I


title: empty vector, 24 hpi, triplicate III

source_name: empty vector, 24 hpi, triplicate III


title: Gentamicin-3, biological rep3

description:
Aerobic conditions
irs_DZ_8749_EC_34101.mas5-Signal

source_name: E. coli_gentamicin_30 min

value: 5 µg/ml gentamicin for 30 min


title: empty vector, 12 hpi, triplicate II

source_name: empty vector, 12 hpi, triplicate II


title: Gentamicin-2, biological rep2

description:
Aerobic conditions
irs_DZ_8749_EC_34097.mas5-Signal


title: Gentamicin-1, biological rep1

description:
Aerobic conditions
irs_DZ_8461_EC_32827.mas5-Signal


title: PGRP-3, biological rep3

description:
Aerobic conditions
irs_DZ_8749_EC_34100.mas5-Signal

source_name: E. coli_PGRP_30 min

value: 100 µg/ml PGRP for 30min


title: empty vector, 6 hpi, triplicate III

source_name: empty vector, 6 hpi, triplicate III


title: ∆rad52_+ARS317_Sector sample 9

source_name: Red sector of a red/pink sectored colony

tag: colony number

source_name: Non-re-replicating strain arrested in mitosis


title: CCCP-1, biological rep1

description:
Aerobic conditions
irs_DZ_8461_EC_32828.mas5-Signal


title: MCF7-normoxia-3

city: Bedford Park

first: Kanchana

middle: Veronika

last: Bandara

state: SA

address: Flinders Drive

department: Renal Department

institute: Flinders University

description:
mammary gland/breast; derived from metastatic site: pleural effusion
Mature miRNA and precursor miRNA expression data

hyb_protocol: Following biotinylation, these fragments were hybridised overnight to a Affymetrix miRNA 3.1 array

scan_protocol: The arrays were then washed, stained using a fluorescently-labelled antibody, and scanned using a high-resolution scanner (GeneChip® Scanner 3000 7G). Affymetrix® GeneChi  p® Command Console® (AGCC) Software

data_processing: Intensity data were analysed using Partek® software (Partek Inc.). Data were normalised by quantile normalisation and log 2 transformed. Differential expression was determined by ANOVA and corrected for false discovery.

source_name: MCF7-hypoxia-21%O2 48h

label_protocol: 100-300 ng of total RNA was used to synthesise double stranded cDNA using random hexamers. The cDNA was then amplified to produce antisense cRNA, which was then reverse transcribed in a second cycle of cDNA synthesis. The second cycle incorporates dUTP into the cDNA sequence, which allows it to be fragmented using uracil DNA glycosylase and apurinic/apyrimidic endonuclease I.

growth_protocol: Breast cancer cell line MCF7 was maintained in RPMI 1640 (Invitrogen) medium supplemented with 10% foetal bovine serum (FBS) (Bovigen), in polystyrene flasks. Cells were maintained at 37 ºC with 5% CO2. All experiments were conducted in triplicate with independent cell cultures.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-8000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.

treatment_protocol: A hypoxic incubator (Coy Laboratory Hypoxic workstation glove box) was used to expose cells to continuous controlled hypoxic conditions. This humidified, temperature controlled (37 ºC) chamber supplemented with 5% CO2, and N2 (as required to maintain controlled O2 levels). Cells were exposed to 0.1% O2 levels for 48 h. Normoxic controls were incubated in parallel in a humidified incubator supplemented with 5% CO2 at 37 ºC. MCF7 cells were seeded at 50 000 cells per well in 24-well plates (1.9 cm2) and grown for 24 h. Cells were transfected with 20 nM siRNA duplexes (Shanghai GenePharma Co., Ltd, China), using Lipofectamine 2000 reagent (Invitrogen) following the manufacturer’s protocol. A second transfection was carried out after 24 h following the same protocol. Cells were harvested 24 h after the second transfection and used for RNA and protein extraction.

tag: cell line

value: normoxia


title: PGRP-2, biological rep2

description:
Aerobic conditions
irs_DZ_8749_EC_34096.mas5-Signal


title: MCF7-normoxia-2


title: PGRP-1, biological rep1

description:
Aerobic conditions
irs_DZ_8461_EC_32826.mas5-Signal


title: ∆rad52_+ARS317_Sector sample 8

source_name: Pink sector of a red/pink sectored colony

tag: sector color


title: Control-3, biological rep3

description:
Aerobic conditions
irs_DZ_8749_EC_34099.mas5-Signal

source_name: E. coli_control_30 min

value: 100 µg/ml BSA for 30min (control)


title: empty vector, 6 hpi, triplicate II

source_name: empty vector, 6 hpi, triplicate II


title: Control-2, biological rep2

description:
Aerobic conditions
irs_DZ_8749_EC_34095.mas5-Signal


title: MCF7-normoxia-1

tag: treatment


title: Control-1, biological rep1

description:
Aerobic conditions
irs_DZ_8461_EC_32825.mas5-Signal


title: SnTox3, 48 hpi, triplicate III

source_name: SnTox3, 48 hpi, triplicate III

tag: protocol


title: ∆rad52_+ARS317_Sector sample 7


title: MCF7-hypoxia-1

source_name: MCF7-hypoxia-0.1%O2 48h

value: hypoxia


title: MCF7-hypoxia-2


title: MCF7-hypoxia-3


title: Pre_unstim_1

description: Splenocytes

source_name: sorted splenic Va14i NKT cells from 12 unstimulated C57BL/6 mice pretreated 4weeks earlier with 4ug aGalCer i.v.

value: C57Bl/6 background

value: 12 weeks

tag: gender

value: female

tag: cell type

value: sorted splenic Va14i NKT cells


title: empty vector, 6 hpi, triplicate I

source_name: empty vector, 6 hpi, triplicate I