title: nf_1672

description: Hybridized to customized Axiom array


title: nf_3150

status: Public on May 02 2016

type: genomic

city: St. John's

first: Guangju

last: Zhai

state: NL

address: 300 Prince Philip Drive

department: Genetics, Medicine

country: Canada

institute: Memorial University of Newfoundland

description: Hybridized to customized Axiom array

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). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: sample

tag: population

value: Newfoundland and Labrador

tag: disease status

value: Healthy

tag: inferred gender

value: Male


title: nf_1602

description: Hybridized to customized Axiom array


title: nf_3146

description: Hybridized to customized Axiom array


title: nf_1638

description: Hybridized to customized Axiom array


title: nf_2901

description: Hybridized to customized Axiom array

value: Female


title: nf_1984

description: Hybridized to customized Axiom array


title: nf_2681

description: Hybridized to customized Axiom array


title: nf_2026

description: Hybridized to customized Axiom array


title: nf_3155

description: Hybridized to customized Axiom array


title: nf_1487

description: Hybridized to customized Axiom array


title: nf_1520

description: Hybridized to customized Axiom array


title: nf_1441

description: Hybridized to customized Axiom array


title: nf_1740

description: Hybridized to customized Axiom array


title: nf_1955

description: Hybridized to customized Axiom array


title: nf_2019

description: Hybridized to customized Axiom array


title: nf_2697

description: Hybridized to customized Axiom array


title: nf_1927

description: Hybridized to customized Axiom array


title: nf_1465

description: Hybridized to customized Axiom array


title: nf_2169

description: Hybridized to customized Axiom array


title: nf_2785

description: Hybridized to customized Axiom array


title: PB_Control_1

status: Public on May 03 2016

type: RNA

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

hyb_protocol: GeneChip hybridisation oven 640 at a final concentration of 23 ng/µL using a GeneChip Hybridization, Wash and Stain Kit (both Affymetrix) in accordance with manufacturer’s instructions.

scan_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip 3000 7G+ scanner and using GeneChip Command Console Software (all Affymetrix), following manufacturer’s instructions.

data_processing: Microarray data were pre-processed using the robust multi-array average (RMA) algorithm, background correction, quartile normalisation and gene-level probe set summation19. Genes differentially expressed between the two groups were identified by Significance Analysis of Microarrays (SAM) analysis with a false discovery rate (FDR) of 0.1 using BRBArrayTools Version 4.4 software Gene networks were generated by Ingenuity Pathway Analysis (IPA) software (Qiagen, Redwood City, CA).

label: biotin

molecule: total RNA

organism: Ovis aries

source_name: Peripheral blood, control

label_protocol: WTPlus Kit (Affymetrix)

growth_protocol: Ovis arise (merino cross) singleton fetuses at 95d gestational age

extract_protocol: PaxGene RNA blood tubes with extraction according to manufacturer's instructions

treatment_protocol: chronic catheterisation followed by intraamniotic exposure of 10mg E.coli lipopolysaccharides (intervention) or sterile saline (control)

tag: treatment

value: Control


title: nf_2838

description: Hybridized to customized Axiom array


title: HLys d3 p.i. (252800518545_2_1)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.6µg labeled samples were hybridized to Agilent-028005 arrays according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution and 20 bit image depth using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies). The extracted txt files were further analyzed with GeneSpring 12.6 GX (Agilent Technologies).

organism: Mus musculus

source_name: lymph node, BCG Berlin ΔureC:: hly, d3 p.i.

label_protocol: Total RNA labeling was performed with the single color Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: All BCG strains were grown in Middlebrook 7H9 broth (Becton Dickinson) supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson), 0.2% glycerol, 0.05% Tween 80 in 1 L roller bottles (450 cm2) at 37°C and 2 rpm to mid log growth or on Middlebrook 7H11 agar (Becton Dickinson) containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson) and 0.2% glycerol.

extract_protocol: Draining lymph nodes were collected and placed immediately into RNAlater (Qiagen). Total RNA was isolated with TRIzol (Life Technologies) according to the supplier's protocol using Glycogen as carrier.

treatment_protocol: Mice were vaccinated subcutaneously at the tail base with 10e6 CFUs of BCG strains in 100 µl PBS.

tag: strain/background

tag: tissue

value: lymph node

tag: infection

value: BCG Berlin delta-ureC::hly

tag: time point (post-infection)

value: day 3


title: nf_2878

description: Hybridized to customized Axiom array


title: nf_2711

description: Hybridized to customized Axiom array


title: nf_1772

description: Hybridized to customized Axiom array


title: nf_2022

description: Hybridized to customized Axiom array


title: nf_2784

description: Hybridized to customized Axiom array


title: nf_3561

description: Hybridized to customized Axiom array


title: nf_1506

description: Hybridized to customized Axiom array


title: nf_2799

description: Hybridized to customized Axiom array


title: nf_1446

description: Hybridized to customized Axiom array


title: nf_2933

description: Hybridized to customized Axiom array


title: nf_1340

description: Hybridized to customized Axiom array


title: nf_1473

description: Hybridized to customized Axiom array


title: nf_1753

description: Hybridized to customized Axiom array


title: nf_2042

description: Hybridized to customized Axiom array


title: nf_2047

description: Hybridized to customized Axiom array


title: nf_2699

description: Hybridized to customized Axiom array


title: nf_2798

description: Hybridized to customized Axiom array


title: nf_2590

description: Hybridized to customized Axiom array


title: nf_2706

description: Hybridized to customized Axiom array


title: nf_1468

description: Hybridized to customized Axiom array


title: nf_1367

description: Hybridized to customized Axiom array


title: nf_2931

description: Hybridized to customized Axiom array


title: nf_2021

description: Hybridized to customized Axiom array


title: nf_2690

description: Hybridized to customized Axiom array


title: nf_2874

description: Hybridized to customized Axiom array


title: nf_1521

description: Hybridized to customized Axiom array


title: nf_1739

description: Hybridized to customized Axiom array


title: nf_1578

description: Hybridized to customized Axiom array


title: nf_1452

description: Hybridized to customized Axiom array


title: nf_1449

description: Hybridized to customized Axiom array


title: nf_2225

description: Hybridized to customized Axiom array


title: nf_2762

description: Hybridized to customized Axiom array


title: nf_2119

description: Hybridized to customized Axiom array


title: nf_2946

description: Hybridized to customized Axiom array


title: nf_2539

description: Hybridized to customized Axiom array


title: nf_1470

description: Hybridized to customized Axiom array


title: nf_1607

description: Hybridized to customized Axiom array


title: nf_2875

description: Hybridized to customized Axiom array


title: nf_1754

description: Hybridized to customized Axiom array


title: nf_1513

description: Hybridized to customized Axiom array


title: nf_1500

description: Hybridized to customized Axiom array


title: nf_2755

description: Hybridized to customized Axiom array


title: nf_1890

description: Hybridized to customized Axiom array


title: nf_1775

description: Hybridized to customized Axiom array


title: nf_2160

description: Hybridized to customized Axiom array


title: nf_1721

description: Hybridized to customized Axiom array


title: nf_2922

description: Hybridized to customized Axiom array


title: nf_1611

description: Hybridized to customized Axiom array


title: nf_3010

description: Hybridized to customized Axiom array


title: nf_1724

description: Hybridized to customized Axiom array


title: nf_1436

description: Hybridized to customized Axiom array


title: nf_2979

description: Hybridized to customized Axiom array


title: nf_2998

description: Hybridized to customized Axiom array


title: nf_3055

description: Hybridized to customized Axiom array


title: nf_1658

description: Hybridized to customized Axiom array


title: nf_2983

description: Hybridized to customized Axiom array


title: nf_2006

description: Hybridized to customized Axiom array


title: nf_2385

description: Hybridized to customized Axiom array


title: nf_1573

description: Hybridized to customized Axiom array


title: nf_1460

description: Hybridized to customized Axiom array


title: nf_1451

description: Hybridized to customized Axiom array


title: nf_1333

description: Hybridized to customized Axiom array


title: nf_1641

description: Hybridized to customized Axiom array


title: nf_1490

description: Hybridized to customized Axiom array


title: nf_2870

description: Hybridized to customized Axiom array


title: nf_1567

description: Hybridized to customized Axiom array


title: nf_1993

description: Hybridized to customized Axiom array


title: nf_1668

description: Hybridized to customized Axiom array


title: nf_3609

description: Hybridized to customized Axiom array


title: nf_2780

description: Hybridized to customized Axiom array


title: nf_1592

description: Hybridized to customized Axiom array


title: nf_3611

description: Hybridized to customized Axiom array


title: nf_1484

description: Hybridized to customized Axiom array


title: nf_1565

description: Hybridized to customized Axiom array


title: nf_2999

description: Hybridized to customized Axiom array


title: nf_1518

description: Hybridized to customized Axiom array


title: nf_1957

description: Hybridized to customized Axiom array


title: nf_1702

description: Hybridized to customized Axiom array


title: nf_2267

description: Hybridized to customized Axiom array


title: nf_3072

description: Hybridized to customized Axiom array


title: nf_1666

description: Hybridized to customized Axiom array


title: nf_2883

description: Hybridized to customized Axiom array


title: nf_1664

description: Hybridized to customized Axiom array


title: nf_1605

description: Hybridized to customized Axiom array


title: nf_3119

description: Hybridized to customized Axiom array


title: nf_1517

description: Hybridized to customized Axiom array


title: nf_3052

description: Hybridized to customized Axiom array


title: nf_1601

description: Hybridized to customized Axiom array


title: nf_1438

description: Hybridized to customized Axiom array


title: nf_1966

description: Hybridized to customized Axiom array


title: nf_1647

description: Hybridized to customized Axiom array


title: nf_2927

description: Hybridized to customized Axiom array


title: nf_3004

description: Hybridized to customized Axiom array


title: nf_1684

description: Hybridized to customized Axiom array


title: nf_2747

description: Hybridized to customized Axiom array


title: nf_1594

description: Hybridized to customized Axiom array


title: nf_3006

description: Hybridized to customized Axiom array


title: nf_1541

description: Hybridized to customized Axiom array


title: nf_3000

description: Hybridized to customized Axiom array


title: nf_1741

description: Hybridized to customized Axiom array


title: nf_1496

description: Hybridized to customized Axiom array


title: nf_1978

description: Hybridized to customized Axiom array


title: nf_2853

description: Hybridized to customized Axiom array


title: nf_1572

description: Hybridized to customized Axiom array


title: nf_2821

description: Hybridized to customized Axiom array


title: nf_1580

description: Hybridized to customized Axiom array


title: nf_2978

description: Hybridized to customized Axiom array


title: nf_2759

description: Hybridized to customized Axiom array


title: nf_1372

description: Hybridized to customized Axiom array


title: nf_1439

description: Hybridized to customized Axiom array


title: nf_1959

description: Hybridized to customized Axiom array


title: nf_2970

description: Hybridized to customized Axiom array


title: nf_1621

description: Hybridized to customized Axiom array


title: nf_2822

description: Hybridized to customized Axiom array


title: nf_1952

description: Hybridized to customized Axiom array


title: nf_1681

description: Hybridized to customized Axiom array


title: nf_2355

description: Hybridized to customized Axiom array


title: nf_2407

description: Hybridized to customized Axiom array


title: nf_2816

description: Hybridized to customized Axiom array


title: nf_2171

description: Hybridized to customized Axiom array


title: nf_1973

description: Hybridized to customized Axiom array


title: nf_1492

description: Hybridized to customized Axiom array


title: nf_3156

description: Hybridized to customized Axiom array


title: nf_1704

description: Hybridized to customized Axiom array


title: nf_1648

description: Hybridized to customized Axiom array


title: nf_1585

description: Hybridized to customized Axiom array


title: nf_2721

description: Hybridized to customized Axiom array


title: nf_2792

description: Hybridized to customized Axiom array


title: nf_2988

description: Hybridized to customized Axiom array


title: nf_2858

description: Hybridized to customized Axiom array


title: nf_1375

description: Hybridized to customized Axiom array


title: nf_1341

description: Hybridized to customized Axiom array


title: nf_2941

description: Hybridized to customized Axiom array


title: nf_2776

description: Hybridized to customized Axiom array


title: nf_1669

description: Hybridized to customized Axiom array


title: nf_1919

description: Hybridized to customized Axiom array


title: nf_1974

description: Hybridized to customized Axiom array


title: nf_1383

description: Hybridized to customized Axiom array


title: Atf2+/+;BrafV600E/V600E;Pten -/- melanoma tumors, replicate 4

city: San Diego

first: brian

last: james

address: 10901 North Torrey Pines Road

country: USA

institute: Sanford Burnham

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: mouse melanoma tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA from tumors was extracted using TRIzol (Ambion, CA, USA).

tag: strain

value: melanoma tumor


title: Atf2+/+;BrafV600E/V600E;Pten -/- melanoma tumors, replicate 1


title: Atf2+/+;BrafV600E/V600E;Pten -/- melanoma tumors, replicate 2


title: Atf2Δ8,9/Δ8,9;BrafV600E/V600E;Pten-/- melanoma tumors, replicate 4


title: Atf2+/+;BrafV600E/V600E;Pten -/- melanoma tumors, replicate 3


title: nf_1747

description: Hybridized to customized Axiom array


title: nf_2802

description: Hybridized to customized Axiom array


title: nf_1604

description: Hybridized to customized Axiom array


title: Atf2Δ8,9/Δ8,9;BrafV600E/V600E;Pten-/- melanoma tumors, replicate 2


title: nf_1976

description: Hybridized to customized Axiom array


title: nf_1610

description: Hybridized to customized Axiom array


title: nf_2932

description: Hybridized to customized Axiom array


title: nf_2769

description: Hybridized to customized Axiom array


title: nf_1935

description: Hybridized to customized Axiom array


title: nf_2876

description: Hybridized to customized Axiom array


title: nf_2928

description: Hybridized to customized Axiom array


title: Atf2Δ8,9/Δ8,9;BrafV600E/V600E;Pten-/- melanoma tumors, replicate 3


title: nf_2742

description: Hybridized to customized Axiom array


title: nf_2925

description: Hybridized to customized Axiom array


title: nf_1926

description: Hybridized to customized Axiom array


title: Bone marrow-derived macrophages isolated from agar culture at 48hr, replicate 2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. HT_MG-430_PM GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: HT_MG-430_PM plate arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1.

label_protocol: Biotin-labeled cRNA was prepared from 100 ng of total RNA according to the standard Affymetrix 3' IVT Express protocol (GeneChip 3' IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

growth_protocol: The TT9423 neuroblastoma cell line was grown as a monolayer in vitro in complete RPMI (Corning) containing 10% fetal bovine serum (Thermo Scientific), 1% penicillin/streptomycin (Invitrogen), and 0.1% gentamycin (Invitrogen). TT9423 cells were collected from the tissue culture plate using trypsin-EDTA (Invitrogen), and 1x10^5 cells were transferred to tissue culture plates coated with 0.5% agar noble in RPMI for overnight sphere development. Subsequent to sphere formation, BMDMs were added to the same cell number as TT9423 cells originating the sphere cultures. Sphere and BMDMs (ivTAMs) were co-cultured for 24 hours. Individual spheres were collected and digested with Tumor digestion media (TDM): 5 mg DNase I (Worthington), 12.5 mg collagenase P (Roche), 12.5 mg collagenase/dispase (Roche), 100 μl B27 (Invitrogen), 50 μl N2 (Invitrogen), made to 5 ml with Neural Basal medium (Invitrogen), followed by 0.22 μm filter sterilization. DNase solution (DS): 7.5 mg DNase I (Worthington), 120 μl 45% glucose solution (Sigma-Aldrich), up to 15 ml with 1x Basal Medium Eagle media (Invitrogen), followed by 0.22 μm filter sterilization. Percoll solution: Percoll (Sigma-Aldrich) was adjusted to a final pH of 7.4 followed by 0.22 μm filter sterilization. After which, macrophages were isolated by CD11b MACs columns and lysed in Trizol.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol.

tag: cell type

value: Bone marrow-derived macrophages outside neuroblastoma neurospheres

tag: timepoint


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 48hr, replicate 2

value: CD11b+ macrophages inside neuroblastoma neurospheres


title: nf_1454

description: Hybridized to customized Axiom array


title: Bone marrow-derived macrophages isolated from agar culture at 24hr, replicate 2


title: nf_1920

description: Hybridized to customized Axiom array


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 48hr, replicate 3


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 48hr, replicate 1


title: Bone marrow-derived macrophages isolated from agar culture at 48hr, replicate 1


title: nf_2849

description: Hybridized to customized Axiom array


title: nf_1503

description: Hybridized to customized Axiom array


title: nf_1475

description: Hybridized to customized Axiom array


title: nf_2257

description: Hybridized to customized Axiom array


title: nf_1856

description: Hybridized to customized Axiom array


title: nf_1950

description: Hybridized to customized Axiom array


title: nf_2894

description: Hybridized to customized Axiom array


title: Bone marrow-derived macrophages isolated from agar culture at 48hr, replicate 3


title: nf_2827

description: Hybridized to customized Axiom array


title: Atf2Δ8,9/Δ8,9;BrafV600E/V600E;Pten-/- melanoma tumors, replicate 1


title: nf_2937

description: Hybridized to customized Axiom array


title: Bone marrow-derived macrophages isolated from agar culture at 24hr, replicate 1


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 24hr, replicate 1


title: nf_2907

description: Hybridized to customized Axiom array


title: nf_2926

description: Hybridized to customized Axiom array


title: Bone marrow-derived macrophages isolated from agar culture at 24hr, replicate 3


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 24hr, replicate 2


title: nf_2942

description: Hybridized to customized Axiom array


title: CD11b+ macrophages isolated from neuroblastoma neurospheres at 24hr, replicate 3


title: nf_2028

description: Hybridized to customized Axiom array


title: nf_2824

description: Hybridized to customized Axiom array


title: nf_1948

description: Hybridized to customized Axiom array


title: nf_2753

description: Hybridized to customized Axiom array


title: nf_1450

description: Hybridized to customized Axiom array


title: ICAR_Non CL_Repeat breeder_4

city: Tsukuba

first: KENGO

last: HAYASHI

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologie

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Intercarunclar endometrium_Contralateral uterine horn_Repeat breeder

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the endometrium using ISOGEN (NipponGene, Tokyo, Japan)  according to the manufacturer's instructions.

tag: breed

value: non-lactating Japanease Black cow

tag: sample group

value: Repeat breeding cows

value: Endometrium

tag: tissue subtype

value: intercarunclar areas in endometrium of contralateral uterine horn

tag: phase

value: Day 15 of estrous cycle

tag: study

value: In vivo


title: nf_2885

description: Hybridized to customized Axiom array

tag: sample

value: Newfoundland and Labrador


title: ICAR_Non CL_Repeat breeder_1


title: ICAR_Non CL_Repeat breeder_2


title: ICAR_Non CL_Normal_4

source_name: Intercarunclar endometrium_Contralateral uterine horn_Normal

value: normally fertile cows


title: ICAR_Non CL_Repeat breeder_3


title: ICAR_Non CL_Normal_3


title: nf_1742

description: Hybridized to customized Axiom array

tag: population

value: Healthy


title: ICAR_Non CL_Normal_2


title: NHF_FB

city: Guangzhou

first: Wenyin

last: HE

state: Guangdong

address: No.63, Duobao road

country: China

institute: The third affiliated hospital of Guangzhou medical university

description:
SAMPLE 12
normal female somatic cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software v3.2

label: Cy3 and Cy5

source_name: fibroblast cell

label_protocol: Labelling with Cy3 and Cy5 according to Standard Illumina Protocol

growth_protocol: cultured in ES medium or mTESR medium in vitro

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: natural growth without treatments

tag: gender

value: Female

tag: cell line

value: somatic cell


title: nf_2760

description: Hybridized to customized Axiom array

tag: disease status

tag: inferred gender

value: Male


title: nf_1985

description: Hybridized to customized Axiom array


title: CAR_Non CL_Repeat breeder_4

source_name: Carunclar endometrium_Contralateral uterine horn_Repeat breeder

tag: tissue

value: carunclar areas in endometrium of contralateral uterine horn


title: CAR_Non CL_Repeat breeder_3


title: Zhao_iPS

description:
SAMPLE 6
normal female iPS cell

source_name: iPSC

value: PBMC-derived iPSC


title: A441_iPS

description:
SAMPLE 10
normal female iPS cell

value: amniotic cell-derived iPSC


title: ate1 ate2 +/- Pst AvrRpm1; 4 hpi; SET 1

city: Dublin

first: Frank

last: Wellmer

address: College Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 1

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1) was used for background subtraction and LOWESS normalization

organism: Arabidopsis thaliana

source_name: (+) Pst AvrRpm1

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: 11-day-old whole seedlings of the at1 ate2 double mutant and of the wild type Col-0 were grown at 22°C under long-day conditions (16 h light/8 h darkness) on 0.5xMS agar medium. P. syringae inoculation assays were performed on plants grown in Jiffy pots with a 9-hour light period and a light intensity of 190 µmol.m-2.s-1.

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: Pseudomonas syringae pv tomato strain AvrRpm1 was grown on KB medium at room temperature. Pseudomonas syringae pv. tomato was inoculated on 4-week-old plants following a high-humidity treatment 12 h before inoculation. A bacterial suspension at 1x105 cfu/mL for Pst DC3000 strain and 5x105 cfu/mL for Pst AvrRpm1 in 10 mM MgCl2 was infiltrated using a blunt syringe into the abaxial side of 4 leaves per plant. For determination of in planta bacterial growth, leaf samples were harvested at 3 dpi and ground in sterile water before plating on selective medium.

tag: developmental stage

value: 4-week old plants

tag: genotype

value: ate1 ate2

source_name: (-) Pst AvrRpm1


title: ate1 ate2 +/- Pst AvrRpm1; 4 hpi; SET 2

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 2


title: YJH-PBMC

description:
SAMPLE 2
normal female somatic cell

source_name: PBMC


title: ate1 ate2 +/- Pst AvrRpm1; 2 hpi; SET 3

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 3


title: ate1 ate2 +/- Pst AvrRpm1; 4 hpi; SET 3

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 3


title: N_iPS

description:
SAMPLE 5
normal female iPS cell

value: adult fibroblast cell-derived iPSC


title: A444_iPS

description:
SAMPLE 4
normal female iPS cell


title: nf_1574

description: Hybridized to customized Axiom array


title: A441_AF

description:
SAMPLE 9
normal female somatic cell

source_name: amnio fluid cell


title: PYH-PBMC

description:
SAMPLE 1
normal female somatic cell


title: nf_1755

description: Hybridized to customized Axiom array


title: XYX_iPS

description:
SAMPLE 7
normal male iPS cell


title: ate1 ate2 +/- Pst AvrRpm1; 4 hpi; SET 4

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 4


title: ate1 ate2 +/- Pst AvrRpm1; 2 hpi; SET 2

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 2


title: CAR_Non CL_Repeat breeder_2

value: non-lactating Japanease Black cow

value: Repeat breeding cows


title: ate1 ate2 +/- Pst AvrRpm1; 2 hpi; SET 1

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 1


title: nf_1946

description: Hybridized to customized Axiom array


title: Chen_iPS

description:
SAMPLE 3
normal female iPS cell


title: nf_1440

description: Hybridized to customized Axiom array


title: NHF_iPS

description:
SAMPLE 11
normal female iPS cell


title: nf_1370

description: Hybridized to customized Axiom array


title: XYX_PBMC

description:
SAMPLE 8
normal male somatic cell


title: CAR_Non CL_Repeat breeder_1

value: Endometrium


title: ate1 ate2 +/- Pst AvrRpm1; 0 hpi; SET 4

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 4


title: ICAR_Non CL_Normal_1

value: intercarunclar areas in endometrium of contralateral uterine horn

value: Day 15 of estrous cycle


title: ate1 ate2 +/- Pst AvrRpm1; 0 hpi; SET 3

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 3


title: ate1 ate2 +/- Pst AvrRpm1; 0 hpi; SET 2

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 2


title: nf_1461

description: Hybridized to customized Axiom array

value: Newfoundland and Labrador


title: CAR_Non CL_Normal_2

source_name: Carunclar endometrium_Contralateral uterine horn_Normal

value: normally fertile cows

value: In vivo


title: ate1 ate2 +/- Pst AvrRpm1; 0 hpi; SET 1

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 1


title: swd1_rep1

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description:
ΔSPAC23H3.05c-KanR (Bioneer)
∆swd1 vs WT

hyb_protocol: Labelled cDNA was hybridized according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePic Pro 6.1 software

data_processing: Background subtraction and lowess normalization was applied according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

organism: Schizosaccharomyces pombe

source_name: swd1 deletion strain

label_protocol: Total RNA was reverse transcribed and labelled according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

growth_protocol: Cells were innoculated at an OD~0.05 in 25mL YES media and collected by vacuum filtration at mid-log-phase growth (OD~0.5). Replicates indicate separately grown biological replicates

extract_protocol: Total RNA was isolated by Acid-phenol extraction followed by ethanol precipitation and resuspension in 50uL TE buffer

tag: strain

value: deltaSPAC23H3.05c-KanR (Bioneer)

source_name: Wild-type reference

value: ED666 (Bioneer)


title: CAR_Non CL_Normal_3


title: nf_2693

description: Hybridized to customized Axiom array

value: Healthy

value: Male


title: CAR_Non CL_Normal_4

value: carunclar areas in endometrium of contralateral uterine horn


title: Col-0 +/- Pst AvrRpm1; 4 hpi; SET 4

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 4

value: wild type Col-0


title: Col-0 +/- Pst AvrRpm1; 4 hpi; SET 3

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 3

value: 4-week old plants


title: CAR_Non CL_Normal_1


title: SPCC162.01c_rep1

description:
ΔSPCC162.01c-KanR (Bioneer)
∆SPCC162.01c vs WT

source_name: SPCC162.01c deletion strain

value: deltaSPCC162.01c-KanR (Bioneer)


title: ssu72_rep1

description:
ΔSPAC3G9.04-KanR (Bioneer)
∆ssu72 vs WT

source_name: ssu72 deletion strain

value: deltaSPAC3G9.04-KanR (Bioneer)


title: ssu72_rep2

description:
ΔSPAC3G9.04-KanR (Bioneer)
∆ssu72 vs WT


title: Col-0 +/- Pst AvrRpm1; 4 hpi; SET 2

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 2


title: Col-0 +/- Pst AvrRpm1; 4 hpi; SET 1

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 4 hpi; Biological Replicate 1


title: ICAR_CL_Repeat breeder_4

source_name: Intercarunclar endometrium_Ipsilateral uterine horn_Repeat breeder

value: non-lactating Japanease Black cow

value: inter carunclar areas in endometrium of ipsilateral uterine horn


title: ICAR_CL_Repeat breeder_3

value: Repeat breeding cows

value: Endometrium


title: SPAC20H4.06c_rep2

description:
ΔSPAC20H4.06c-KanR (Bioneer)
∆SPAC20H4.06c vs WT

source_name: SPAC20H4.06c deletion strain

value: deltaSPAC20H4.06c-KanR (Bioneer)


title: SPAC20H4.06c_rep1


title: Col-0 +/- Pst AvrRpm1; 2 hpi; SET 4

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 4


title: ICAR_CL_Repeat breeder_2

value: Day 15 of estrous cycle


title: nf_3134

description: Hybridized to customized Axiom array

source_name: peripheral blood sample

value: Newfoundland and Labrador


title: nf_1569

description: Hybridized to customized Axiom array


title: nf_1600

description: Hybridized to customized Axiom array


title: Col-0 +/- Pst AvrRpm1; 2 hpi; SET 3

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 3


title: SPAC18G6.13_rep2

description:
ΔSPAC18G6.13-KanR (Bioneer)
∆SPAC18G6.13 vs WT

source_name: SPAC18G6.13 deletion strain

value: deltaSPAC18G6.13-KanR (Bioneer)


title: nf_2855

description: Hybridized to customized Axiom array


title: ICAR_CL_Repeat breeder_1

value: In vivo


title: ICAR_CL_Normal_3

source_name: Intercarunclar endometrium_Ipsilateral uterine horn_Normal

value: normally fertile cows

value: intercarunclar areas in endometrium of ipsilateral uterine horn


title: ICAR_CL_Normal_4


title: ICAR_CL_Normal_2


title: Col-0 +/- Pst AvrRpm1; 2 hpi; SET 2

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 2


title: nf_1437

description: Hybridized to customized Axiom array

value: Healthy

value: Female


title: nf_2985

description: Hybridized to customized Axiom array


title: smd3_rep1

description:
ΔSPBC19C2.14-KanR (Bioneer)
∆smd3 vs WT

source_name: smd3 deletion strain

value: deltaSPBC19C2.14-KanR (Bioneer)

value: ED666 (Bioneer)


title: Col-0 +/- Pst AvrRpm1; 2 hpi; SET 1

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 1

value: 4-week old plants

value: wild type Col-0


title: pwi1_rep1

description:
ΔSPCC825.05c-KanR (Bioneer)
∆pwi1 vs WT

source_name: pwi1 deletion strain

value: deltaSPCC825.05c-KanR (Bioneer)


title: Col-0 +/- Pst AvrRpm1; 0 hpi; SET 4

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 4


title: SPAC18G6.13_rep1


title: CAR_CL_Repeat breeder_4

source_name: Carunclar endometrium_Ipsilateral uterine horn_Repeat breeder

value: non-lactating Japanease Black cow

value: carunclar areas in endometrium of ipsilateral uterine horn


title: pwi1_rep2

description:
ΔSPCC825.05c-KanR (Bioneer)
∆pwi1 vs WT


title: ICAR_CL_Normal_1

value: Endometrium


title: ppn1_rep2

description:
ΔSPCC74.02c-KanR (Bioneer)
∆ppn1 vs WT

source_name: ppn1 deletion strain

value: deltaSPCC74.02c-KanR (Bioneer)


title: nf_1964

description: Hybridized to customized Axiom array

value: Male


title: nf_1603

description: Hybridized to customized Axiom array

value: Newfoundland and Labrador


title: NP_Pax6_rep2

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure

scan_protocol: Scanning was performed with NimbleScan.

data_processing: For each oligo, the log2 ratio of IP over input intensities were calculated. Arrays were then loess normalized using R and Bioconductor package limma.

source_name: Pax6 ChIP DNA from NP cells

label_protocol: According to Nimblegen guidelines

growth_protocol: Wild-type embryonic stem cells (129-C57Bl/6) and derived neuronal progenitor cells were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments for Pax6 were performed as previously described (Weber et al., 2007, PMID: 17334365).

value: brain

tag: cell type

value: neural progenitor

tag: antibody

value: anti-Pax6 (Covance PRB-278P)

source_name: Input DNA from NP cells

value: None, input DNA


title: nf_1433

description: Hybridized to customized Axiom array

value: Healthy


title: smd3_rep2

description:
ΔSPBC19C2.14-KanR (Bioneer)
∆smd3 vs WT


title: nf_1616

description: Hybridized to customized Axiom array

value: Female


title: nf_1932

description: Hybridized to customized Axiom array


title: ate1 ate2 +/- Pst AvrRpm1; 2 hpi; SET 4

description: mock-treated ate1 ate2 plants vs. ate1 ate2 plants infiltrated with Pst AvrRpm1; 2 hpi; Biological Replicate 4

source_name: (-) Pst AvrRpm1

value: ate1 ate2

source_name: (+) Pst AvrRpm1


title: Col-0 +/- Pst AvrRpm1; 0 hpi; SET 3

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 3


title: CAR_CL_Repeat breeder_3

tag: breed

value: Repeat breeding cows

value: Day 15 of estrous cycle

value: In vivo


title: NP_Pax6_rep3


title: CAR_CL_Repeat breeder_2

tag: sample group


title: Col-0 +/- Pst AvrRpm1; 0 hpi; SET 1

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 1

value: 4-week old plants

value: wild type Col-0


title: nf_2974

description: Hybridized to customized Axiom array


title: Col-0 +/- Pst AvrRpm1; 0 hpi; SET 2

description: mock-treated Col-0 plants vs. Col-0 plants infiltrated with Pst AvrRpm1; 0 hpi; Biological Replicate 2


title: nf_2886

description: Hybridized to customized Axiom array


title: pht1_rep1

description:
ΔSPBC11B10.10c-KanR (Bioneer)
∆pht1 vs WT

source_name: pht1 deletion strain

value: deltaSPBC11B10.10c-KanR (Bioneer)

value: ED666 (Bioneer)


title: ppn1_rep1

description:
ΔSPCC74.02c-KanR (Bioneer)
∆ppn1 vs WT

value: deltaSPCC74.02c-KanR (Bioneer)

source_name: Wild-type reference


title: ctr1_rep2

description:
ΔSPAC140.04-KanR (Bioneer)
∆ctr1 vs WT

source_name: ctr1 deletion strain

value: deltaSPAC140.04-KanR (Bioneer)


title: CAR_CL_Normal_3

source_name: Carunclar endometrium_Ipsilateral uterine horn_Normal

value: non-lactating Japanease Black cow

value: normally fertile cows

value: Endometrium

tag: tissue subtype

value: carunclar areas in endometrium of ipsilateral uterine horn


title: ate1 ate2 vs. wild type untreated SET 5

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 5

source_name: wild type Col-0

value: seedling (11-d old)

source_name: ate1 ate2


title: nf_3078

description: Hybridized to customized Axiom array

source_name: peripheral blood sample

value: Newfoundland and Labrador

value: Healthy


title: ash2_rep1

description:
ΔSPBC13G1.08c-KanR (Bioneer)
∆ash2 vs WT

source_name: ash2 deletion strain

value: deltaSPBC13G1.08c-KanR (Bioneer)


title: ctr1_rep1

description:
ΔSPAC140.04-KanR (Bioneer)
∆ctr1 vs WT


title: NP_Pax6_rep1

value: brain

value: neural progenitor

value: anti-Pax6 (Covance PRB-278P)

value: None, input DNA


title: ate1 ate2 vs. wild type untreated SET 3

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 3

value: ate1 ate2

value: wild type Col-0


title: nf_3079

description: Hybridized to customized Axiom array

value: Male


title: CAR_CL_Normal_2

tag: phase

value: Day 15 of estrous cycle

value: In vivo


title: CAR_CL_Normal_1

value: non-lactating Japanease Black cow

tag: study


title: ate1 ate2 vs. wild type untreated SET 1

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 1


title: aar2_rep1

description:
ΔSPAC3H5.04-KanR (Bioneer)
∆aar2 vs WT

source_name: aar2 deletion strain

value: deltaSPAC3H5.04-KanR (Bioneer)

value: ED666 (Bioneer)


title: aar2_rep2

description:
ΔSPAC3H5.04-KanR (Bioneer)
∆aar2 vs WT


title: ate1 ate2 vs. wild type untreated SET 2

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 2


title: SKR_3

status: Public on May 01 2016

city: Singapore

first: Shyh-Chang

last: Ng

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description: replicate 2

hyb_protocol: Illumina standard hybridisation for Illumina MouseWG-6 v2.0 expression beadchip [GPL6887]

scan_protocol: Illumina Beadarray Reader - Sentrix scan for Illumina MouseWG-6 v2.0 expression beadchip [GPL6887] at Gain 4.5

data_processing: Exported with Illumina Genome Studio Gene Expression module 1.9.0

source_name: Mouse quadriceps muscle, rxf393 injection

label_protocol: Ambion Total Prep RNA for Illumina

growth_protocol: NOD-SCID mice were fed ad libitum

extract_protocol: Ambion standard Trizol extraction.

treatment_protocol: NOD-SCID mice were subcutaneously transplanted with 5.0x10^6 cancer cells

tag: cells injected

value: RXF393 cells

tag: cachectic cancer cells

value: Yes

value: NOD-SCID


title: RXF_3

description: replicate 3


title: SKR_2

description: replicate 3

source_name: Mouse quadriceps muscle, skrc39 injection

value: SKRC39 cells

value: No


title: mor_in_40

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with preprocessCore in R.

source_name: Striatum of 6-10 week old C57BL/6J mice

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: striatum

tag: chronic treatment

value: MOR

tag: acute treatment


title: sach_8

value: SACH

value: SAL


title: RXF_1

description: replicate 2


title: sach_in_6


title: sach_5


title: sach_in_7


title: mor_38


title: mor_in_35


title: SKR_1

description: replicate 1


title: mor_33


title: mor_37


title: mor_in_34


title: mor_in_39


title: sach_in_4


title: RXF_2

description: replicate 1


title: sach_in_9


title: mor_41


title: sach_3


title: mor_32


title: sach_in_12


title: ate1 ate2 vs. wild type untreated SET 6

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 6

value: seedling (11-d old)

value: ate1 ate2


title: patient 60 tumor

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: The Hybridization and Wash Kit (Affymetrix) was used to hybridize all samples to Human Gene ST 1.0 arrays (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

data_processing: RMA algorithm implementation of oligo package (R statistical software).

source_name: tumor biopsy from hepatocellular carcinoma patient

label_protocol: Total RNA, 250 ng, was reverse transcribed and biotinylated with the whole-transcript Expression Kit (Ambion) and whole transcript Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using Qiazol reagent and RNAeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

value: tumor

tag: disease state

value: hepatocellular carcinoma patient


title: mor_in_31


title: patient 59 non-tumor

source_name: liver parenchyma biopsy from hepatocellular carcinoma patient

value: liver parenchyma


title: patient 56 non-tumor


title: sach_2


title: patient 58 tumor


title: mor_30


title: patient 53 non-tumor


title: patient 54 tumor


title: sach_in_11


title: patient 54 non-tumor


title: sach_1


title: patient 53 tumor


title: patient 60 non-tumor


title: patient 55 non-tumor


title: patient 56 tumor


title: patient 58 non-tumor


title: patient 59 tumor


title: patient 57 tumor


title: mor_in_29


title: patient 57 non-tumor


title: patient 52 tumor


title: patient 55 tumor


title: patient 52 non-tumor


title: patient 51 tumor


title: patient 51 non-tumor


title: patient 48 non-tumor


title: patient 48 tumor


title: patient 47 non-tumor


title: patient 49 non-tumor


title: patient 49 tumor


title: patient 46 non-tumor


title: patient 45 non-tumor


title: patient 44 tumor


title: patient 50 non-tumor


title: patient 44 non-tumor


title: patient 46 tumor


title: patient 47 tumor


title: patient 42 tumor


title: patient 42 non-tumor


title: patient 43 tumor


title: patient 43 non-tumor


title: patient 50 tumor


title: patient 45 tumor


title: CAR_CL_Normal_4

value: non-lactating Japanease Black cow

value: normally fertile cows

value: Endometrium

value: carunclar areas in endometrium of ipsilateral uterine horn

value: Day 15 of estrous cycle

value: In vivo


title: patient 41 tumor


title: patient 40 tumor


title: ate1 ate2 vs. wild type untreated SET 4

description: ate1 ate2 vs. wild type 11-day old seedlings; Biological Replicate 4

value: wild type Col-0


title: CAR_CL_Repeat breeder_1

source_name: Carunclar endometrium_Ipsilateral uterine horn_Repeat breeder

value: Repeat breeding cows


title: patient 40 non-tumor


title: patient 41 non-tumor


title: patient 37 tumor


title: patient 35 tumor


title: patient 38 tumor


title: patient 37 non-tumor


title: patient 38 non-tumor


title: patient 33 tumor


title: patient 32 tumor


title: patient 39 tumor


title: patient 36 non-tumor


title: patient 34 non-tumor


title: patient 31 non-tumor


title: patient 31 tumor


title: patient 36 tumor


title: patient 30 tumor


title: patient 29 tumor


title: patient 33 non-tumor


title: patient 34 tumor


title: patient 32 non-tumor


title: patient 27 non-tumor


title: sach_10

value: striatum


title: patient 28 tumor


title: patient 27 tumor


title: patient 28 non-tumor


title: patient 35 non-tumor


title: patient 26 tumor


title: patient 30 non-tumor


title: patient 29 non-tumor


title: patient 24 tumor


title: patient 25 non-tumor


title: patient 22 non-tumor


title: patient 20 tumor


title: patient 22 tumor


title: patient 25 tumor


title: patient 23 non-tumor


title: patient 23 tumor


title: patient 21 tumor


title: patient 20 non-tumor


title: patient 18 non-tumor


title: patient 18 tumor


title: patient 19 non-tumor


title: patient 21 non-tumor


title: patient 24 non-tumor


title: patient 15 tumor


title: patient 19 tumor


title: patient 17 non-tumor


title: patient 16 non-tumor


title: patient 14 tumor


title: patient 13 tumor


title: patient 14 non-tumor


title: patient 13 non-tumor


title: patient 15 non-tumor


title: patient 12 non-tumor


title: patient 11 non-tumor


title: patient 12 tumor


title: patient 17 tumor


title: patient 10 non-tumor


title: patient 16 tumor


title: patient 9 non-tumor


title: patient 26 non-tumor


title: patient 8 non-tumor


title: patient 8 tumor


title: patient 6 non-tumor


title: patient 7 tumor


title: patient 9 tumor


title: patient 6 tumor


title: patient 7 non-tumor


title: patient 5 non-tumor


title: patient 5 tumor


title: patient 11 tumor


title: patient 2 tumor


title: patient 4 non-tumor


title: normal3

source_name: normal liver biopsy

value: liver

value: normal


title: patient 4 tumor


title: patient 10 tumor


title: patient 1 non-tumor


title: patient 2 non-tumor


title: patient 3 tumor


title: normal4


title: normal5


title: patient 1 tumor


title: patient 3 non-tumor


title: normal2


title: SUBM2 Patient, Control

city: Tucson

first: Haiquan

last: Li

state: AZ

address: 1657 E Helen Street

department: Medicine

institute: University of Arizona

description: Gene expression data

hyb_protocol: Hybridization were performed following Affymetrix protocols

scan_protocol: standard Affymetrix protocol

data_processing: The raw data were normalized according to the Robust Multiple-array Average (RMA) normalization. The normalization was applied on each patient data independently (2 paired samples at a time, to avoid bias in the single-patient experiments) using Affymetrix Power Tools (APT).

source_name: PBMC

label_protocol: Labeling of cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: The live PBMCs were isolated from blood samples collected from four human subjects under a protocol approved by The University of Arizona Internal Review Board. Whole blood was obtained from donors and placed in Becton Dickenson’s CPT tubes that were centrifuged according to standard protocols to obtain PBMCs, then each aliquoted in two paired samples. Each sample of the pair was subsequently exposed to and incubated with either (i) Human Rhinovirus serotype 16 (ex vivo infected sample) or to (ii) sterile medium (control ex vivo non-infected sample) and incubated at 37°C in 5% CO2 for 24 hours. This protocol resulted in 23 ex vivo infected + 23 ex vivo controls = 46 paired samples. RNA was extracted from these samples, amplified, tagged, and hybridized on Affymetrix Human Gene 1.0 ST microarrays according to standard operating procedures.

value: Peripheral blood mononuclear cell

tag: treatment

value: control


title: SUB7 Patient, Rhinovirus-exposed

description: Gene expression data

value: rhinovirus-exposed


title: SUBM2 Patient, Rhinovirus-exposed

description: Gene expression data


title: patient 39 non-tumor

tag: tissue


title: SUB7 Patient, Control

description: Gene expression data


title: SUB21 Patient, Rhinovirus-exposed

description: Gene expression data


title: normal1


title: SUB26 Patient, Control

description: Gene expression data


title: SUB2 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB17 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB2 Patient, Control

description: Gene expression data


title: SUB26 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB17 Patient, Control

description: Gene expression data


title: SUB14 Patient, Control

description: Gene expression data


title: SUB14 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB16 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB16 Patient, Control

description: Gene expression data


title: SUB13 Patient, Control

description: Gene expression data


title: SUB04 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB10 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB21 Patient, Control

description: Gene expression data


title: SUB04 Patient, Control

description: Gene expression data


title: SUB13 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB05 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUBM1 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUBM1 Patient, Control

description: Gene expression data


title: SUB30 Patient, Control

description: Gene expression data


title: SUB29 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB10 Patient, Control

description: Gene expression data


title: SUB30 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB23 Patient, Control

description: Gene expression data


title: SUB05 Patient, Control

description: Gene expression data


title: SUB29 Patient, Control

description: Gene expression data


title: SUB25 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB23 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB22 Patient, Control

description: Gene expression data


title: SUB25 Patient, Control

description: Gene expression data


title: SUB15 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB20 Patient, Rhinovirus-exposed

description: Gene expression data


title: SUB20 Patient, Control

description: Gene expression data


title: SUB12 Patient, Control

description: Gene expression data


title: SUB12 Patient, Rhinovirus-exposed

description: Gene expression data


title: jurkat_stim

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description: Jurkat cells stimulated for 4h with PMA and Ionomycin

hyb_protocol: Samples were hybridised as per Affymetrix standard protocols

scan_protocol: Samples were scanned as per Affymetrix standard protocols

data_processing: RMA normalised using the Affy package in R and only the ‘main’ probes were used.

source_name: Jurkat cell line

label_protocol: Samples were labelled as per Affymetrix standard protocols

growth_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete RPMI medium with FCS.

extract_protocol: Total mRNA extracted  using TriZol® Reagent (Invitrogen, 15596-018) followed by chloroform extraction (Sigma, C2432) and precipitation with isopropanol.

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187). The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting.

tag: cell line

value: Jurkat

value: PMA and Ionomycin


title: 102670-001-023

city: Leiden

first: attje

middle: sietske

last: hoekstra

address: Einthovenweg 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: biological replicate sample 23 and 24

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridized to the Illumina HumanHT-12 v4 BeadChip according to standard Illumina hybridization protocol

scan_protocol: Scanning was performed on the Illumina iScan according to standard Illumina scanning protocol

data_processing: Normalization and quality control was performed using the Bioconductor lumi package of R (lumi)

source_name: SHSY5Y cells_SDHD+SLC22A18

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: SNB19 cells were grown in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin. SHSY5Y cells were grown in DMEM-F12 supplemented with 10% fetal bovine serum and penicillin/streptomycin

extract_protocol: Total RNA from cells was isolated using the Nucleospin RNA II kit

treatment_protocol: SNB19 and SHSY5Y cells were transduced with shRNAs to create stable knockdown of SDHD, CDKN1C or SLC22A18. Scrambled shRNA was taken as control.

value: neuroblastoma cells

tag: shRNA


title: 102670-001-020

description: biological replicate sample 19 and 20

source_name: SHSY5Y cells_SLC22A18


title: SUB22 Patient, Rhinovirus-exposed

description: Gene expression data


title: 102670-001-021

description: biological replicate sample 21 and 22

source_name: SHSY5Y cells_SDHD+CDKN1C


title: jurkat_nonstim

description: Non stimulated Jurkat cells


title: 102670-001-024

description: biological replicate sample 23 and 24


title: 102670-001-015

description: biological replicate sample 15 and 16

source_name: SHSY5Y cells_SDHD

value: SDHD


title: M3 Patient, Control

description: Gene expression data


title: SUB15 Patient, Control

description: Gene expression data


title: SUB09 Patient, Control

description: Gene expression data


title: 102670-001-019

description: biological replicate sample 19 and 20


title: 102670-001-022

description: biological replicate sample 21 and 22


title: jurkat_resting

description: Jurkat cells stimulated for 4h with PMA and Ionomycin and then washed and cultured for 9 days

value: prestimulation


title: SUB09 Patient, Rhinovirus-exposed

description: Gene expression data


title: M3 Patient, Rhinovirus-exposed

description: Gene expression data


title: 102670-001-016

description: biological replicate sample 15 and 16


title: 102670-001-018

description: biological replicate sample 17 and 18

source_name: SHSY5Y cells_CDKN1C


title: 102670-001-011

description: biological replicate sample 11 and 12

source_name: SNB19 cells_SDHD+SLC22A18

value: glioblastoma cells


title: jurkat_re-stim

description: Jurkat cells stimulated for 4h with PMA and Ionomycin and then washed and cultured for 9 days and restimulated with PMA and Ionomycin for 2 h.

value: prestimulation and PMA and Ionomycin


title: 102670-001-012

description: biological replicate sample 11 and 12


title: 102670-001-014

description: biological replicate sample 13 and 14

source_name: SHSY5Y cells_scrambled control

value: scrambled control


title: 102670-001-009

description: biological replicate sample 9 and 10

source_name: SNB19 cells_SDHD+CDKN1C


title: 102670-001-017

description: biological replicate sample 17 and 18


title: 102670-001-010

description: biological replicate sample 9 and 10


title: 102670-001-013

description: biological replicate sample 13 and 14


title: 102670-001-007

description: biological replicate sample 7 and 8

source_name: SNB19 cells_SLC22A18


title: 102670-001-008

description: biological replicate sample 7 and 8


title: 102670-001-004

description: biological replicate sample 3 and 4

source_name: SNB19 cells_SDHD


title: hskm_early myotube_RXF_2

description: RXF replicate 2

hyb_protocol: Illumina standard hybridisation for Illumina HumanHT-12 v4.0 expression beadchip [GPL10558]

scan_protocol: Illumina Beadarray Reader - Sentrix scan for Illumina HumanHT-12 v4.0 expression beadchip [GPL10558]

source_name: human skeletal muscle early myotube

growth_protocol: Muscle stem cells were derived in a 100 mm dish containing growth medium, maintained, and differentiated according to previously published protocols. Early myotubes were obtained after 6 days of growth and differentiation in conditioned media.

treatment_protocol: Conditioned media were obtained by culturing 1.6 × 10^6 cells for 72-96 hours in a 150 mm dish containing 20 ml of RPMI1640 (Gibco) media with 10% fetal bovine serum (Hyclone), then sterile filtered.

tag: conditioned media

value: RXF-conditioned media

tag: cachectic conditioned media

value: Yes


title: 102670-001-006

description: biological replicate sample 5 and 6

source_name: SNB19 cells_CDKN1C

tag: cell type


title: hskm_early myotube_RXF_3

description: RXF replicate 3


title: hskm_early myotube_SKR_3

description: SKR replicate 3

value: SKR-conditioned media

value: No


title: 102670-001-002

description: biological replicate sample 1 and 2

source_name: SNB19 cells_scrambled control


title: hskm_early myotube_SKR_1

description: SKR replicate 1


title: 102670-001-001

description: biological replicate sample 1 and 2


title: 102670-001-005

description: biological replicate sample 5 and 6


title: hskm_early myotube_RXF_1

description: RXF replicate 1


title: hskm_early myotube_SKR_2

description: SKR replicate 2


title: Cervix_D0 [9982865068_J]

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

description:
D0
9982865068_J

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

organism: Macaca mulatta

source_name: Subject: 181_08

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: 44 outbred, Indian-origin, adult or juvenile female rhesus monkeys (Macaca mulatta) were genotyped and selected as negative for the protective MHC class I alleles Mamu-A*01, Mamu-B*08, and Mamu-B*17.  Animals were randomly allocated to groups.  All monkeys were housed at Bioqual, Rockville, MD.

extract_protocol: Plasma SIV RNA levels were measured using a gag targeted quantitative real-time RT-PCR assay, and tissue levels of SIV RNA and DNA were measured using gag targeted, nested quantitative hybrid real time/digital RT-PCR and PCR assays, essentially as described (Hansen et al., 2013). SIV-specific cellular immune responses in blood and tissues were assessed by multiparameter ICS assays essentially as previously described (Baden et al., 2015; Barouch et al., 2012; Li et al., 2011).  9-color ICS assays were performed with predetermined titers of mAbs against CD3 (SP34; Alexa700), CD4 (L200; AmCyan), CD8 (SK1; allophycocyanin-cyanine 7 [APC-Cy7]), CD28 (L293; peridinin chlorophyll-A-cyanine 5.5 [PerCP-Cy5.5]), CD95 (DX2; phycoerythrin [PE]), CD69 (TP1.55.3; phycoerythrin-Texas Red [energy coupled dye; ECD]; Beckman Coulter), IFN-γ (B27; phycoerythrin-cyanine 7 [PE-Cy7]), IL-2 (MQ1-17H12; allophycocyanin [APC]) and TNF-α (Mab11; fluorescein isothiocya [FITC]). IFN-γ backgrounds were consistently <0.01% in PBMC and <0.05% in tissues.

treatment_protocol: Animals were infected with 5x104 TCID50 of our SIVmac251 challenge stock (Barouch et al., 2012; Liu et al., 2010; Liu et al., 2009) by the intravaginal route and were necropsied on day 0, 1, 3, 7, or 10 following infection.

tag: name used in manuscript

value: FRT

value: Cervix

tag: status

value: Healthy

tag: subset


title: 102670-001-003

description: biological replicate sample 3 and 4


title: Colon_D0 [9982865068_H]

description:
D0
9982865068_H

value: Colon


title: Colon_D0 [9982865068_F]

description:
D0
9982865068_F

source_name: Subject: 258_09


title: Spleen_D0 [9982865068_K]

description:
D0
9982865068_K

source_name: Subject: 189_08

value: Spleen


title: Tonsil_D0 [9982865068_I]

description:
D0
9982865068_I

value: Tonsil


title: axillary_LN_D0 [9982865068_A]

description:
D0
9982865068_A

value: LN


title: genital_pelvic_LN_D0 [9982865068_C]

description:
D0
9982865068_C


title: Blood_D0 [9982865068_G]

description:
D0
9982865068_G

source_name: Subject: 271_09

value: Blood


title: mesenteric_LN_D0 [9982865068_B]

description:
D0
9982865068_B


title: Jejunum_D0 [9982865068_D]

description:
D0
9982865068_D

value: GI

value: Jejunum


title: mesenteric_LN_D0 [9982865061_J]

description:
D0
9982865061_J


title: Colon_D0 [9982865061_K]

description:
D0
9982865061_K


title: Blood_D0 [9982865061_H]

description:
D0
9982865061_H


title: Jejunum_D0 [9982865068_E]

description:
D0
9982865068_E


title: Tonsil_D0 [9982865061_I]

description:
D0
9982865061_I


title: Bone_Marrow_D0 [9982865061_F]

description:
D0
9982865061_F


title: axillary_LN_D0 [9982865061_B]

description:
D0
9982865061_B


title: Mid_Vagina_D0 [9982865061_G]

description:
D0
9982865061_G


title: axillary_LN_D0 [9982865061_D]

description:
D0
9982865061_D


title: Cervix_D0 [9982865061_L]

description:
D0
9982865061_L


title: genital_pelvic_LN_D0 [9982865061_A]

description:
D0
9982865061_A


title: Spleen_D0 [9982865068_L]

description:
D0
9982865068_L


title: Spleen_D0 [9980097056_F]

description:
D0
9980097056_F


title: axillary_LN_D0 [9982865061_C]

description:
D0
9982865061_C


title: Blood_D0 [9980097056_E]

description:
D0
9980097056_E


title: Jejunum_D0 [9980097056_C]

description:
D0
9980097056_C


title: Bone_Marrow_D0 [9980097056_B]

description:
D0
9980097056_B


title: Cervix_D0 [9980097056_A]

description:
D0
9980097056_A


title: Mid_Vagina_D0 [9980097039_J]

description:
D0
9980097039_J


title: Bone_Marrow_D0 [9980097039_I]

description:
D0
9980097039_I


title: mesenteric_LN_D0 [9980097039_L]

description:
D0
9980097039_L


title: Tonsil_D0 [9980097039_E]

description:
D0
9980097039_E


title: Blood_D0 [9980097039_H]

description:
D0
9980097039_H


title: mesenteric_LN_D0 [9980097039_F]

description:
D0
9980097039_F


title: Spleen_D0 [9980097039_G]

description:
D0
9980097039_G


title: genital_pelvic_LN_D3 [9377361036_I]

description:
D3
9377361036_I

source_name: Subject: Monkey_PZH

value: SIV


title: pararectal_paracolonic_D3 [9377361036_J]

description:
D3
9377361036_J


title: genital_pelvic_LN_D0 [9980097039_D]

description:
D0
9980097039_D


title: Bone_Marrow_D0 [9980097039_C]

description:
D0
9980097039_C


title: genital_pelvic_LN_D3 [9377361036_K]

description:
D3
9377361036_K

source_name: Subject: Monkey_PZV


title: Rectum_D3 [9377361036_F]

description:
D3
9377361036_F

value: Rectum


title: Colon_D3 [9377361036_L]

description:
D3
9377361036_L


title: Splenocytes_D3 [9377361036_H]

description:
D3
9377361036_H

value: Splenocytes


title: Jejunum_D0 [9980097039_B]

description:
D0
9980097039_B


title: Tonsil_D0 [9980097039_A]

description:
D0
9980097039_A


title: axillary_LN_D3 [9377361033_K]

description:
D3
9377361033_K


title: Brain_lymphocytes_D3 [9377361036_C]

description:
D3
9377361036_C


title: genital_pelvic_LN_D0 [9980097039_K]

description:
D0
9980097039_K


title: Bone_Marrow_D3 [9377361036_D]

description:
D3
9377361036_D


title: pararectal_paracolonic_D3 [9377361036_B]

description:
D3
9377361036_B

source_name: Subject: Monkey_PMT


title: Blood_D3 [9377361036_G]

description:
D3
9377361036_G


title: mesenteric_LN_D3 [9377361033_L]

description:
D3
9377361033_L


title: Thymus_D3 [9377361033_B]

description:
D3
9377361033_B

value: Thymus


title: Liver_D3 [9377361036_A]

description:
D3
9377361036_A

value: Liver


title: Ileum_D3 [9377361033_H]

description:
D3
9377361033_H

value: Ileum


title: Inguinal_LN_D1 [9377361031_H]

description:
D1
9377361031_H

source_name: Subject: Monkey_KIB


title: Blood_D3 [9377361033_J]

description:
D3
9377361033_J


title: Mid_Vagina_D0 [9980097056_D]

description:
D0
9980097056_D


title: Lung_D1 [9377361031_J]

description:
D1
9377361031_J

source_name: Subject: Monkey_MA2

value: Lung


title: genital_pelvic_LN_D3 [9377361033_A]

description:
D3
9377361033_A


title: Thymus_D3 [9377361033_E]

description:
D3
9377361033_E


title: Colon_D1 [9377361031_D]

description:
D1
9377361031_D

source_name: Subject: Monkey_ME4


title: Thymus_D1 [9377361031_I]

description:
D1
9377361031_I


title: Splenocytes_D1 [9377361031_K]

description:
D1
9377361031_K

source_name: Subject: Monkey_MZJ


title: Ileum_D1 [9377361008_K]

description:
D1
9377361008_K


title: Brain_lymphocytes_D1 [9377361008_L]

description:
D1
9377361008_L


title: Cecum_D1 [9377361031_E]

description:
D1
9377361031_E

value: Cecum


title: Liver_D1 [9377361031_G]

description:
D1
9377361031_G


title: Bone_Marrow_D1 [9377361031_B]

description:
D1
9377361031_B


title: genital_pelvic_LN_D1 [9377361031_A]

description:
D1
9377361031_A


title: Colon_D1 [9377361031_C]

description:
D1
9377361031_C


title: pararectal_paracolonic_D1 [9377361008_B]

description:
D1
9377361008_B


title: genital_pelvic_LN_D1 [9377361008_J]

description:
D1
9377361008_J


title: Liver_D1 [9377361008_F]

description:
D1
9377361008_F


title: Rectum_D1 [9377361008_E]

description:
D1
9377361008_E


title: axillary_LN_D1 [9377361008_I]

description:
D1
9377361008_I


title: Liver_D1 [9377361008_H]

description:
D1
9377361008_H


title: ileocecal_LN_D1 [9377361008_G]

description:
D1
9377361008_G


title: Uterus_D1 [9377361008_C]

description:
D1
9377361008_C

value: Uterus


title: Brain_lymphocytes_D1 [9377361008_A]

description:
D1
9377361008_A


title: Tonsil_D1 [9377361008_D]

description:
D1
9377361008_D


title: Lung_D3 [9377361003_C]

description:
D3
9377361003_C

source_name: Subject: Monkey_AR79


title: Rectum_D3 [9377361003_D]

description:
D3
9377361003_D


title: Splenocytes_D3 [9377358073_I]

description:
D3
9377358073_I


title: Cervix_D3 [9377361003_B]

description:
D3
9377361003_B

value: FRT

value: Cervix


title: Cecum_D3 [9377358073_D]

description:
D3
9377358073_D


title: pararectal_paracolonic_D1 [9377358071_K]

description:
D1
9377358071_K


title: mesenteric_LN_D1 [9377358071_J]

description:
D1
9377358071_J


title: Uterus_D1 [9377358071_I]

description:
D1
9377358071_I


title: PBMC_pre_challenge_D3 [9377358073_E]

description:
D3
9377358073_E


title: Uterus_D1 [9377358071_B]

description:
D1
9377358071_B


title: Inguinal_LN_D1 [9377358071_D]

description:
D1
9377358071_D


title: PBMC_pre_challenge_D1 [9377358071_E]

description:
D1
9377358071_E


title: Uterus_D1 [9377358071_F]

description:
D1
9377358071_F


title: ileocecal_LN_D3 [9377358069_H]

description:
D3
9377358069_H


title: Ileum_D1 [9377358066_I]

description:
D1
9377358066_I


title: Rectum_D1 [9377358066_J]

description:
D1
9377358066_J


title: Lung_D1 [9377358066_L]

description:
D1
9377358066_L


title: Thymus_D1 [9377358066_G]

description:
D1
9377358066_G


title: Colon_D1 [9377358071_H]

description:
D1
9377358071_H

value: Colon


title: Mid_Vagina_D1 [9377358071_A]

description:
D1
9377358071_A


title: Lung_D1 [9377358066_B]

description:
D1
9377358066_B


title: PBMC_pre_challenge_D3 [9377358065_D]

description:
D3
9377358065_D


title: Cecum_D1 [9377358066_C]

description:
D1
9377358066_C


title: Jejunum_D3 [9377358065_J]

description:
D3
9377358065_J


title: Ileum_D1 [9377358066_H]

description:
D1
9377358066_H


title: Jejunum_D1 [9377358066_A]

description:
D1
9377358066_A


title: Inguinal_LN_D3 [9377358065_I]

description:
D3
9377358065_I


title: Splenocytes_D3 [9377358065_F]

description:
D3
9377358065_F


title: Tonsil_D3 [9377358065_K]

description:
D3
9377358065_K

value: Tonsil


title: Bone_Marrow_D1 [9377358066_F]

description:
D1
9377358066_F


title: Inguinal_LN_D1 [9377358066_K]

description:
D1
9377358066_K


title: mesenteric_LN_D3 [9377358065_C]

description:
D3
9377358065_C

value: LN


title: Rectum_D1 [9377358071_G]

description:
D1
9377358071_G


title: Lung_D3 [9377358065_E]

description:
D3
9377358065_E


title: ileocecal_LN_D3 [9377358065_G]

description:
D3
9377358065_G


title: Splenocytes_D1 [9377358063_K]

description:
D1
9377358063_K


title: axillary_LN_D3 [9377358065_B]

description:
D3
9377358065_B


title: Cecum_D3 [9377358065_A]

description:
D3
9377358065_A


title: Duodenum_D1 [9377358063_F]

description:
D1
9377358063_F

value: Duodenum


title: Liver_D3 [9377358058_G]

description:
D3
9377358058_G


title: Lung_D1 [9377358063_C]

description:
D1
9377358063_C


title: ileocecal_LN_D1 [9377358063_G]

description:
D1
9377358063_G


title: axillary_LN_D3 [9377358058_H]

description:
D3
9377358058_H


title: mesenteric_LN_D3 [9377358053_J]

description:
D3
9377358053_J


title: Duodenum_D3 [9377358058_E]

description:
D3
9377358058_E


title: Bone_Marrow_D3 [9377358032_A]

description:
D3
9377358032_A


title: Duodenum_D3 [9377358026_L]

description:
D3
9377358026_L


title: genital_pelvic_LN_D3 [9377358058_D]

description:
D3
9377358058_D


title: Tonsil_D1 [9377358063_A]

description:
D1
9377358063_A


title: Brain_lymphocytes_D3 [9377358053_G]

description:
D3
9377358053_G


title: Cervix_D3 [9377358053_H]

description:
D3
9377358053_H


title: Ileum_D3 [9377358053_K]

description:
D3
9377358053_K


title: Uterus_D3 [9377358053_F]

description:
D3
9377358053_F


title: Colon_D3 [9377358032_K]

description:
D3
9377358032_K


title: Blood_D1 [9377358063_I]

description:
D1
9377358063_I

value: Blood


title: Uterus_D3 [9377358026_F]

description:
D3
9377358026_F


title: Colon_D3 [9377358053_E]

description:
D3
9377358053_E


title: Colon_D3 [9377358053_L]

description:
D3
9377358053_L


title: Lung_D3 [9377358026_I]

description:
D3
9377358026_I


title: Bone_Marrow_D3 [9377358053_C]

description:
D3
9377358053_C


title: Splenocytes_D3 [9377358026_J]

description:
D3
9377358026_J


title: Jejunum_D1 [9377358063_B]

description:
D1
9377358063_B

value: GI

value: Jejunum


title: Jejunum_D3 [9377358053_D]

description:
D3
9377358053_D

value: SIV


title: Duodenum_D3 [9377358026_K]

description:
D3
9377358026_K


title: Duodenum_D3 [9377358026_G]

description:
D3
9377358026_G


title: Jejunum_D1 [9372962074_L]

description:
D1
9372962074_L


title: Ileum_D3 [9377358019_I]

description:
D3
9377358019_I


title: Uterus_D3 [9377358019_E]

description:
D3
9377358019_E


title: Lung_D3 [9377358026_D]

description:
D3
9377358026_D


title: Duodenum_D1 [9372962074_H]

description:
D1
9372962074_H


title: Tonsil_D3 [9377358019_G]

description:
D3
9377358019_G


title: Bone_Marrow_D1 [9372962074_C]

description:
D1
9372962074_C


title: mesenteric_LN_D1 [9372962074_D]

description:
D1
9372962074_D


title: Thymus_D3 [9377358025_K]

description:
D3
9377358025_K


title: Liver_D3 [9377358026_C]

description:
D3
9377358026_C


title: Splenocytes_D1 [9372962074_J]

description:
D1
9372962074_J

value: Splenocytes


title: axillary_LN_D3 [9377358019_J]

description:
D3
9377358019_J


title: Duodenum_D1 [9372962066_K]

description:
D1
9372962066_K


title: genital_pelvic_LN_D1 [9372962074_A]

description:
D1
9372962074_A


title: Mid_Vagina_D3 [9377358019_K]

description:
D3
9377358019_K


title: Jejunum_D3 [9377358019_L]

description:
D3
9377358019_L


title: Blood_D1 [9372962074_K]

description:
D1
9372962074_K


title: pararectal_paracolonic_D3 [9377358019_B]

description:
D3
9377358019_B


title: Duodenum_D1 [9372962066_J]

description:
D1
9372962066_J


title: ileocecal_LN_D3 [9377358019_D]

description:
D3
9377358019_D


title: Brain_lymphocytes_D1 [9372962074_F]

description:
D1
9372962074_F


title: Jejunum_D1 [9372962074_G]

description:
D1
9372962074_G


title: Mid_Vagina_D1 [9372962074_B]

description:
D1
9372962074_B


title: pararectal_paracolonic_D1 [9372962074_I]

description:
D1
9372962074_I


title: Brain_lymphocytes_D3 [9377358025_A]

description:
D3
9377358025_A


title: Cecum_D1 [9372962066_I]

description:
D1
9372962066_I


title: Mid_Vagina_D3 [9377358019_A]

description:
D3
9377358019_A


title: axillary_LN_D1 [9372962074_E]

description:
D1
9372962074_E


title: genital_pelvic_LN_D1 [9372962047_H]

description:
D1
9372962047_H


title: Blood_D3 [9377358026_E]

description:
D3
9377358026_E


title: axillary_LN_D1 [9372962066_C]

description:
D1
9372962066_C


title: ileocecal_LN_D1 [9372962066_D]

description:
D1
9372962066_D


title: Rectum_D1 [9372962047_C]

description:
D1
9372962047_C

value: Rectum


title: Tonsil_D1 [9372962066_B]

description:
D1
9372962066_B


title: PBMC_pre_challenge_D1 [9372962047_G]

description:
D1
9372962047_G


title: Liver_D1 [9372962066_L]

description:
D1
9372962066_L

value: Liver


title: Sacral_LN_D1 [9372962047_F]

description:
D1
9372962047_F


title: Ileum_D1 [9372962029_J]

description:
D1
9372962029_J

value: Ileum


title: Blood_D1 [9372962047_J]

description:
D1
9372962047_J


title: Cervix_D1 [9372962047_I]

description:
D1
9372962047_I


title: Inguinal_LN_D1 [9372962066_A]

description:
D1
9372962066_A


title: Bone_Marrow_D1 [9372962047_E]

description:
D1
9372962047_E


title: pararectal_paracolonic_D1 [9372962047_L]

description:
D1
9372962047_L


title: Colon_D1 [9372962047_B]

description:
D1
9372962047_B


title: Tonsil_D1 [9372962066_H]

description:
D1
9372962066_H


title: Cervix_D1 [9372962066_G]

description:
D1
9372962066_G


title: Sacral_LN_D1 [9372962029_H]

description:
D1
9372962029_H


title: mesenteric_LN_D1 [9372962029_G]

description:
D1
9372962029_G


title: Thymus_D1 [9372962047_K]

description:
D1
9372962047_K

value: Thymus


title: Blood_D1 [9372962029_I]

description:
D1
9372962029_I


title: mesenteric_LN_D1 [9372962029_L]

description:
D1
9372962029_L


title: PBMC_pre_challenge_D1 [9372962029_D]

description:
D1
9372962029_D


title: Blood_D1 [9372962029_E]

description:
D1
9372962029_E


title: Cervix_D1 [9372962066_F]

description:
D1
9372962066_F


title: Mid_Vagina_D1 [9372962047_A]

description:
D1
9372962047_A


title: Thymus_D1 [9372962029_F]

description:
D1
9372962029_F


title: Splenocytes_D1 [9372962047_D]

description:
D1
9372962047_D


title: Cervix_D1 [9372962029_K]

description:
D1
9372962029_K


title: axillary_LN_D1 [9372962029_C]

description:
D1
9372962029_C


title: Liver_D3 [9372535086_I]

description:
D3
9372535086_I


title: Rectum_D3 [9372535086_K]

description:
D3
9372535086_K


title: Tonsil_D3 [9372535050_D]

description:
D3
9372535050_D


title: Cecum_D1 [9372962029_A]

description:
D1
9372962029_A

value: Cecum


title: ileocecal_LN_D3 [9287078060_K]

description:
D3
9287078060_K

source_name: Subject: Monkey_AS23


title: Inguinal_LN_D3 [9372535086_B]

description:
D3
9372535086_B


title: Rectum_D3 [9372535086_A]

description:
D3
9372535086_A


title: Cervix_D3 [9372535050_G]

description:
D3
9372535050_G


title: Cecum_D3 [9372535050_J]

description:
D3
9372535050_J


title: Cervix_D3 [9372535050_A]

description:
D3
9372535050_A


title: axillary_LN_D3 [9287078060_I]

description:
D3
9287078060_I

source_name: Subject: Monkey_5349


title: Inguinal_LN_D3 [9372535086_E]

description:
D3
9372535086_E


title: Thymus_D3 [9372535086_C]

description:
D3
9372535086_C


title: ileocecal_LN_D1 [9372962029_B]

description:
D1
9372962029_B


title: Uterus_D3 [9287078060_L]

description:
D3
9287078060_L

source_name: Subject: Monkey_AQ90

value: Uterus


title: ileocecal_LN_D3 [9372535086_D]

description:
D3
9372535086_D


title: ileocecal_LN_D3 [9287078060_J]

description:
D3
9287078060_J

source_name: Subject: Monkey_5359


title: Bone_Marrow_D3 [9372535050_B]

description:
D3
9372535050_B


title: Cervix_D3 [9287078060_F]

description:
D3
9287078060_F

value: FRT


title: Inguinal_LN_D3 [9287078060_E]

description:
D3
9287078060_E


title: mesenteric_LN_D3 [9287078060_G]

description:
D3
9287078060_G


title: Liver_D3 [9287078051_H]

description:
D3
9287078051_H


title: Rectum_D3 [9287078051_I]

description:
D3
9287078051_I


title: Duodenum_D3 [9287078060_A]

description:
D3
9287078060_A


title: Uterus_D3 [9287078051_K]

description:
D3
9287078051_K


title: Liver_D3 [9287078060_D]

description:
D3
9287078060_D


title: Uterus_D3 [9287078051_J]

description:
D3
9287078051_J


title: Rectum_D3 [9287078060_C]

description:
D3
9287078060_C


title: Jejunum_D3 [9287078051_L]

description:
D3
9287078051_L


title: Cecum_D3 [9372535050_F]

description:
D3
9372535050_F


title: Bone_Marrow_D3 [9287078051_F]

description:
D3
9287078051_F


title: Thymus_D3 [9287078051_E]

description:
D3
9287078051_E


title: Splenocytes_D3 [9287078048_I]

description:
D3
9287078048_I


title: Colon_D3 [9287078048_K]

description:
D3
9287078048_K


title: genital_pelvic_LN_D3 [9287078051_C]

description:
D3
9287078051_C


title: Cervix_D3 [9287078048_L]

description:
D3
9287078048_L

value: Cervix


title: Blood_D3 [9287078051_D]

description:
D3
9287078051_D


title: Lung_D3 [9287078041_L]

description:
D3
9287078041_L

value: Lung


title: Mid_Vagina_D3 [9287078048_B]

description:
D3
9287078048_B


title: Jejunum_D3 [9287078048_J]

description:
D3
9287078048_J


title: Thymus_D3 [9287078048_G]

description:
D3
9287078048_G


title: Ileum_D3 [9287078051_G]

description:
D3
9287078051_G


title: mesenteric_LN_D3 [9287078041_J]

description:
D3
9287078041_J


title: severe chronic hepatitis C, male, C676

city: North Bethesda

first: Kentaro

last: Matsuura

state: Maryland

address: 5411 McGrath Blvd.

department: Department of Transfusion Medicine

institute: National Institutes of Health

hyb_protocol: The biotin-labeled samples with hybridization master mix were hybridized at 48 °C and 60 rpm for 16 hours on Affymetrix GeneChip miRNA 4.0 Array,  following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix) . Thereafter, the GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix), following the manufacturer’s instructions.

scan_protocol: The GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix), following the manufacturer’s instructions.

data_processing: Raw microarray data (CEL files) were imported into Partek Genomics Suite (Partek Inc., St. Louis, MO), and probe set summaries were computed using Robust Multi-Array algorithm. To adjust for differences in labeling intensities and hybridization, a global normalization was made by aligning signal intensities of data arrays across the medians.

source_name: plasma

label_protocol: Total RNA derived from 400 μL of plasma in each subject was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single and double-stranded DNA molecule conjugated to biotin) using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

extract_protocol:
We extracted RNAs from plasma samples in 16 healthy controls, 16 CHC patients with mild fibrosis and 16 with significant fibrosis.
Total RNAs including miRNAs in plasma were purified with miRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany) respectively, following the manufacturer’s instructions.

tag: gender

value: male

tag: age

tag: ishak fiborosis score


title: severe chronic hepatitis C, male, C727


title: Cecum_D3 [9287078048_E]

description:
D3
9287078048_E


title: Lung_D3 [9287078041_K]

description:
D3
9287078041_K


title: Colon_D3 [9287078041_H]

description:
D3
9287078041_H

value: Colon


title: Tonsil_D3 [9287078048_D]

description:
D3
9287078048_D

value: Tonsil


title: Blood_D3 [9287078051_A]

description:
D3
9287078051_A

value: Blood


title: Splenocytes_D3 [9287078041_I]

description:
D3
9287078041_I


title: severe chronic hepatitis C, male, C288


title: genital_pelvic_LN_D3 [9287078041_G]

description:
D3
9287078041_G

value: LN


title: axillary_LN_D3 [9287078048_C]

description:
D3
9287078048_C


title: severe chronic hepatitis C, male, C133


title: severe chronic hepatitis C, male, C466


title: severe chronic hepatitis C, male, C322


title: pararectal_paracolonic_D3 [9287078048_H]

description:
D3
9287078048_H


title: Liver_D3 [9287078041_F]

description:
D3
9287078041_F


title: Jejunum_D3 [9287078041_D]

description:
D3
9287078041_D

value: GI

value: Jejunum


title: Colon_D3 [9287078041_C]

description:
D3
9287078041_C

value: SIV


title: severe chronic hepatitis C, female, C719

value: female


title: mesenteric_LN_D3 [9287078041_E]

description:
D3
9287078041_E


title: severe chronic hepatitis C, male, C115


title: Duodenum_D3 [9287078041_A]

description:
D3
9287078041_A

value: Duodenum


title: mild chronic hepatitis C, male, C437


title: severe chronic hepatitis C, female, C303


title: severe chronic hepatitis C, female, C289


title: severe chronic hepatitis C, female, C446


title: severe chronic hepatitis C, female, C477


title: severe chronic hepatitis C, male, C296


title: Jejunum_D3 [9287078038_K]

description:
D3
9287078038_K


title: mild chronic hepatitis C, male, C739


title: mesenteric_LN_D3 [9287078041_B]

description:
D3
9287078041_B


title: Duodenum_D3 [9287078038_B]

description:
D3
9287078038_B


title: mild chronic hepatitis C, male, C327


title: mild chronic hepatitis C, male, C481


title: severe chronic hepatitis C, female, C170


title: mild chronic hepatitis C, male, C557


title: Blood_D3 [9287078038_E]

description:
D3
9287078038_E


title: axillary_LN_D3 [9287078038_J]

description:
D3
9287078038_J


title: Colon_D3 [9287078038_I]

description:
D3
9287078038_I


title: Inguinal_LN_D3 [9287078038_F]

description:
D3
9287078038_F


title: severe chronic hepatitis C, female, C166


title: pararectal_paracolonic_D3 [9287078038_H]

description:
D3
9287078038_H


title: Inguinal_LN_D3 [9287078038_D]

description:
D3
9287078038_D


title: PBMC_pre_challenge_D3 [9287078038_C]

description:
D3
9287078038_C


title: Cervix_D3 [9287078038_G]

description:
D3
9287078038_G


title: severe chronic hepatitis C, female, C642


title: mild chronic hepatitis C, male, C224


title: Splenocytes_D3 [9287078036_L]

description:
D3
9287078036_L

value: Splenocytes


title: mild chronic hepatitis C, male, C203


title: mild chronic hepatitis C, male, C267


title: Liver_D3 [9287078036_K]

description:
D3
9287078036_K

value: Liver


title: mild chronic hepatitis C, female, C053


title: Thymus_D3 [9287078036_J]

description:
D3
9287078036_J

value: Thymus


title: pararectal_paracolonic_D3 [9287078036_C]

description:
D3
9287078036_C


title: mild chronic hepatitis C, female, C114


title: mild chronic hepatitis C, female, C315


title: mild chronic hepatitis C, female, C028


title: Mid_Vagina_D3 [9287078038_A]

description:
D3
9287078038_A


title: mild chronic hepatitis C, female, C237


title: Rectum_D3 [9287078036_D]

description:
D3
9287078036_D

value: Rectum


title: Cervix_D3 [9287078036_B]

description:
D3
9287078036_B

value: FRT


title: Rectum_D3 [9287078036_A]

description:
D3
9287078036_A


title: mild chronic hepatitis C, female, C521


title: Ileum_D3 [9287078036_F]

description:
D3
9287078036_F

value: Ileum


title: healthy donor, male, 9

value: not applicable


title: healthy donor, male, 6

value: male


title: PBMC_pre_challenge_D3 [9287078036_H]

description:
D3
9287078036_H


title: Tonsil_D3 [9287078036_G]

description:
D3
9287078036_G


title: mild chronic hepatitis C, female, C208


title: mild chronic hepatitis C, female, C113


title: Cecum_D3 [9287078036_E]

description:
D3
9287078036_E

value: Cecum


title: healthy donor, male, 8


title: Blood_D3 [9287078036_I]

description:
D3
9287078036_I


title: axillary_LN_D3 [9287078028_L]

description:
D3
9287078028_L


title: healthy donor, male, 7


title: genital_pelvic_LN_D3 [9287078028_K]

description:
D3
9287078028_K


title: healthy donor, male, 4


title: Lung_D3 [9287078028_J]

description:
D3
9287078028_J

value: Lung


title: healthy donor, male, 3


title: healthy donor, male, 1


title: healthy donor, female, 8


title: healthy donor, male, 5


title: healthy donor, female, 7


title: healthy donor, female, 10


title: genital_pelvic_LN_D3 [9287078028_H]

description:
D3
9287078028_H


title: Splenocytes_D3 [9287078028_I]

description:
D3
9287078028_I


title: Cecum_D3 [9287078028_D]

description:
D3
9287078028_D


title: Inguinal_LN_D3 [9287078028_E]

description:
D3
9287078028_E


title: Sp70

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: CGH-Agilent-10rpm : 4000.0 ng at 65 degree_C during 24 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing

organism: Ehrlichia ruminantium

label_protocol: CGH Agilent/bioprime

extract_protocol: Trizol

value: Elementary bodies (EB)

tag: amount in (µg)

tag: strain

value: attenuated Senegal


title: Bone_Marrow_D3 [9287078028_A]

description:
D3
9287078028_A


title: healthy donor, female, 6


title: pararectal_paracolonic_D3 [9287078028_G]

description:
D3
9287078028_G


title: PBMC_Pre_challenge_D3 [9287078028_B]

description:
D3
9287078028_B


title: Uterus_D3 [9287078026_L]

description:
D3
9287078026_L

value: Uterus


title: Ileum_D3 [9287078028_C]

description:
D3
9287078028_C


title: Tonsil_D3 [9287078026_J]

description:
D3
9287078026_J

value: Tonsil


title: healthy donor, female, 2


title: healthy donor, female, 4


title: Bone_Marrow_D3 [9287078028_F]

description:
D3
9287078028_F

value: SIV


title: healthy donor, female, 1

value: female


title: healthy donor, female, 3


title: Ileum_D3 [9287078026_I]

description:
D3
9287078026_I


title: Sp8b

value: virulent Senegal


title: ileocecal_LN_D3 [9287078026_D]

description:
D3
9287078026_D


title: Sp8a


title: Gp44

value: virulent gardel


title: Lung_D3 [9287078026_H]

description:
D3
9287078026_H


title: Bone_Marrow_D3 [9287078026_E]

description:
D3
9287078026_E


title: Sp77


title: Tonsil_D3 [9287078026_C]

description:
D3
9287078026_C


title: Duodenum_D3 [9287078026_F]

description:
D3
9287078026_F

value: Duodenum


title: Cecum_D3 [9287078026_A]

description:
D3
9287078026_A


title: Gp43


title: Gp243

value: attenuated Gardel


title: Gp251


title: Sp7b


title: Sp75


title: Splenocytes_D7 [9031313032_L]

description:
D7
9031313032_L

source_name: Subject: Monkey_5442

value: Splenocytes


title: Cecum_D7 [9031313032_E]

description:
D7
9031313032_E


title: ileocecal_LN_D3 [9287078026_B]

description:
D3
9287078026_B


title: Brain_Lymphocyte_D10 [9031313032_B]

description:
D10
9031313032_B

source_name: Subject: Monkey_5443


title: Gp38


title: pararectal_paracolonic_D10 [9031313032_I]

description:
D10
9031313032_I

source_name: Subject: Monkey_5441


title: Colon_D7 [9031313032_G]

description:
D7
9031313032_G

source_name: Subject: Monkey_5355

value: Colon


title: Gp238


title: Liver_D10 [9031313032_H]

description:
D10
9031313032_H

value: Liver


title: pararectal_paracolonic_D7 [9031313023_K]

description:
D7
9031313023_K

source_name: Subject: Monkey_5439


title: Cecum_D10 [9031313032_D]

description:
D10
9031313032_D


title: Duodenum_D10 [9031313032_A]

description:
D10
9031313032_A


title: Lung_D7 [9031313032_C]

description:
D7
9031313032_C


title: pararectal_paracolonic_D10 [9031313023_L]

description:
D10
9031313023_L

source_name: Subject: Monkey_5440


title: Bone_Marrow_D7 [9031313023_H]

description:
D7
9031313023_H


title: mesenteric_LN_D10 [9031313023_I]

description:
D10
9031313023_I

value: LN


title: ileocecal_LN_D10 [9031313023_J]

description:
D10
9031313023_J


title: Bone_Marrow_D7 [9031313023_G]

description:
D7
9031313023_G

source_name: Subject: Monkey_5438


title: Tonsil_D7 [9031313023_E]

description:
D7
9031313023_E


title: FK1-2

city: Chiayi

first: Shou-Tsung

last: Wang

address: No. 300, Syuefu Rd.

country: Taiwan

institute: National Chiayi University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Agilent G2505C scanner and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Balb/c_female_ketamine_20 wks

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

tag: strain background

value: Balb/c

tag: treated with

value: ketamine hydrochloride (100 mg/kg/day) for 20 wks

value: urinary bladders


title: Rectum_D7 [9031313023_B]

description:
D7
9031313023_B

value: Rectum


title: Lung_D10 [9031313023_F]

description:
D10
9031313023_F

value: Lung


title: pararectal_paracolonic_D7 [9031313023_C]

description:
D7
9031313023_C


title: FC2-2

source_name: Balb/c_female_saline control

value: normal saline


title: FC1-2


title: Mid_Vagina_D7 [9031313023_D]

description:
D7
9031313023_D

value: FRT


title: FK2-1


title: Mid_Vagina_D10 [9031313015_L]

description:
D10
9031313015_L

value: SIV


title: FC2-1

value: female


title: FK2-2


title: FC1-1


title: Inguinal_LN_D7 [9031313015_I]

description:
D7
9031313015_I


title: Jejunum_D7 [9031313023_A]

description:
D7
9031313023_A

value: GI

value: Jejunum


title: MK2-1

source_name: Balb/c_male_ketamine_20 wks

value: male


title: Brain_Lymphocyte_D10 [9031313015_J]

description:
D10
9031313015_J


title: genital_pelvic_LN_D7 [9031313015_K]

description:
D7
9031313015_K


title: Jejunum_D10 [9031313015_H]

description:
D10
9031313015_H


title: MK1-1


title: MK1-2


title: MK2-2


title: Colon_D7 [9031313015_E]

description:
D7
9031313015_E


title: MC2-2

source_name: Balb/c_male_saline control


title: FK1-1


title: MC1-1


title: MC2-1


title: axillary_LN_D7 [9031313015_G]

description:
D7
9031313015_G


title: Liver_D10 [9031313015_B]

description:
D10
9031313015_B


title: axillary_LN_D7 [9031313015_C]

description:
D7
9031313015_C


title: Cecum_D7 [9031313015_D]

description:
D7
9031313015_D

value: Cecum


title: Ileum_D7 [9031313015_F]

description:
D7
9031313015_F

value: Ileum


title: MC1-2


title: Splenocytes_D7 [9031313013_L]

description:
D7
9031313013_L

value: Splenocytes


title: axillary_LN_D10 [9031313013_K]

description:
D10
9031313013_K


title: Tonsil_D7 [9031313013_I]

description:
D7
9031313013_I

value: Tonsil


title: Liver_D7 [9031313013_J]

description:
D7
9031313013_J

value: Liver


title: Duodenum_D10 [9031313013_C]

description:
D10
9031313013_C

value: Duodenum


title: ileocecal_LN_D7 [9031313013_E]

description:
D7
9031313013_E


title: Thymus_D10 [9031313013_D]

description:
D10
9031313013_D

value: Thymus


title: Ileum_D7 [9031313015_A]

description:
D7
9031313015_A


title: Tonsil_D10 [9031313013_G]

description:
D10
9031313013_G


title: IND 8199 d42

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: monkey no. 8199

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. Arrays were normalized to the mean of trimmed positive non-flagged/non-control Reporters.

source_name: d42 post immunization

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA from whole blood was isolated by the PAXgene protocol (PreAnalytiX)

treatment_protocol: PAXgene tubes were used for whole blood sampling.

value: whole blood

tag: spectrotype

value: Indian


title: Tonsil_D7 [9031313012_K]

description:
D7
9031313012_K

tag: tissue


title: axillary_LN_D7 [9031313012_I]

description:
D7
9031313012_I

value: LN


title: Blood_D10 [9031313013_F]

description:
D10
9031313013_F

value: Blood


title: Thymus_D7 [9031313013_B]

description:
D7
9031313013_B