title: LB_AG_M_V_D3_R3

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Agria cactus. 16 days DEVT flies were collected.

value: virgin

value: whole organism


title: LB_AG_M_V_D2_R1

status: Public on Aug 21 2015

type: RNA

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

country: USA

institute: University of Nevada

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Agria cactus. 15 days DEVT flies were collected.

hyb_protocol: Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.

scan_protocol: Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Drosophila mojavensis

source_name: Drosophila mojavensis LB09

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA.  Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: population

value: Las Bocas, Sonora

tag: host diet

value: Agria

tag: gender

value: male

tag: group

tag: length of egg to adult development time

value: 15 day DEVT

tag: tissue


title: LB_AG_M_V_D3_R2

value: 16 day DEVT


title: PP_AG_F_V_D1_R3

description: This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin females were raised on fermented Agria cactus. 14 days DEVT flies were collected.

source_name: Drosophila mojavensis PP08

value: Punta Prieta, Baja California

value: female

value: 14 day DEVT


title: LB_AG_M_V_D4_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Agria cactus. 17 days DEVT flies were collected.

value: 17 day DEVT


title: LB_AG_M_V_D2_R2


title: LB_AG_M_V_D3_R1


title: LB_AG_M_V_D3_R4


title: LB_AG_M_V_D2_R3


title: LB_AG_M_V_D2_R4


title: PDAC2

city: London

first: Jenny

last: Cook

address: John Vane Science Centre, Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

description: Gene expression data from CD14++ CD16- classical monocytes from peripheral blood of patient with pancreatic ductal adenocarcinoma

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human 2.0 plus U133 Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneScan 3000 7G.

data_processing: The data were analyzed with R-lab using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Homo sapiens

source_name: NAIVEPANC2_315_CD14++CD16- monocytes

label_protocol: cDNA product was biotinylated using the NuGen Encore biotin module and then prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA extraction was performed using Qiagen micro extraction kit according to the manufacturer's instructions. RNA was amplified using the NuGen Ovation pico WTA 3300 kit.

treatment_protocol: Peripheral blood was collected in EDTA vacutainers, blood was subject to red blood cell lysis and the classical CD14++ CD16- monocytes isolated using fluorescence assisted cell sorting (FACS).

tag: disease state

value: Locally advanced, unresectable Pancreatic Ductal Adenocarcinoma (PDAC) prior to any chemotherapy treatment

tag: treatment

tag: age

tag: Sex

value: f

value: monocytes


title: LB_AG_M_V_D1_R3

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin males were raised on fermented Agria cactus. 14 days DEVT flies were collected.


title: HEALTHY2

description: Gene expression data from CD14++ CD16- classical monocytes from peripheral blood healthy volunteer

source_name: HEALTHY2_47_CD14++CD16- monocytes

value: Healthy

value: m


title: LB_AG_M_V_D1_R1

value: virgin

value: whole organism


title: LB_AG_M_M_D2_R3

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated males were raised on fermented Agria cactus. 15 days DEVT flies were collected.

value: Wild-type

value: normal

value: mated


title: LB_AG_M_V_D1_R2

value: Las Bocas, Sonora

value: Agria

value: male


title: LB_AG_M_M_D1_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated males were raised on fermented Agria cactus. 14 days DEVT flies were collected.


title: LB_AG_F_V_D3_R4

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Agria cactus. 16 days DEVT flies were collected.

value: 16 day DEVT


title: LB_AG_M_M_D2_R1

value: 15 day DEVT


title: LB_AG_M_M_D2_R2


title: LB_AG_F_V_D3_R3

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Agria cactus. 15 days DEVT flies were collected.

value: female


title: LB_AG_M_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated males were raised on fermented Agria cactus. 16 days DEVT flies were collected.


title: LB_AG_F_V_D2_R5


title: LB_AG_F_V_D1_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised on fermented Agria cactus. 14 days DEVT flies were collected.

value: 14 day DEVT


title: LB_AG_F_V_D2_R3


title: LB_AG_F_V_D3_R1


title: LB_AG_F_V_D2_R1


title: LB_AG_F_V_D2_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These virgin females were raised onfermented Agria cactus. 15 days DEVT flies were collected.


title: LB_AG_F_V_D3_R2


title: LB_AG_F_V_D2_R4


title: LB_AG_F_M_D1_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated females were raised on fermented Agria cactus. 14 day DEVT flies were collected.


title: LB_AG_F_M_D2_R2

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated females were raised on fermented Agria cactus. 15 days DEVT flies were collected.


title: LB_AG_F_V_D1_R1


title: LB_AG_F_M_D3_R1

description: This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These mated females were raised on fermented Agria cactus. 16 days DEVT flies were collected.


title: LB_AG_F_M_D2_R1


title: LB_AG_F_M_D3_R2


title: ColXN617K HZ_3

city: Parkville

first: Trevor

middle: L

last: Cameron

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

description: replicate 3

hyb_protocol: All aRNA samples were hybridized to MouseWG-6_V2 whole genome microarrays (Illumina) in strict accordance with the manufacturer’s specifications

scan_protocol: Microarrays were scanned using an Illumina iScan Reader with Illumina Control Software v3.3.28 at 0.53µm resolution

data_processing: Microarray data were analyzed using the package Limma from the statistical language R. Background correction and quantile normalization were performed using the necq function. Probes that did not have above background expression in at least three samples were removed from the analysis after normalization. Probes that were classified as bador no matchfrom illuminaMousev2.db were also removed.

organism: Mus musculus

source_name: Tibial growth plate hypertrophic zone, ColXN617K HZ

label_protocol: Amplified RNA samples (4ug) were labelled with BIO-ULS (Kreatech), according to the manufacturer’s specifications.

growth_protocol: Col10a1 p.Asn617Lys mice (ColXN617K) were crossed with mice in which Xbp1 mRNA is inactivated by the Cre recombinase-mediated deletion of exon 2 in Col2a1-expressing cells (Xbp1CartΔEx2) to generate the compound mutant, Col10a1 p.Asn617Lys/Xbp1CartΔEx2 (C/X). These mice were viable, fertile, and bred normally and were house under pathogen-free conditions. Hind legs were harvested from ColXN617K, Xbp1CartΔEx2, C/X, and wildtype mice at 2 weeks of age.

extract_protocol: Microdissected tissues were collected in TRIzol reagent (Invitrogen) for RNA extraction and purification, which was performed following the manufacturer’s specifications.  All total RNA samples were subjected to two rounds of linear amplification using the ampULSe RNA Amplification and Labeling Kit with Biotin ULS (Kreatech), following the manufacturer’s protocol. 100-150ng of first-round amplified aRNA was used as template for each second round amplification. Following total RNA extraction and amplification, the yield, purity, and integrity of all RNA samples were validated by capillary electrophoresis with a TapeStation 2200 (Agilent Technologies), using a High Sensitivity R6K ScreenTape (Agilent Technologies), according to the manufacturer’s specifications.

treatment_protocol: Dissected limbs were embedded in Tissue-Tek OCT (Sakura Fine Technical), snap-frozen on liquid nitrogen, and stored at -80°C. 10um cryosections were prepared using a cryostat (Leica CM1850), mounted on RNAse-free SuperFrost Plus slides (Biolab Scientific), and stored at -80°C. Immediately prior to microdissection, tissues were fixed in 70% ethanol, rinsed in RNAse-free water, and dehydrated in 70%, 95%, and 100% ethanol for 30 seconds each.  They were then air-dried and the tissue of interest was microdissected using an ophthalmic scalpel (Feather) fixed to the scanning xy-object guide.  Light microscopy was performed using an Eclipse 80i light microscope (Nikon).

tag: strain

value: mixed background

tag: genotype/variation

value: ColXN617K HZ

value: 2 weeks

value: Growth plate hypertrophic zone


title: PB_Control_2

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

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).

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)

value: Control

value: blood


title: C/X HZ_3

description: replicate 2

source_name: Tibial growth plate hypertrophic zone, C/X HZ

value: C/X HZ


title: PB_Intervention_4

source_name: Peripheral blood, intervention

value: Intervention


title: PB_Control_3


title: PB_Control_1


title: PB_Intervention_1


title: PB_Control_4


title: PB_Intervention_2


title: Xbp1CartΔEx2 HZ_3

description: replicate 1

source_name: Tibial growth plate hypertrophic zone, Xbp1CartΔEx2 HZ

value: Xbp1Cart{delta}Ex2 HZ


title: LB_AG_F_M_D1_R1

value: Wild-type

value: normal

value: mated

value: whole organism


title: Wt HZ_2

description: replicate 3

source_name: Tibial growth plate hypertrophic zone, Wt HZ

value: Wt HZ


title: Xbp1CartΔEx2 HZ_2

description: replicate 1


title: ColXN617K HZ_1

description: replicate 2


title: C/X HZ_1

description: replicate 2


title: Wt HZ_1

description: replicate 1


title: Xbp1CartΔEx2 HZ_1

description: replicate 3


title: PB_Intervention_3


title: ColXN617K HZ_2

description: replicate 2


title: Wt HZ_3

description: replicate 3


title: Early stage lung squamous cell carcinoma sample EU50_Sty

status: Public on Aug 20 2015

type: genomic

city: San Sebastian

first: Angel

last: Rubio

state: GUIPÚZCOA

address: Paseo Mikeletegi, Nº 48

department: Bioinformatics

country: Spain

institute: CEIT

description: Hybridized to 250K_Sty

hyb_protocol: Labeled samples were applied to microarrays and hybridized during 18 h at 49 0C in the hybridization oven

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

data_processing:
Copy number normalization, to produce log2ratios for individual SNPs was performed using ACNE and NSA R packages. Tumor purity was estimated for each patient using GPHMM software. Circular Binary Segmentation was applied using DNAcopy R package on log2ratio data. Segmented log2ratio was adjusted by estimated tumor purity.
Log2ratio segments may fall within the same gene for a given sample. To solve this problem, a single value was assigned to each gene. A weighted median was performed to the log2ratio values of the segments within the analyzed gene, where the weights correspond to the length of the corresponding segments within the gene.
The Ensembl 54 reference gene set was used (http://may2009.archive.ensembl.org/)
Segmented log2ratio adjusted by tumor purity and summarized by gene (according to Ensembl 54 gene annotation)

label: Biotin

molecule: genomic DNA

label_protocol: 500 ng of DNA were separately digested with Nsp I and Sty I restriction enzymes. After adaptors ligation, DNA was amplified in a GeneAmp PCR System 9700 using the TITANIUM DNA Amplification Kit. Following amplification, DNA was fragmented with DNAse I and subsequently biotin end-labeled.

extract_protocol: DNA was extrated from a minimum area of 20 mm2 from microdissected frozen tissue sections (10 μm) using the QIAamp DNA Micro Kit

value: Lung

tag: cell type

value: Lung squamous cell carcinoma

value: Male

tag: tumor stage

value: IB


title: Early stage lung squamous cell carcinoma sample Eu44_Sty

description: Hybridized to 250K_Sty

value: IA


title: Early stage lung squamous cell carcinoma sample Eu23_Sty

description: Hybridized to 250K_Sty

value: IIA


title: Early stage lung squamous cell carcinoma sample VB57_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample VB121_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu27_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu22_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample VB108_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample VB65_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu21_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu93_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample VB118_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample VB78_Sty

description: Hybridized to 250K_Sty

source_name: Early stage lung adenocarcinoma sample

value: Lung adenocarcinoma


title: C/X HZ_2

description: replicate 1

value: mixed background

value: 2 weeks

value: Growth plate hypertrophic zone


title: Early stage lung adenocarcinoma sample VB95_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu85_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu15_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample BN02_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu36_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample VB93_Sty

description: Hybridized to 250K_Sty

value: Female


title: Early stage lung squamous cell carcinoma sample Eu51_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu68_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu120_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu16_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu13_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample EU88_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample Eu94_Sty

description: Hybridized to 250K_Sty


title: Early stage lung squamous cell carcinoma sample Eu63_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample VB71_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample Eu41_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample Eu47_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample VB90_Sty

description: Hybridized to 250K_Sty


title: Ckit positive (Ckit+) cells at time T2 on OP9-Dll4, biological rep2

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2p_D (kit+D) R2

hyb_protocol: biotinylated cDNA was hybridized to Affymetrix GeneChip® Mouse Gene 1.0 ST arrays

scan_protocol: GenChips were scanned using the GCS3000 Affymetrix Platform

data_processing: Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy” by RMA normalization.

source_name: Ckit+ CD31+CD45- cell population from AGM regions obtained from E11.5 mouse embryos after 2h incubation on OP9-Dll4

label_protocol: 5ng of total RNA from each sample was amplified using the Ovation™  Pico WTA System (NuGEN Technologies, San Carlos, CA) and sense transcript cDNA (ST-cDNA) was generated using the WT-Ovation™ Exon Module (NuGEN Technologies). After, ST-cDNA was fragmented and labelled with the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies)

extract_protocol: Total RNA from the different populations was extracted using Qiagen RNeasy Midi Kit (Qiagen). following manufacturer’s instructions.

treatment_protocol: Sorted CD31+CD45-Ter119- cells were incubated for 2 hours on OP9-Jag1 and OP9-Dll4 stromal cells, harvested and sorted again into CD31+CD45-ckit+(kit+J; kit+D) and CD31+CD45-ckit- (kit-J; kit-D).Incubation was performed in Iscoves medium  (Gibco, Life Technologies) supplemented with 10% inactivated FBS, 10ng/ml IL3, 10ng/ml SCF, 20ng/ml IL6, 10ng/ml IGF-1, 10ng/ml FGF-β, 10ng/ml VEGF, 2U/ml Erythropoietin, 4.5x10-4 M monothioglycerol,  10μg/ml Heparin and 50ng/ml bovine pituitary extract.

tag: source tissue

value: E11.5 mouse AGM pool

tag: cell population

value: Ckit+ CD31+CD45-


title: Ckit positive (Ckit+) cells at time T2 on OP9-Jag1, biological rep1

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2p_J (kit+J) R1

source_name: Ckit+ CD31+CD45- cell population from AGM regions obtained from E11.5 mouse embryos after 2h incubation on OP9-Jag1


title: Early stage lung adenocarcinoma sample Eu60_Sty

description: Hybridized to 250K_Sty


title: Ckit positive (Ckit+) cells at time T2 on OP9-Dll4, biological rep1

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2p_D (kit+D) R1


title: Ckit positive (Ckit+) cells at time T2 on OP9-Jag1, biological rep3

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2p_J (kit+J) R3


title: Early stage lung adenocarcinoma sample Eu001_Sty

description: Hybridized to 250K_Sty


title: Ckit positive (Ckit+) cells at time T2 on OP9-Dll4, biological rep3

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T2p_D (kit+D) R3


title: Ckit negative (Ckit-) cells at time T2 on OP9-Dll4, biological rep2

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T2n_D (kit-D) R2

source_name: Ckit- CD31+CD45- cell population from AGM regions obtained from E11.5 mouse embryos after 2h incubation on OP9-Dll4

value: Ckit- CD31+CD45-


title: Ckit positive (Ckit+) cells at time T2 on OP9-Jag1, biological rep2

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2p_J (kit+J) R2


title: Ckit negative (Ckit-) cells at time T2 on OP9-Jag1, biological rep2

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2n_J (kit-J) R2

source_name: Ckit- CD31+CD45- cell population from AGM regions obtained from E11.5 mouse embryos after 2h incubation on OP9-Jag1


title: Ckit negative (Ckit-) cells at time T2 on OP9-Jag1, biological rep1

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2n_J (kit-J) R1


title: Early stage lung squamous cell carcinoma sample Eu58_Sty

description: Hybridized to 250K_Sty


title: Ckit negative (Ckit-) cells at time T2 on OP9-Dll4, biological rep3

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T2n_D (kit-D) R3


title: Ckit positive (Ckit+) cells at time T0, biological rep1

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T0p_R1

source_name: Ckti+ CD31+CD45- cell from AGM regions obtained from E11.5 mouse embryos

value: Ckti+ CD31+CD45-


title: Early stage lung adenocarcinoma sample BN05_Sty

description: Hybridized to 250K_Sty


title: Ckit negative (Ckit-) cells at time T0, biological rep1

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T0n_R1

source_name: Ckit- CD31+CD45- cell population from AGM regions obtained from E11.5 mouse embryos


title: Early stage lung adenocarcinoma sample Eu004_Sty

description: Hybridized to 250K_Sty


title: Ckit negative (Ckit-) cells at time T0, biological rep3

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T0n_R3


title: Ckit positive (Ckit+) cells at time T0, biological rep2

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T0p_R2


title: Early stage lung adenocarcinoma sample BN03_Sty

description: Hybridized to 250K_Sty


title: Ckit negative (Ckit-) cells at time T0, biological rep2

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T0n_R2


title: Early stage lung adenocarcinoma sample BN04_Sty

description: Hybridized to 250K_Sty


title: Early stage lung adenocarcinoma sample Eu118_Sty

description: Hybridized to 250K_Sty


title: Ckit negative (Ckit-) cells at time T2 on OP9-Dll4, biological rep1

description:
Gene expression data from total RNA of Ckit- cell from AGM regions obtained from E11.5 embryos by dissection
T2n_D (kit-D) R1


title: Early Stage Non Small Lung Cancer patient TTran_251469365052

hyb_protocol: Hybridization of genomic DNA onto the Agilent 244K CGH (Agilent Technologies) was performed according to Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

data_processing:
Normalized and background corrected intensities were used to calculate log2 ratios for each probe.
Circular Binary Segmentation was applied using DNAcopy R package on log2ratio data. Segmented log2ratio was adjusted by estimated tumor purity. Tumor purity was provided for each patient.
Log2ratio segments may fall within the same gene for a given sample. To solve this problem, a single value was assigned to each gene. A weighted median was performed to the log2ratio values of the segments within the analyzed gene, where the weights correspond to the length of the corresponding segments within the gene.
The Ensembl 54 reference gene set was used (http://may2009.archive.ensembl.org/)
Segmented log2ratio adjusted by tumor purity and summarized by gene (according to Ensembl 54 gene annotation)

source_name: Early stage lung squamous cell carcinoma sample

label_protocol: DNA concentration was assessed using the Quant-iT PicoGreen dsDNA Assay kit (Life Technologies). 2.5 ug of tumor DNA (A260/A280ratio of 1.8–2.0) was labelled with Cy5 (red). The normal reference (Human Genomic DNA, Female, Promega, Inc., Cat #G1521). was labeled with Cy3 (green). Labelled DNA was hybridized on Agilent Human Genome CGH Microarray 244A (high-definition 244K array).

extract_protocol: Snap-Frozen tumor tissue were processed on cryostat to generate multiple 5-micron thick shavings. After trimming excess OCT the shavings are homogenized and further processed using the Qiagen QIAamp DNA Mini kit (Qiagen Inc.) according to the manufacturer’s instructions.


title: Early Stage Non Small Lung Cancer patient TTran_251469365033

source_name: Human Genomic DNA, Female, Promega, Inc., Cat #G1521


title: Early Stage Non Small Lung Cancer patient TTran_251469365366


title: Early Stage Non Small Lung Cancer patient TTran_251469364536

value: IIB


title: Early Stage Non Small Lung Cancer patient TTran_251469365113


title: Early Stage Non Small Lung Cancer patient TTran_251469365034


title: Early Stage Non Small Lung Cancer patient TTran_251469365147


title: Early Stage Non Small Lung Cancer patient TTran_251469365158


title: Early Stage Non Small Lung Cancer patient TTran_251469372843


title: Early Stage Non Small Lung Cancer patient TTran_251469365114


title: Early Stage Non Small Lung Cancer patient TTran_251469372512


title: Early Stage Non Small Lung Cancer patient TTran_251469372868


title: Early Stage Non Small Lung Cancer patient TTran_251469372871


title: Early Stage Non Small Lung Cancer patient TTran_251469365365


title: Early Stage Non Small Lung Cancer patient TTran_251469365031


title: Early Stage Non Small Lung Cancer patient TTran_251469365161


title: Early Stage Non Small Lung Cancer patient TTran_251469365138


title: Early Stage Non Small Lung Cancer patient TTran_251469365254


title: Early Stage Non Small Lung Cancer patient TTran_251469364561


title: Early Stage Non Small Lung Cancer patient TTran_251469365051


title: Ckit positive (Ckit+) cells at time T0, biological rep3

description:
Gene expression data from total RNA of Ckit+ cell from AGM regions obtained from E11.5 embryos by dissection
T0p_R3


title: Early Stage Non Small Lung Cancer patient TTran_251469364873


title: Early Stage Non Small Lung Cancer patient TTran_251469372841


title: Early Stage Non Small Lung Cancer patient TTran_251469364562


title: Early Stage Non Small Lung Cancer patient TTran_251469372645


title: Early Stage Non Small Lung Cancer patient TTran_251469365170


title: Early Stage Non Small Lung Cancer patient TTran_251469364778


title: Early Stage Non Small Lung Cancer patient TTran_251469365171


title: Early Stage Non Small Lung Cancer patient TTran_251469364519


title: Early Stage Non Small Lung Cancer patient TTran_251469365112


title: Early Stage Non Small Lung Cancer patient TTran_251469364779


title: Early Stage Non Small Lung Cancer patient TTran_251469365111


title: Early Stage Non Small Lung Cancer patient TTran_251469365169


title: Early Stage Non Small Lung Cancer patient TTran_251469364518


title: Early Stage Non Small Lung Cancer patient TTran_251469364888


title: Early Stage Non Small Lung Cancer patient TTran_251469364517


title: Early Stage Non Small Lung Cancer patient TTran_251469365442


title: Early Stage Non Small Lung Cancer patient TTran_251469365177


title: Early Stage Non Small Lung Cancer patient TTran_251469365179


title: Early Stage Non Small Lung Cancer patient TTran_251469365117


title: Early Stage Non Small Lung Cancer patient TTran_251469365036


title: Early Stage Non Small Lung Cancer patient TTran_251469365213


title: Early Stage Non Small Lung Cancer patient TTran_251469365443


title: Early Stage Non Small Lung Cancer patient TTran_251469365176


title: Early Stage Non Small Lung Cancer patient TTran_251469365049


title: Early Stage Non Small Lung Cancer patient TTran_251469365120


title: Early Stage Non Small Lung Cancer patient TTran_251469365070


title: Early Stage Non Small Lung Cancer patient TTran_251469365210


title: Early Stage Non Small Lung Cancer patient TTran_251469364557


title: Early Stage Non Small Lung Cancer patient TTran_251469365125


title: NRCWE-033.28.162 Sample 70

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Colombine Dr

country: Canada

institute: Health Canada

hyb_protocol: Equal amount (300 ng) of labelled cRNA from each experimental sample was hybridized to Agilent Sureprint G3 Mouse GE 4x44K microarrays (agilent Technologies Inc., Mississuaga, ON, Canada) at 65°C for 17 hours in the Agilent SureHyb Hybridization chamber.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Mouse lung tissue, middle dose, day 28

label_protocol: Agilent Linear Amplification Kit (Agilent Technologies Inc., Mississauga, ON, Canada) was used to synthesize cDNA and labelled cRNA from 200 ng of total RNA derived from each individual mouse lungs and commercially available Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada). Cyanine-labelled cRNA was in vitro transcribed using T7 RNA polymerase and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). Experimental samples were labelled with Cyanine-5 and the UMRR was labelled with Cyanine-3.

extract_protocol: In brief, a small frozen section of lung tissue was homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) using the Retsch Mixer MM 400. RNA was isolated using chloroform, precipitated using isopropyl alcohol and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). All RNA showed high integrity with a A260/280 ratio between 2.0 and 2.2 and RNA integrity number above 7.0.

treatment_protocol: each mouse received 54, 162 or 486 µg of sanding dusts of paint consisting of TiO2NPs or only the vehicle via single intratracheal instillation. Mice were anaesthetised and intratracheally instilled with particle suspensions as described previously (Saber et al 2012, Particle and Fiber Toxicology). Whole lung tissues were collected 24 h and 28 d post exposure, flash frozen in liquid nitrogen and stored at -80°C until the analysis.

tag: sample id

tag: genetic background

value: lung

tag: dose

value: middle dose

tag: time

value: day 28

tag: sample type


title: Early Stage Non Small Lung Cancer patient TTran_251469365083

value: Lung

tag: gender


title: Early Stage Non Small Lung Cancer patient TTran_251469365253

tag: tissue

value: Male


title: Early Stage Non Small Lung Cancer patient TTran_251469365106

value: IB


title: Early Stage Non Small Lung Cancer patient TTran_251469364567


title: Early Stage Non Small Lung Cancer patient TTran_251469365244

value: IIA


title: NRCWE-032.28.54 Sample 67

source_name: Mouse lung tissue, low dose, day 28

value: low dose

source_name: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Early Stage Non Small Lung Cancer patient TTran_251469365122

value: Lung adenocarcinoma


title: NRCWE-032.28.486 Sample 68

source_name: Mouse lung tissue, high dose, day 28

value: high dose

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Early Stage Non Small Lung Cancer patient TTran_251469365129

value: Female


title: Early Stage Non Small Lung Cancer patient TTran_251469364875

value: IA


title: NRCWE-033.1.486 Sample 69

source_name: Mouse lung tissue, high dose, day 1

value: day 1


title: Early Stage Non Small Lung Cancer patient TTran_251469364558


title: NRCWE-033.1.162 Sample 60

source_name: Mouse lung tissue, middle dose, day 1


title: NRCWE-033.28.54 Sample 63


title: Early Stage Non Small Lung Cancer patient TTran_251469365134


title: NRCWE-033.1.54 Sample 65

source_name: Mouse lung tissue, low dose, day 1


title: NRCWE-032.28.162 Sample 62


title: NRCWE-033.28.486 Sample 54


title: Early Stage Non Small Lung Cancer patient TTran_251469365356


title: NRCWE-033.28.162 Sample 59


title: Early Stage Non Small Lung Cancer patient TTran_251469365041


title: NRCWE-032.1.162 Sample 56


title: NRCWE-033.1.162 Sample 64


title: NRCWE-032.28.162 Sample 66


title: Early Stage Non Small Lung Cancer patient TTran_251469365133


title: NRCWE-033.1.486 Sample 55


title: NRCWE-032.28.54 Sample 61


title: NRCWE-032.28.486 Sample 53


title: NRCWE-033.1.54 Sample 51


title: NRCWE-032.28.54 Sample 50


title: NRCWE-032.1.486 Sample 52


title: Early Stage Non Small Lung Cancer patient TTran_251469364570


title: NRCWE-033.1.54 Sample 58


title: NRCWE-033.28.54 Sample 48


title: NRCWE-032.1.54 Sample 49


title: NRCWE-032.1.162 Sample 46


title: NRCWE-033.1.486 Sample 44


title: NRCWE-032.1.54 Sample 57


title: NRCWE-032.28.486 Sample 41


title: Donor 2 Tx.8hrs.3

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: Dendritic cell was treated by Tx for 8 Hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were median normalized

source_name: Dendritic cell

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: RNA was isolated with the RNeasyPLUS kit (Qiagen) according to the manufacture’s instructions

value: Dendritic cell

value: Tx

tag: time (hours)


title: NRCWE-033.28.162 Sample 38

tag: treatment


title: Early Stage Non Small Lung Cancer patient TTran_251469365175

source_name: Early stage lung adenocarcinoma sample

tag: age


title: NRCWE-033.28.486 Sample 42


title: NRCWE-033.1.162 Sample 45


title: Donor 2 Tx.8hrs.1


title: NRCWE-032.1.486 Sample 43


title: Control.28.0 Sample 40

source_name: Negative Control

value: Negative Control

value: Control


title: NRCWE-033.28.54 Sample 37

value: lung


title: NRCWE-032.28.162 Sample 47

value: middle dose

value: day 28


title: Donor 2 Tx.8hrs.2


title: NRCWE-032.1.54 Sample 34


title: Donor 2 Tx.7hrs.1

description: Dendritic cell was treated by Tx for 7 Hours


title: NRCWE-033.28.486 Sample 39


title: Donor 2 Tx.7hrs.3


title: NRCWE-032.1.486 Sample 35


title: NRCWE-032.28.486 Sample 31


title: NRCWE-032.1.162 Sample 36


title: Donor 2 Tx.6hrs.3

description: Dendritic cell was treated by Tx for 6 Hours


title: NRCWE-032.28.162 Sample 30


title: Donor 2 Tx.6hrs.2


title: Donor 2 Tx.7hrs.2


title: Donor 2 Tx.6hrs.1


title: Control.28.0 Sample 32


title: Control.1.0 Sample 33


title: NRCWE-032.28.54 Sample 29


title: NRCWE-033.28.54 Sample 21


title: NRCWE-033.1.54 Sample 28


title: Control.1.0 Sample 27


title: Donor 2 Tx.5hrs.2

description: Dendritic cell was treated by Tx for 5 Hours


title: NRCWE-033.1.162 Sample 26


title: Control.28.0 Sample 23


title: NRCWE-033.28.162 Sample 22


title: Donor 2 Tx.3.3hrs.3

description: Dendritic cell was treated by Tx for 3.3 Hours


title: Donor 2 Tx.5hrs.3


title: Donor 2 Tx.4hrs.2

description: Dendritic cell was treated by Tx for 4 Hours


title: NRCWE-032.1.486 Sample 20


title: NRCWE-033.1.486 Sample 25


title: Donor 2 Tx.3.3hrs.2


title: Donor 2 Tx.5hrs.1


title: Donor 2 Tx.3.3hrs.1


title: NRCWE-032.1.162 Sample 19


title: Donor 2 Tx.4hrs.3


title: NRCWE-032.1.54 Sample 17


title: Donor 2 Tx.2.7hrs.3

description: Dendritic cell was treated by Tx for 2.7 Hours


title: Donor 2 Tx.4hrs.1


title: Donor 2 Tx.2hrs.3

description: Dendritic cell was treated by Tx for 2 Hours


title: Donor 2 Tx.2.7hrs.1


title: Control.28.0 Sample 16


title: Control.1.0 Sample 18


title: Donor 2 Tx.2.7hrs.2


title: NRCWE-033.28.486 Sample 24


title: NRCWE-033.28.54 Sample 8


title: NRCWE-032.28.54 Sample 14


title: Donor 2 NC.6hrs.1

description: Dendritic cell was treated by NC for 6 Hours

value: NC


title: NRCWE-033.1.486 Sample 10


title: Donor 2 NC.6hrs.3


title: Donor 2 Tx.2hrs.2


title: NRCWE-033.1.162 Sample 11


title: Donor 2 NC.5hrs.1

description: Dendritic cell was treated by NC for 5 Hours


title: Donor 2 NC.8hrs.1

description: Dendritic cell was treated by NC for 8 Hours


title: NRCWE-033.28.486 Sample 7


title: Donor 2 NC.7hrs.2

description: Dendritic cell was treated by NC for 7 Hours


title: Donor 2 NC.5hrs.2


title: Donor 2 NC.8hrs.3


title: Donor 2 NC.5hrs.3


title: Control.28.0 Sample 6


title: NRCWE-032.1.54 Sample 3


title: Donor 2 NC.6hrs.2


title: NRCWE-033.28.162 Sample 5


title: Donor 2 Tx.2hrs.1


title: NRCWE-032.1.162 Sample 2


title: NRCWE-033.1.54 Sample 12


title: NRCWE-032.28.486 Sample 15


title: NRCWE-032.1.486 Sample 4


title: NRCWE-032.28.162 Sample 13


title: Control.1.0 Sample 9


title: Donor 2 NC.7hrs.1


title: Donor 2 NC.4hrs.3

description: Dendritic cell was treated by NC for 4 Hours


title: Donor 2 NC.7hrs.3


title: Donor 2 NC.8hrs.2


title: NRCWE-030.1.162 Sample 69

source_name: Mouse lung tisue, high dose, day1

treatment_protocol: each mouse received 18, 54, or 162 µg of TiO2NPs or only the vehicle via single intratracheal instillation. Mice were anaesthetised and intratracheally instilled with particle suspensions as described previously (Saber et al 2012, Particle and Fiber Toxicology). Whole lung tissues were collected 24 h and 28 d post exposure, flash frozen in liquid nitrogen and stored at -80°C until the analysis.


title: NRCWE-030.1.162 Sample 63


title: NRCWE-030.1.18 Sample 67

source_name: Mouse lung tisue, low dose, day1


title: Donor 2 NC.3.3hrs.2

description: Dendritic cell was treated by NC for 3.3 Hours


title: NRCWE-025.28.162 Sample 66

source_name: Mouse lung tisue, high dose, day28


title: Donor 2 NC.3.3hrs.1


title: Donor 2 NC.2hrs.3

description: Dendritic cell was treated by NC for 2 Hours


title: NRCWE-030.1.18 Sample 56


title: NRCWE-025.28.18 Sample 65

source_name: Mouse lung tisue, low dose, day28


title: Control.1.0 Sample 1


title: Donor 2 Cal.8hrs.3

description: Dendritic cell was treated by Cal for 8 Hours

value: Cal


title: Donor 2 NC.2.7hrs.3

description: Dendritic cell was treated by NC for 2.7 Hours


title: NRCWE-025.28.54 Sample 64

source_name: Mouse lung tisue, middle dose, day28


title: NRCWE-025.1.162 Sample 68


title: Donor 2 NC.4hrs.2


title: Donor 2 NC.3.3hrs.3


title: NRCWE-030.1.18 Sample 61


title: NRCWE-025.1.162 Sample 60


title: Donor 2 NC.2.7hrs.1


title: Donor 2 NC.4hrs.1


title: Donor 2 NC.2hrs.1


title: Donor 2 NC.2.7hrs.2


title: NRCWE-025.1.18 Sample 62


title: Control .1.0 Sample 58

source_name: Negative control

value: Negative control

value: control


title: Donor 2 NC.2hrs.2


title: NRCWE-030.1.162 Sample 59


title: Donor 2 Cal.8hrs.1


title: Donor 2 Cal.7hrs.2

description: Dendritic cell was treated by Cal for 7 Hours


title: NRCWE-025.28.54 Sample 55


title: NRCWE-025.28.18 Sample 54

value: low dose


title: NRCWE-030.1.54 Sample 57

source_name: Mouse lung tisue, middle dose, day1


title: Donor 2 Cal.7hrs.1


title: 30 min Streptococcus gordonii and hyphal Candida alicans interaction, biological replicate one (BR1)

city: Buffalo

first: M

middle: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Periodontics and Endodontics

institute: University at Buffalo

description: Pellet of Streptococcus gordonii and CSB  incubated for 30 minutes at 36ºC with 5% CO2 versus a mixed pellet of Streptococcus gordonii and hyphal Candida alicans, incubated together for 30 minutes at 36ºC with 5% CO2

hyb_protocol: cDNA probes were hybridized to aminosilane-coated glass slides spotted with unique 70-mers representing each open reading frame from the S. gordonii strain CH1 genome sequence (Genbank number CP000725.1) in replicates of six (obtained from the Pathogen Functional Genomics Resource Center; NIDCR Oral Microbe Microarray Initiative; GPL10584); each slide contained a total of 500 Arabidopsis thaliana 70-mers as controls. Slides were blocked during prehybridization at 42°C in blocking buffer (5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7.4), 0.1% w/v SDS, 1% w/v bovine serum albumen (BSA), then washed successively with water and isopropanol before drying via centrifugation prior to hybridization.  To accommodate potential increases in cDNA quantity based upon contributions from the C. albicans hyphae 2-fold more cDNA from the interaction samples was mixed with DL1-CSB samples for each interaction comparison. To account for biases during the labeling process, flip-dyes, in which the fluorescent labeling is reversed for each sample, were used.  Cy3 labeled DL1-CSB cDNA was combined with Cy 5-labeled DL1-C. albicans cDNA in appropriate ratios; similarly Cy5-labled DL1-CSB and Cy3 labeled DL1-C. albicans cDNAs were combined. The dye-labeled cDNA mixtures were dried, resuspended in 50 µl of hybridization buffer (40% v/v formamide, 5x SSC, 0.1% SDS, 0.6 ug/uL Salmon Sperm DNA), heated at 95°C for 10 min, placed on ice, and individual mixtures added to each microarray slide under a Lifterslip (Erie Scientific Company, Portsmouth, NH, USA). Each slide was incubated at 42°C for 16 h in a sealed hybridization chamber (Corning Life Sciences, Tewksbury, MA, USA), then washed successively in 0.1% w/v SDS-2x SSC, 0.1% SDS-0.1x SSC, and 0.1x SSC and dried by centrifugation.

scan_protocol: The Axon 4200A (Axon Instruments, Foster City, CA, USA) was used to obtain digital images of the microarrays.

data_processing: Data were analyzed using the TM4 Microarray Software Suite, consisting of Spotfinder, Midas, and MeV (http://www.tm4.org/). The fluorescence signals from the flip-dye hybridizations were measured using Spotfinder. Normalization and regularization of the data were performed using Midas (Lowess normalization, block mode, smooth parameter of 0.33, Cy3 reference; standard deviation regularization, block mode, Cy3 reference; flip-dye consistency checking and combination, using the data trim option of the standard deviation mode and keeping all data within 2.0 standard deviations; replicate spots were averaged to be used in the determination of the final ratio for each spot). Using MeV, with 100 permutations and a P value cutoff of 0.05 the final expression ratios were generated and used to determine the fold change for hybridization of each probe; fold changes were ranked from the greatest increase to the greatest decrease. Experimental cDNA probes from DL1 cells incubated with hyphae that hybridized to the oligonucleotide spots with average fold changes 1.6-times greater than or 1.6-times less than fold changes of DL1-CSB controls in two biologically independent experiments were considered to be potentially up- or down- regulated, respectively.

organism: Streptococcus gordonii

source_name: Streptococcus gordonii, alone, versus Streptococcus gordonii and hyphal Candida alicans

label_protocol: cDNA was reverse transcribed using Superscript III (Life Technologies, Grand Island, NY, USA), end-labeled via amino-allyl-labeling (Life Technologies, Grand Island, NY, USA) and Cye-dye coupled (GE Healthcare/Amersham, Piscataway, NY, USA) to make microarray probes as previously described. Probes were purified over QIAgen PCR purification columns (QIAgen) to remove excess dye before use.

growth_protocol: Streptococcus gordonii strain Challis DL1 cells were grown to mid-log phase (approximately 108 cells/ml) in TY (5g/L Tryptone, 5 g/L yeast extract, 23 mM K2HPO4, pH 7.5) medium plus 5g/liter glucose (TY-G) under stationary conditions at 36ºC, aerobically with 5% CO2. Candida albicans strain UB1843 (SC5314) cells were grown overnight in YPD medium (1% w/v yeast extract, 2% w/v mycological peptone, 2% w/v glucose) shaking at 225 rpm, 37ºC aerobically for 16 hours to OD600 ~2.6. The resulting C. albicans cells were harvested by centrifugation (1,370 xg for 5 minutes), washed once in complete Salts-Biotin (CSB) nutrient-limited medium (7.5 mM Ammonium sulfate, 15 mM KH2PO4, 0.1 mM MgSO4•7H2O, 3.6µg/ml Biotin, 0.05 mg/ml CaCl2, 0.5% glucose, pH 6.5), resuspended in fresh CSB to OD600 ~ 1.0 (approximately 107 cells/ml) and incubated at 37oC aerobically with 225 rpm shaking for 16 hours to induce starvation. Candida hyphae formation was then induced by the addition of 1/10 volume 10% w/v aqueous glucose to the C. albicans culture. Incubation continued at 37ºC, 225 rpm for 3 hr and the final OD and pH were measured.

extract_protocol: RNA was prepared from the pelleted DL1-CSB and DL1-hyphae cell mixtures with a FastPrep120 Instrument (MP Biomedicals, Santa Ana, CA, USA) and RNAPro Blue RNA Extraction Kit (MP Biomedicals) for prokaryotic cells according to the manufacturer's directions. The extracted RNA was digested with DNase (Roche Applied Science, Indianapolis, IN, USA) and purified with QIAgen RNA mini spin columns (QIAgen, Germantown, MD, USA) according to the manufacturer's directions. RNA integrity was confirmed by comparison of the ratios of absorbance at 260/280 nm and 260/230 nm as quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA).

treatment_protocol: Equal volumes of the DL1 cultures and C. albicans hyphae, or final pH-adjusted fresh CSB medium as a control, were mixed, centrifuged (3,800 xg for 5 minutes) and the resulting loose pellets were incubated for 30 minutes at 36ºC aerobically in 5% CO2 without shaking to allow the S. gordonii cells to interact with the C. albicans hyphae in close proximity.


title: 30 min Streptococcus gordonii and hyphal Candida alicans interaction, biological replicate two (BR2)


title: NRCWE-030.1.54 Sample 51


title: Donor 2 Cal.8hrs.2


title: NRCWE-030.28.18 Sample 52


title: Donor 2 Cal.6hrs.3

description: Dendritic cell was treated by Cal for 6 Hours


title: NRCWE-030.28.54 Sample 53


title: Donor 2 Cal.7hrs.3


title: Donor 2 Cal.5hrs.1

description: Dendritic cell was treated by Cal for 5 Hours


title: Donor 2 Cal.6hrs.1


title: Donor 2 Cal.5hrs.3


title: Donor 2 Cal.5hrs.2


title: NRCWE-025.1.162 Sample 48

value: high dose


title: NRCWE-025.1.54 Sample 49

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: NRCWE-030.1.162 Sample 50


title: NRCWE-025.28.162 Sample 46


title: Donor 2 Cal.4hrs.2

description: Dendritic cell was treated by Cal for 4 Hours


title: Donor 2 Cal.4hrs.3


title: NRCWE-030.28.162 Sample 47


title: Donor 2 Cal.6hrs.2


title: Donor 2 Cal.3.3hrs.3

description: Dendritic cell was treated by Cal for 3.3 Hours


title: Donor 2 Cal.3.3hrs.1


title: Donor 2 Cal.2.7hrs.2

description: Dendritic cell was treated by Cal for 2.7 Hours


title: NRCWE-030.28.54 Sample 40


title: NRCWE-025.28.54 Sample 43


title: NRCWE-030.1.18 Sample 39


title: Donor 2 Cal.2hrs.1

description: Dendritic cell was treated by Cal for 2 Hours


title: NRCWE-030.28.162 Sample 41


title: NRCWE-025.28.162 Sample 42


title: Donor 2 Brevig.8hrs.2

description: Dendritic cell was treated by Brevig for 8 Hours

value: Brevig


title: Donor 2 Brevig.8hrs.3


title: Donor 2 Cal.2hrs.3


title: Donor 2 Cal.3.3hrs.2


title: Donor 2 Cal.2.7hrs.3


title: Donor 2 Cal.2.7hrs.1


title: NRCWE-025.1.18 Sample 37


title: NRCWE-030.28.162 Sample 33


title: control .28.0 Sample 32


title: Donor 2 Brevig.7hrs.3

description: Dendritic cell was treated by Brevig for 7 Hours


title: NRCWE-025.1.54 Sample 38


title: NRCWE-030.1.54 Sample 36


title: Donor 2 Cal.2hrs.2


title: NRCWE-030.28.18 Sample 34


title: NRCWE-030.28.18 Sample 45


title: NRCWE-030.28.54 Sample 35


title: Pst DC3000-0h

city: Hangzhou

first: Dayong

last: Li

state: Zhejiang

address: 866 Yuhangtang Rd

department: Institute of Biotechnology

country: China

institute: Zhejiang University

description:
control
SAMPLE 11

data_processing: Bio-Rad CFX manager. The relative expression levels were calculated using the 2-ΔΔCT method. For the normalization it uses the housekeeping gene: SlActin (accession number AB199316). Target gene signals normalized to housekeeping genes, using the 2-ΔΔCT method.

label: SYBR Green

organism: Solanum lycopersicum

source_name: cv. Suhong 2003

label_protocol: SYBR Premix Ex TaqTM kits (TaKaRa, Dalian, China)

growth_protocol: Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1.

extract_protocol: Total RNA from different organs was extracted using TRIzol reagent (Invitrogen, Shanghai, China) and treated with RNase-free DNase (TaKaRa, Dalian, China) to erase any genomic DNA in the RNA samples according to the manufactures’ instructions.

treatment_protocol: For analysis of gene expression, 4-week-old tomato plants were treated by foliar spraying with 100 μM methyl jasmonate (MeJA), 100 μM 1-amino cyclopropane-1-carboxylic acid (ACC), 100 μM SA or 0.1% ethanol as a control and samples were collected at indicated time points after treatment. For analysis of gene expression in response to pathogen infection, whole plant inoculation assays for B. cinerea (spore density of 1×105 spores/mL) and vacuum infiltrated inoculation assays for Pst DC3000 along with corresponding mock inoculation controls were performed.

value: various


title: Pst DC3000-24h

description:
test
SAMPLE 12


title: Pst DC3000-48h

description:
test
SAMPLE 13


title: Bc-48h

description:
test
SAMPLE 10


title: Bc-24h

description:
test
SAMPLE 9


title: Donor 2 Cal.4hrs.1


title: ACC-24h

description:
test
SAMPLE 7


title: ACC-12h

description:
test
SAMPLE 6


title: Bc-0h

description:
control
SAMPLE 8


title: SA-24h

description:
test
SAMPLE 3


title: SA-12h

description:
test
SAMPLE 2


title: SA-0h

description:
control
SAMPLE 1


title: MeJA-12h

description:
test
SAMPLE 4


title: Donor 2 Brevig.7hrs.2


title: NRCWE-025.1.18 Sample 30

source_name: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Donor 2 Brevig.7hrs.1


title: control .28.0 Sample 27


title: Donor 2 Brevig.8hrs.1


title: NRCWE-025.1.54 Sample 31


title: Donor 2 Brevig.6hrs.3

description: Dendritic cell was treated by Brevig for 6 Hours


title: NRCWE-025.28.162 Sample 29


title: MeJA-24h

description:
test
SAMPLE 5


title: NRCWE-025.28.54 Sample 26


title: Donor 2 Brevig.5hrs.2

description: Dendritic cell was treated by Brevig for 5 Hours


title: Donor 2 Brevig.6hrs.1


title: NRCWE-030.1.54 Sample 25


title: NRCWE-025.28.18 Sample 28


title: NRCWE-025.28.18 Sample 44


title: Donor 2 Brevig.5hrs.3


title: NRCWE-030.1.18 Sample 22


title: NRCWE-030.1.162 Sample 23


title: NRCWE-030.28.54 Sample 19


title: NRCWE-030.28.18 Sample 20


title: Donor 2 Brevig.4hrs.2

description: Dendritic cell was treated by Brevig for 4 Hours


title: Donor 2 Brevig.2.7hrs.3

description: Dendritic cell was treated by Brevig for 2.7 Hours


title: control .1.0 Sample 24


title: Donor 2 Brevig.3.3hrs.2

description: Dendritic cell was treated by Brevig for 3.3 Hours


title: control .28.0 Sample 18


title: Donor 2 Brevig.3.3hrs.3


title: Donor 2 Brevig.3.3hrs.1


title: Donor 2 Brevig.4hrs.3


title: NRCWE-025.1.54 Sample 16


title: Donor 2 Brevig.4hrs.1


title: Donor 2 Brevig.2.7hrs.1


title: NRCWE-030.28.162 Sample 21


title: Donor 2 Brevig.2.7hrs.2


title: Donor 2 Brevig.2hrs.3

description: Dendritic cell was treated by Brevig for 2 Hours


title: Donor 2 Brevig.2hrs.2


title: control .1.0 Sample 17


title: Donor 2 Brevig.2hrs.1


title: control .28.0 Sample 13


title: Donor 2 Brevig.6hrs.2


title: Donor 2 AlaF.8hrs.3

description: Dendritic cell was treated by AlaF for 8 Hours

value: AlaF


title: NRCWE-025.28.54 Sample 11


title: control .1.0 Sample 10


title: NRCWE-030.1.54 Sample 9


title: NRCWE-025.28.18 Sample 12


title: Donor 2 Brevig.5hrs.1

value: Dendritic cell


title: NRCWE-025.1.18 Sample 15


title: NRCWE-030.28.54 Sample 6


title: Donor 2 AlaF.6hrs.3

description: Dendritic cell was treated by AlaF for 6 Hours


title: Donor 2 AlaF.8hrs.2


title: NRCWE-025.1.162 Sample 14


title: Donor 2 AlaF.5hrs.3

description: Dendritic cell was treated by AlaF for 5 Hours


title: Donor 2 AlaF.6hrs.2


title: NRCWE-030.28.18 Sample 5


title: Donor 2 AlaF.8hrs.1


title: NRCWE-025.1.18 Sample 4


title: NRCWE-030.28.162 Sample 8


title: Donor 2 AlaF.4hrs.2

description: Dendritic cell was treated by AlaF for 4 Hours


title: control .28.0 Sample 7


title: Donor 2 AlaF.5hrs.2


title: Donor 2 AlaF.6hrs.1


title: TiO2 NRCWE 001 Umodificeret.28.18 Sample 67

source_name: mouse lung tissue, low dose, day 28

value: TiO2 NRCWE 001


title: Donor 2 AlaF.3.3hrs.3

description: Dendritic cell was treated by AlaF for 3.3 Hours


title: TiO2 NRCWE 002 Modificeret.1.162 Sample 69

source_name: mouse lung tissue, high dose, day 1

value: day 1

value: TiO2 NRCWE 002


title: TiO2 NRCWE 001 Umodificeret.28.162 Sample 68

source_name: mouse lung tissue, high dose, day 28

value: lung


title: NRCWE-025.1.162 Sample 1


title: Donor 2 AlaF.3.3hrs.1


title: NRCWE-025.1.54 Sample 2

value: middle dose


title: Donor 2 AlaF.4hrs.1


title: Donor 2 AlaF.3.3hrs.2


title: Donor 2 AlaF.4hrs.3


title: TiO2 NRCWE 002 Modificeret.1.162 Sample 65


title: Donor 2 AlaF.2hrs.3

description: Dendritic cell was treated by AlaF for 2 Hours


title: TiO2 NRCWE 002 Modificeret.1.162 Sample 66


title: Negativ control (H2O).1.0 Sample 64

source_name: negative

value: negative

value: Negativ control


title: TiO2 NRCWE 002 Modificeret.1.18 Sample 63

source_name: mouse lung tissue, low dose, day 1


title: Donor 2 AlaF.5hrs.1

source_name: Dendritic cell


title: TiO2 NRCWE 002 Modificeret.1.54 Sample 62

source_name: mouse lung tissue, middle dose, day 1


title: Donor 2 AlaF.2.7hrs.2

description: Dendritic cell was treated by AlaF for 2.7 Hours


title: Donor 2 AlaF.2.7hrs.1


title: Donor 2 AlaF.2.7hrs.3


title: Donor 2 AlaF.2hrs.1


title: Donor 2 Control.0hrs.2

description: Dendritic cell Control

value: Control


title: TiO2 NRCWE 001 Umodificeret.28.162 Sample 59

value: day 28


title: TiO2 NRCWE 001 Umodificeret.28.54 Sample 60

source_name: mouse lung tissue, middle dose, day 28


title: TiO2 NRCWE 002 Modificeret.1.54 Sample 61


title: TiO2 NRCWE 002 Modificeret.1.162 Sample 58


title: TiO2 NRCWE 001 Umodificeret.28.162 Sample 57


title: Donor 1 Tx.7hrs.3

description: Dendritic cell was treated by Tx for 7 Hours

value: Tx


title: control .1.0 Sample 3

value: Negative control

value: control


title: Donor 2 Control.0hrs.3

description: Dendritic cell Control


title: Donor 1 Tx.8hrs.1

description: Dendritic cell was treated by Tx for 8 Hours


title: Donor 2 Control.0hrs.1

description: Dendritic cell Control


title: Donor 1 Tx.7hrs.1


title: TiO2 NRCWE 002 Modificeret.1.18 Sample 51

value: low dose

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: TiO2 NRCWE 002 Modificeret.28.54 Sample 56


title: Donor 1 Tx.8hrs.3


title: Donor 1 Tx.6hrs.2

description: Dendritic cell was treated by Tx for 6 Hours


title: TiO2 NRCWE 002 Modificeret.28.162 Sample 54

value: high dose


title: Donor 1 Tx.7hrs.2


title: Donor 1 Tx.6hrs.3


title: Donor 2 AlaF.2hrs.2

value: AlaF


title: TiO2 NRCWE 001 Umodificeret.1.54 Sample 53


title: TiO2 NRCWE 002 Modificeret.28.18 Sample 48


title: TiO2 NRCWE 001 Umodificeret.1.162 Sample 50


title: Donor 1 Tx.6hrs.1

value: Dendritic cell


title: TiO2 NRCWE 001 Umodificeret.28.18 Sample 49

value: TiO2 NRCWE 001


title: TiO2 NRCWE 001 Umodificeret.28.54 Sample 55


title: TiO2 NRCWE 002 Modificeret.28.54 Sample 47


title: TiO2 NRCWE 001 Umodificeret.28.18 Sample 41


title: Donor 1 Tx.4hrs.1

description: Dendritic cell was treated by Tx for 4 Hours


title: Donor 1 Tx.3.3hrs.2

description: Dendritic cell was treated by Tx for 3.3 Hours


title: Donor 1 Tx.4hrs.3


title: Donor 1 Tx.4hrs.2


title: TiO2 NRCWE 002 Modificeret.1.18 Sample 44

value: day 1


title: Donor 1 Tx.5hrs.2

description: Dendritic cell was treated by Tx for 5 Hours


title: TiO2 NRCWE 001 Umodificeret.1.162 Sample 38


title: Donor 1 Tx.3.3hrs.1


title: Donor 1 Tx.2.7hrs.2

description: Dendritic cell was treated by Tx for 2.7 Hours


title: TiO2 NRCWE 002 Modificeret.28.18 Sample 36

value: TiO2 NRCWE 002


title: Donor 1 Tx.3.3hrs.3


title: TiO2 NRCWE 002 Modificeret.1.54 Sample 42

value: lung


title: Donor 1 Tx.5hrs.1


title: TiO2 NRCWE 001 Umodificeret.28.162 Sample 39


title: Donor 1 Tx.5hrs.3


title: Donor 1 Tx.2hrs.3

description: Dendritic cell was treated by Tx for 2 Hours


title: TiO2 NRCWE 001 Umodificeret.1.18 Sample 35


title: TiO2 NRCWE 002 Modificeret.28.162 Sample 37


title: Donor 1 Tx.2.7hrs.3


title: Donor 1 Tx.2.7hrs.1


title: TiO2 NRCWE 001 Umodificeret.1.54 Sample 45

value: middle dose


title: TiO2 NRCWE 001 Umodificeret.28.54 Sample 46


title: TiO2 NRCWE 002 Modificeret.1.18 Sample 40


title: Negativ control (H2O).28.0 Sample 34

value: negative


title: Donor 1 Tx.2hrs.2


title: TiO2 NRCWE 002 Modificeret.28.18 Sample 33


title: Donor 1 Tx.2hrs.1


title: TiO2 NRCWE 002 Modificeret.28.162 Sample 31


title: TiO2 NRCWE 002 Modificeret.28.54 Sample 32


title: TiO2 NRCWE 001 Umodificeret.1.18 Sample 43


title: TiO2 NRCWE 002 Modificeret.1.54 Sample 28


title: Negativ control (H2O).1.0 Sample 30

value: Negativ control


title: Donor 1 NC.7hrs.2

description: Dendritic cell was treated by NC for 7 Hours

value: NC


title: Donor 1 NC.7hrs.3


title: TiO2 NRCWE 002 Modificeret.1.18 Sample 29


title: Donor 1 NC.8hrs.1

description: Dendritic cell was treated by NC for 8 Hours


title: Negativ control (H2O).28.0 Sample 26


title: TiO2 NRCWE 002 Modificeret.1.162 Sample 27


title: Donor 1 NC.8hrs.2


title: TiO2 NRCWE 001 Umodificeret.28.54 Sample 25

value: day 28


title: Donor 1 NC.7hrs.1


title: Donor 1 NC.6hrs.2

description: Dendritic cell was treated by NC for 6 Hours


title: Donor 1 NC.6hrs.1


title: Donor 1 NC.6hrs.3


title: TiO2 NRCWE 001 Umodificeret.28.18 Sample 24


title: TiO2 NRCWE 001 Umodificeret.28.18 Sample 23


title: Donor 1 NC.8hrs.3


title: TiO2 NRCWE 001 Umodificeret.28.162 Sample 22


title: Donor 1 NC.5hrs.1

description: Dendritic cell was treated by NC for 5 Hours


title: TiO2 NRCWE 001 Umodificeret.28.54 Sample 20


title: Donor 1 NC.5hrs.2


title: Donor 1 Tx.8hrs.2

value: Tx


title: TiO2 NRCWE 001 Umodificeret.1.162 Sample 18


title: TiO2 NRCWE 002 Modificeret.1.54 Sample 52


title: Donor 1 NC.4hrs.3

description: Dendritic cell was treated by NC for 4 Hours


title: TiO2 NRCWE 001 Umodificeret.1.54 Sample 19


title: Negativ control (H2O).1.0 Sample 17


title: Donor 1 NC.4hrs.1


title: TiO2 NRCWE 002 Modificeret.28.54 Sample 15


title: TiO2 NRCWE 002 Modificeret.28.162 Sample 14


title: Donor 1 NC.3.3hrs.3

description: Dendritic cell was treated by NC for 3.3 Hours


title: Donor 1 NC.5hrs.3


title: TiO2 NRCWE 001 Umodificeret.1.18 Sample 16


title: Donor 1 NC.3.3hrs.2


title: Donor 1 NC.2.7hrs.3

description: Dendritic cell was treated by NC for 2.7 Hours


title: Donor 1 NC.4hrs.2


title: TiO2 NRCWE 001 Umodificeret.1.162 Sample 11


title: Donor 1 NC.3.3hrs.1


title: Donor 1 NC.2.7hrs.1


title: Negativ control (H2O).1.0 Sample 12


title: Donor 1 NC.2hrs.2

description: Dendritic cell was treated by NC for 2 Hours


title: Donor 1 NC.2.7hrs.2


title: TiO2 NRCWE 001 Umodificeret.1.54 Sample 10


title: Donor 1 NC.2hrs.3


title: Negativ control (H2O).28.0 Sample 21


title: TiO2 NRCWE 002 Modificeret.28.18 Sample 8


title: TiO2 NRCWE 002 Modificeret.28.162 Sample 7


title: TiO2 NRCWE 002 Modificeret.28.18 Sample 13


title: TiO2 NRCWE 001 Umodificeret.1.18 Sample 9


title: Donor 1 NC.2hrs.1


title: TiO2 NRCWE 001 Umodificeret.1.18 Sample 4


title: Donor 1 Cal.8hrs.3

description: Dendritic cell was treated by Cal for 8 Hours

value: Cal


title: Negativ control (H2O).28.0 Sample 6


title: Donor 1 Cal.8hrs.1


title: Donor 1 Cal.7hrs.3

description: Dendritic cell was treated by Cal for 7 Hours


title: TiO2 NRCWE 002 Modificeret.28.54 Sample 5


title: Donor 1 Cal.8hrs.2


title: TiO2 NRCWE 001 Umodificeret.1.54 Sample 3


title: Donor 1 Cal.7hrs.2


title: Donor 1 Cal.7hrs.1


title: Donor 1 Cal.6hrs.3

description: Dendritic cell was treated by Cal for 6 Hours


title: Negativ control (H2O).1.0 Sample 1


title: TiO2 NRCWE 001 Umodificeret.1.162 Sample 2


title: Indoor-NanoTiO2 28d-H4

source_name: Mouse lung tissue, 486 ug, day 28

treatment_protocol: Each mouse received 54, 162 or 486 µg of sanding dusts of paints consisting of TiO2NPs or only the vehicle via single intratracheal instillation. Mice were anaesthetised and intratracheally instilled with particle suspensions as described previously (Saber et al 2012, Particle and Fiber Toxicology). Whole lung tissues were collected 24 h and 28 d post exposure, flash frozen in liquid nitrogen and stored at -80°C until the analysis.


title: Indoor-NanoTiO2 28d-M3

source_name: Mouse lung tissue, 162 ug, day 28


title: Donor 1 Cal.5hrs.2

description: Dendritic cell was treated by Cal for 5 Hours


title: Donor 1 Cal.5hrs.1


title: Donor 1 Cal.6hrs.1


title: Indoor-NanoTiO2 28d-L2

source_name: Mouse lung tissue, 54 ug, day 28


title: Control 28d-C2

value: Control


title: Indoor-R 1d-M1

source_name: Mouse lung tissue, 162 ug, day 1

value: Indoor-R


title: Indoor-R 1d-L4

source_name: Mouse lung tissue, 54 ug, day 1

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Donor 1 Cal.6hrs.2


title: Donor 1 Cal.5hrs.3


title: Donor 1 Cal.4hrs.1

description: Dendritic cell was treated by Cal for 4 Hours


title: Donor 1 Cal.3.3hrs.2

description: Dendritic cell was treated by Cal for 3.3 Hours


title: Indoor-NanoTiO2 28d-M1


title: Indoor-R 1d-H4

source_name: Mouse lung tissue, 486 ug, day 1


title: Donor 1 Cal.3.3hrs.3


title: Indoor-NanoTiO2 1d-M1


title: Donor 1 Cal.2.7hrs.2

description: Dendritic cell was treated by Cal for 2.7 Hours


title: Donor 1 Cal.4hrs.2


title: Indoor-NanoTiO2 1d-H1


title: Indoor-R 1d-L1


title: Donor 1 Cal.4hrs.3


title: Indoor-R 28d-M1


title: Indoor-R 28d-L5


title: Donor 1 Cal.2.7hrs.3


title: Donor 1 Cal.2hrs.3

description: Dendritic cell was treated by Cal for 2 Hours


title: Donor 1 Cal.3.3hrs.1


title: Donor 1 Cal.2hrs.2


title: Donor 1 Cal.2.7hrs.1


title: Control 1d-C4

source_name: Negative control


title: Donor 1 Brevig.8hrs.2

description: Dendritic cell was treated by Brevig for 8 Hours

value: Brevig


title: Donor 1 Brevig.7hrs.3

description: Dendritic cell was treated by Brevig for 7 Hours


title: Donor 1 Cal.2hrs.1


title: Indoor-NanoTiO2 1d-L1


title: Indoor-NanoTiO2 1d-L4


title: Donor 1 Brevig.7hrs.1


title: Donor 1 Brevig.8hrs.3


title: Indoor-R 1d-L5


title: Donor 1 Brevig.6hrs.2

description: Dendritic cell was treated by Brevig for 6 Hours


title: Indoor-R 28d-M2


title: Indoor-NanoTiO2 28d-M4


title: Indoor-NanoTiO2 28d-L4


title: Indoor-R 1d-M3


title: Indoor-NanoTiO2 28d-H2


title: Donor 1 Brevig.6hrs.1


title: Indoor-R 28d-H1


title: Donor 1 Brevig.5hrs.2

description: Dendritic cell was treated by Brevig for 5 Hours


title: Donor 1 Brevig.6hrs.3


title: Indoor-R 28d-H4


title: Indoor-NanoTiO2 1d-M5


title: Indoor-R 28d-L3


title: Donor 1 Brevig.5hrs.3


title: Donor 1 Brevig.7hrs.2


title: Donor 1 Brevig.8hrs.1


title: Flower

description: SAMPLE 4

data_processing:
Bio-Rad CFX manager. The relative expression levels were calculated using the 2-ΔΔCT method. For the normalization it uses the housekeeping gene: SlActin (accession number AB199316). Target gene signals normalized to housekeeping genes, using the 2-ΔΔCT method.
Fold Change = test/control ratios. One of the gene which has the lowest expression was treated as a control.

source_name: Flower

growth_protocol: Tomato (Solanum lycopersicum) cv. Suhong 2003 were reared in growth chambers at 24 ± 1 °C with a photoperiod of 14 h light/10 h dark and light intensity of 200 μE m2 s-1. The roots, stem,leaves,  flower, and fruits were collected from flowering plants for tissue expression analysis.

tag: cultivar

value: cv. Suhong 2003

value: Flower


title: Indoor-R 28d-H2

source_name: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: Stem

description: SAMPLE 2

source_name: Stem

value: Stem


title: Root

description: SAMPLE 1

source_name: Root

value: Root


title: Fruit

description: SAMPLE 5

source_name: Fruit

value: Fruit


title: Leave

description: SAMPLE 3

source_name: Leave

value: Leave


title: Indoor-R 1d-H2

value: lung


title: Donor 1 Brevig.4hrs.2

description: Dendritic cell was treated by Brevig for 4 Hours

value: Dendritic cell


title: Donor 1 Brevig.4hrs.1


title: Indoor-R 28d-L1


title: Donor 1 Brevig.5hrs.1


title: Donor 1 Brevig.3.3hrs.2

description: Dendritic cell was treated by Brevig for 3.3 Hours


title: Indoor-NanoTiO2 28d-H5


title: Donor 1 Brevig.3.3hrs.3


title: Donor 1 Brevig.3.3hrs.1


title: Donor 1 Brevig.2.7hrs.1

description: Dendritic cell was treated by Brevig for 2.7 Hours


title: Indoor-NanoTiO2 28d-M2


title: Indoor-R 1d-L3


title: Indoor-NanoTiO2 1d-H2


title: Indoor-NanoTiO2 1d-L5


title: Donor 1 Brevig.4hrs.3


title: Donor 1 Brevig.2.7hrs.3


title: Indoor-NanoTiO2 1d-H3


title: Donor 1 Brevig.2hrs.2

description: Dendritic cell was treated by Brevig for 2 Hours


title: Indoor-NanoTiO2 1d-M4


title: Donor 1 Brevig.2hrs.3


title: Donor 1 AlaF.8hrs.3

description: Dendritic cell was treated by AlaF for 8 Hours

value: AlaF


title: Indoor-R 28d-L4


title: Donor 1 AlaF.8hrs.2


title: Indoor-R 1d-M5


title: Donor 1 Brevig.2.7hrs.2


title: Indoor-NanoTiO2 28d-H1


title: Indoor-NanoTiO2 28d-L5


title: Donor 1 AlaF.8hrs.1


title: Donor 1 AlaF.6hrs.2

description: Dendritic cell was treated by AlaF for 6 Hours


title: Indoor-R 28d-M3


title: Indoor-R 1d-M2


title: Control 28d-C5


title: Indoor-NanoTiO2 28d-L1


title: Indoor-R 1d-L2


title: Indoor-R 1d-H3


title: Indoor-R 1d-H1


title: Donor 1 AlaF.5hrs.3

description: Dendritic cell was treated by AlaF for 5 Hours


title: Donor 1 AlaF.6hrs.1


title: Donor 1 AlaF.5hrs.1


title: Donor 1 AlaF.4hrs.3

description: Dendritic cell was treated by AlaF for 4 Hours


title: Control 1d-C5


title: Donor 1 AlaF.3.3hrs.3

description: Dendritic cell was treated by AlaF for 3.3 Hours


title: Indoor-R 28d-M4


title: Donor 1 AlaF.6hrs.3


title: Control 28d-C3


title: Donor 1 AlaF.4hrs.2


title: Indoor-R 28d-H5


title: Donor 1 AlaF.4hrs.1


title: Control 1d-C2


title: Donor 1 AlaF.3.3hrs.2


title: Indoor-NanoTiO2 1d-H5


title: Indoor-NanoTiO2 1d-L3


title: male SD rat_pulmonary arterial_4generation_hypoxia+quercetin_rep3

city: wuhan

first: he

middle: yuan

last: zhou

address: Huazhong University of Science and Technology,

institute: Tongji Hospital of Tongji Medical College

description: Gene expression after male SD rat  pulmonary arterial smooth muscle cell treatment with hypoxia and quercetin

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 9.5.3 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 10.0 (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: pulmonary arterial smooth muscle cell

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: cells were plated on 25 cm2 cell culture flasks and incubated in a 37 °C, 5% CO2 humidified incubator Hypoxic conditions for PASMCs were achieved by placing cells in an airtight chamber (Billups-Rothberg) with a gas mixture containing 1% O2, 5% CO2. The control plates were placed in a normoxic incubator at 37°C. PASMCs seeded on 6-well plates were induced with serum deprivation by incubating cells in DMEM-F12 without serum for 24 h. The cells were then treated with quercetin(Sigma-Aldrich, China) or DMSO (0.1%) in DMEM-F12 containing 10% FBS for 24 h.

tag: strain

value: SD

value: male

value: pulmonary arterial

tag: generation

value: hypoxia+quercetin


title: Indoor-R 28d-L2


title: Donor 1 AlaF.3.3hrs.1

source_name: Dendritic cell

tag: cell type


title: Donor 1 AlaF.2.7hrs.3

description: Dendritic cell was treated by AlaF for 2.7 Hours


title: Donor 1 AlaF.2.7hrs.2


title: Donor 1 AlaF.2.7hrs.1


title: Control 28d-C1

value: Control


title: Indoor-R 28d-M5

value: Indoor-R


title: Indoor-NanoTiO2 1d-M3

value: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)


title: male SD rat_pulmonary arterial_4generation_hypoxia+quercetin_rep2


title: Control 28d-C4


title: male SD rat_pulmonary arterial_4generation_hypoxia+quercetin_rep1


title: Indoor-NanoTiO2 28d-M5


title: Indoor-R 28d-H3


title: male SD rat_pulmonary arterial_4generation_hypoxia_rep3

description: Gene expression after male SD rat  pulmonary arterial smooth muscle cell in hypoxia

value: hypoxia


title: Donor 1 Control.0hrs.3

description: Dendritic cell Control


title: male SD rat_pulmonary arterial_4generation_hypoxia_rep1


title: Donor 1 AlaF.2hrs.1

description: Dendritic cell was treated by AlaF for 2 Hours


title: Donor 1 AlaF.2hrs.3


title: male SD rat_pulmonary arterial_4generation_hypoxia_rep2


title: Donor 1 AlaF.2hrs.2


title: Microvesicles derived from and 24-month-old Fisher344 rats MSC -2

city: Nanjing

first: Yan

last: Wang

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: 24-month-old Fisher344 rats MSC

label_protocol: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: BM-MSCs were extracted from 3-month-old and 24-month-old Fisher344 rats,The isolated primary BM-MSCs were cultured in complete medium (Cyagen Bioscience Inc., USA). After the cells were passaged to P3,Cells were starved overnight in serum-free medium supplemented with 0.5% BSA (Sigma, USA) prior to collection of MVs.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs.

treatment_protocol: Cell debris was removed from the supernatant after centrifugation at 2,000g for 20 min. The supernatant was collected and centrifuged at 100,000g at 4°C for 1 h using a high-speed refrigerated centrifuge (HITACHI CP100WX, Japan).

value: Bone Marrow Mesenchymal Stem Cell-derived Microvesicles


title: Indoor-NanoTiO2 28d-L3


title: Microvesicles derived from and 24-month-old Fisher344 rats MSC -3


title: Microvesicles derived from and 24-month-old Fisher344 rats MSC -1


title: Indoor-NanoTiO2 28d-H3


title: male SD rat_pulmonary arterial_4generation_normoxia_rep2

description: Gene expression after male SD rat  pulmonary arterial smooth muscle cell in normoxia

value: normoxia


title: Microvesicles derived from 3-month-old Fisher344 rats MSC -3

source_name: 3-month-old Fisher344 rats MSC


title: Microvesicles derived from 3-month-old Fisher344 rats MSC -2


title: male SD rat_pulmonary arterial_4generation_normoxia_rep3


title: Microvesicles derived from 3-month-old Fisher344 rats MSC -1


title: Arid1a d/d 3

city: Grand Rapids

first: Jae-Wook

last: Jeong

address: 333 Bostwick Avenue NE

department: Department of Obstetrics, Gynecology & Reproductive Biology

institute: Michigan State University

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

source_name: uteri of Arid1a d/d at E3.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect intact 3.5 dpc mice

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

tag: genotype

value: Arid1a (d/d)

value: uterus

value: Female

tag: developmental stage

value: E3.5 dpc


title: Donor 1 Control.0hrs.2

description: Dendritic cell Control


title: Arid1a d/d 2


title: male SD rat_pulmonary arterial_4generation_normoxia_rep1


title: Indoor-R 1d-H5

value: lung


title: Indoor-R 1d-M4


title: Arid1a d/d 1


title: Control 1d-C1


title: Control 1d-C3


title: Arid1a f/f 2

source_name: uteri of Arid1a f/f at E3.5

value: Arid1a (f/f)


title: Arid1a f/f 3


title: Donor 1 Brevig.2hrs.1

value: Brevig

value: Dendritic cell


title: Donor 1 Control.0hrs.1

description: Dendritic cell Control


title: Indoor-NanoTiO2 1d-M2


title: Indoor-NanoTiO2 1d-L2


title: Infected, anti-IL17RA, biological rep2-4

city: San Francisco

first: Antony

last: Symons

address: 1120 Veterans Boulevard

department: Inflammation TA

institute: Amgen Inc.

description:
mdr s2 anti-IL-17RA-4
Gene expression data from diseased mice treated with different blocking antibodies.

hyb_protocol: Labelled cDNA was hybridized onto Affymetrix mouse HT_MG430_PM arrays according to Affymetrix technical protocol.

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

data_processing: The data were analyzed with OmicSoft ArrayStudios.

source_name: colon tissue in infected mice treated with anti-IL17RA

label_protocol: Amplified cDNA was labeled using the FL Ovation™ cDNA Biotin Module V2 (Nugen, Inc.) according to manufacturer recommendations.

extract_protocol: Snap-frozen colon tissue was homogenized with a TissueLyser (Qiagen, Valencia, CA) and total RNA extracted using the RNeasy Mini kit (Qiagen).

treatment_protocol: mdr1a-deficient mice were infected with 1x10^7 cfu of H. bilis bacteria by oral gavage on day 0 and 7 to accelerate colitis development. Antagonist antibody treatment began on day 0 and continued on a regular schedule thereafter.

tag: strain/background

value: FVB

tag: genotype/variation

value: mdr1a KO

value: colon

tag: antibody treatment

tag: h. bilis infection

value: infected

tag: study #


title: Infected, anti-IL17RA, biological rep2-3

description:
mdr s2 anti-IL-17RA-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Indoor-NanoTiO2 1d-H4

tag: genetic background

tag: time

tag: sample type


title: Arid1a f/f 1

tag: tissue

tag: gender


title: Infected, anti-IL17RA, biological rep2-1

description:
mdr s2 anti-IL-17RA-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL17RA, biological rep2-2

description:
mdr s2 anti-IL-17RA-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL17A, biological rep2-4

description:
mdr s2 anti-IL-17A-4
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue in infected mice treated with anti-IL17A


title: Infected, anti-IL17A, biological rep2-5

description:
mdr s2 anti-IL-17A-5
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample VB65_Nsp

description: Hybridized to 250K_Nsp

value: Lung

value: Lung squamous cell carcinoma

tag: age

value: Male

tag: tumor stage

value: IB


title: Infected, anti-IL17RA, biological rep2-5

description:
mdr s2 anti-IL-17RA-5
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL17A, biological rep2-2

description:
mdr s2 anti-IL-17A-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3123

city: Uppsala

first: Sven

last: Nelander

address: Rudbecklab

country: Sweden

institute: Uppsala Universitet

hyb_protocol: GeneChip® ST Arrays ( GeneChip® Human Exon 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were normalized with the RMA method.

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit( P/N 4425209 Rev C 09/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 6, Affymetrix Inc., Santa Clara, CA)

growth_protocol: Fresh tumor tissue was minced, dissociated, washed and then cultured in neural stem cell media. After 5-7 days, cells or spheres were plated onto laminin-coated dishes. Cells were maintained and passaged as adherent cultures.

extract_protocol: RNeasy Mini kit (Qiagen)

treatment_protocol: not applicable

tag: cell line


title: Early stage lung squamous cell carcinoma sample VB121_Nsp

description: Hybridized to 250K_Nsp


title: Infected, anti-IL17A, biological rep2-3

description:
mdr s2 anti-IL-17A-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL17A, biological rep2-1

description:
mdr s2 anti-IL-17A-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3121


title: U3118


title: Early stage lung squamous cell carcinoma sample VB118_Nsp

description: Hybridized to 250K_Nsp

value: IA


title: Infected, control mIgG, biological rep2-4

description:
mdr s2 mIgG1-4
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue in infected mice treated with control IgG


title: Early stage lung squamous cell carcinoma sample Eu93_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample Eu63_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample Eu68_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample VB108_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample VB57_Nsp

description: Hybridized to 250K_Nsp


title: Infected, control mIgG, biological rep2-3

description:
mdr s2 mIgG1-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Donor 1 AlaF.5hrs.2

description: Dendritic cell was treated by AlaF for 5 Hours

tag: treatment

value: AlaF

tag: time (hours)


title: Infected, control mIgG, biological rep2-2

description:
mdr s2 mIgG1-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample Eu58_Nsp

description: Hybridized to 250K_Nsp

tag: cell type


title: U3117


title: U3110


title: Early stage lung squamous cell carcinoma sample Eu85_Nsp

description: Hybridized to 250K_Nsp

value: IIA


title: Early stage lung squamous cell carcinoma sample Eu51_Nsp

description: Hybridized to 250K_Nsp

value: Female


title: Early stage lung squamous cell carcinoma sample EU50_Nsp

description: Hybridized to 250K_Nsp


title: U3088


title: U3101


title: U3085


title: Early stage lung squamous cell carcinoma sample Eu44_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample Eu36_Nsp

description: Hybridized to 250K_Nsp


title: U3086


title: Infected, control mIgG, biological rep2-1

description:
mdr s2 mIgG1-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, PBS, biological rep2-2

description:
mdr s2 PBS-2
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue in infected mice treated with PBS

value: PBS


title: U3084


title: Uninfected, biological rep2-3

description:
mdr s2 naive-3
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue from uninfected mice

value: naive

value: uninfected


title: Uninfected, biological rep2-2

description:
mdr s2 naive-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample Eu23_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample Eu27_Nsp

description: Hybridized to 250K_Nsp


title: U3082


title: U3078


title: Infected, PBS, biological rep2-3

description:
mdr s2 PBS-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample Eu22_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung squamous cell carcinoma sample Eu21_Nsp

description: Hybridized to 250K_Nsp


title: Infected, anti-IL17RA, biological rep1-5

description:
mdr s1 anti-IL-17RA-5
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3073


title: Early stage lung squamous cell carcinoma sample Eu16_Nsp

description: Hybridized to 250K_Nsp


title: U3088

hyb_protocol: standard protocols for Affymetrix Cytoscan™ HD arrays (Affymetrix® Cytoscan User Guide (P/N 703038 Rev4.) Hybridized probes were captured by streptavidin-phycoerythrin conjugates using the GeneChip® Fluidics Station 450.

data_processing: Data processing of CEL files was performed using Rawcopy software

label_protocol: 250 ng total genomic DNA was digested with the restriction enzyme Nsp I, then ligated to an Nsp I adaptor and further subjected to PCR amplification using a single primer. After fragmentation, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase (TdT)

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: Dneasy blood and tissue kit (Qiagen)


title: Uninfected, biological rep2-1

description:
mdr s2 naive-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample Eu15_Nsp

description: Hybridized to 250K_Nsp


title: Infected, PBS, biological rep2-1

description:
mdr s2 PBS-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3110


title: Infected, anti-IL17RA, biological rep1-4

description:
mdr s1 anti-IL-17RA-4
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3121


title: U3071


title: U3129


title: U3101


title: U3086


title: U3118


title: U3082


title: U3068


title: Infected, anti-IL17RA, biological rep1-3

description:
mdr s1 anti-IL-17RA-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung squamous cell carcinoma sample Eu13_Nsp

description: Hybridized to 250K_Nsp


title: U3085


title: U3065


title: U3084


title: U3117


title: Infected, anti-IL17RA, biological rep1-2

description:
mdr s1 anti-IL-17RA-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3062


title: U3060


title: Infected, anti-IL12/23p40, biological rep1-3

description:
mdr s1 anti-p40-3
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue in infected mice treated with anti-IL12/23p40


title: U3056


title: Infected, anti-IL17RA, biological rep1-1

description:
mdr s1 anti-IL-17RA-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3054


title: Early stage lung squamous cell carcinoma sample Eu120_Nsp

description: Hybridized to 250K_Nsp


title: Infected, anti-IL12/23p40, biological rep1-2

description:
mdr s1 anti-p40-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL12/23p40, biological rep1-1

description:
mdr s1 anti-p40-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3053


title: Early stage lung adenocarcinoma sample VB78_Nsp

description: Hybridized to 250K_Nsp

source_name: Early stage lung adenocarcinoma sample

value: Lung adenocarcinoma


title: Early stage lung adenocarcinoma sample VB93_Nsp

description: Hybridized to 250K_Nsp


title: U3051


title: U3078


title: Infected, anti-IL23p19, biological rep1-4

description:
mdr s1 anti-p19-4
Gene expression data from diseased mice treated with different blocking antibodies.

source_name: colon tissue in infected mice treated with anti-IL23p19


title: Infected, anti-IL23p19, biological rep1-5

description:
mdr s1 anti-p19-5
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3068


title: Early stage lung adenocarcinoma sample VB90_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung adenocarcinoma sample VB95_Nsp

description: Hybridized to 250K_Nsp


title: U3071


title: U3062


title: Early stage lung adenocarcinoma sample VB71_Nsp

description: Hybridized to 250K_Nsp


title: U3048


title: U3065


title: U3047


title: U3046


title: Infected, anti-IL23p19, biological rep1-3

description:
mdr s1 anti-p19-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Infected, anti-IL23p19, biological rep1-2

description:
mdr s1 anti-p19-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung adenocarcinoma sample Eu94_Nsp

description: Hybridized to 250K_Nsp


title: U3060


title: Early stage lung squamous cell carcinoma sample BN02_Nsp

description: Hybridized to 250K_Nsp


title: Infected, anti-IL23p19, biological rep1-1

description:
mdr s1 anti-p19-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3042


title: Infected, control mIgG, biological rep1-3

description:
mdr s1 mIgG1-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung adenocarcinoma sample Eu47_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung adenocarcinoma sample Eu60_Nsp

description: Hybridized to 250K_Nsp


title: Early stage lung adenocarcinoma sample EU88_Nsp

description: Hybridized to 250K_Nsp


title: Infected, control mIgG, biological rep1-2

description:
mdr s1 mIgG1-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3073


title: U3037


title: Early stage lung adenocarcinoma sample Eu41_Nsp

description: Hybridized to 250K_Nsp


title: U3123


title: U3035


title: Early stage lung adenocarcinoma sample Eu004_Nsp

description: Hybridized to 250K_Nsp


title: U3039


title: Infected, PBS, biological rep1-3

description:
mdr s1 PBS-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung adenocarcinoma sample Eu118_Nsp

description: Hybridized to 250K_Nsp


title: U3054


title: U3056


title: Infected, control mIgG, biological rep1-1

description:
mdr s1 mIgG1-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3034


title: Early stage lung adenocarcinoma sample Eu001_Nsp

description: Hybridized to 250K_Nsp


title: U3031


title: Infected, PBS, biological rep1-2

description:
mdr s1 PBS-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3033


title: Infected, PBS, biological rep1-1

description:
mdr s1 PBS-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: Early stage lung adenocarcinoma sample BN05_Nsp

description: Hybridized to 250K_Nsp


title: U3051


title: Uninfected, biological rep1-3

description:
mdr s1 naive-3
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3065

hyb_protocol: GeneChip® ST Arrays (GeneChip® Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual ( P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA).

growth_protocol: Neonatal NOD/SCID mice (P1-3) were injected intracerebrally with three different human GC lines (U3020MG, U3047MG and U3065MG), two mice with each cell line and sacrificed upon any sign of illness. The tumor tissue was dissected out and one portion stored at -70° C for later RNA extraction (samples labelled with T) and another portion dissociated enzymatically into single cells and for establishment of a glioma cell culture subjected to two passages (samples lablled with C). Injected and explanted cells were both cultured adherently in neural stem cell media.

extract_protocol: miRNeasy Mini kit (Qiagen)


title: Uninfected, biological rep1-2

description:
mdr s1 naive-2
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3029


title: U3028


title: U3046


title: U3020


title: U3048


title: Uninfected, biological rep1-1

description:
mdr s1 naive-1
Gene expression data from diseased mice treated with different blocking antibodies.


title: U3027


title: Early stage lung adenocarcinoma sample BN03_Nsp

description: Hybridized to 250K_Nsp


title: U3047


title: Early stage lung adenocarcinoma sample BN04_Nsp

description: Hybridized to 250K_Nsp


title: D_48hr_3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: 48h after dox treatment, rep 3

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: Analysis of the microarray was performed using GenomeStudio software (Illumina) and included quality control checks of hybridization and signal generation using sample-independent controls, background subtraction, and array normalization using quantile normalization.

source_name: Pancreatic ductal adenocarcinoma (PDAC) cell line BxPC3

label_protocol: According to Illumina protocol.

growth_protocol: BxPC3 was cultured in RPMI 1640 media (Life Technologies) with 10% Tetracycline-free Fetal Bovine Serum (FBS) (Clontech) and 1% Penicillin Streptomycin (Life Technologies).

treatment_protocol: BxPC3 was infected by pINDUCER-SMAD4-Puro virus.The resluting BxPC3-pINS4c5 cells were seeded in 6-well plates to reach 60% confluence. After 24h, 1µg/ml doxycycline was added to experimental wells. 8h, 24h, and 48h after doxycycline treatment, RNA was isolated using RNeasy Mini Kit (Quiagen) with DNase I treatment from three wells at each time point and from three untreated wells.

tag: time point

tag: agent

value: 1µg/ml doxycycline


title: Tumor-U3047-rep2

source_name: U3047, tumor

value: U3047, tumor


title: U3037


title: D_48hr_1

description: 48h after dox treatment, rep 1

extract_protocol: 8h, 24h, and 48h after doxycycline treatment, RNA was isolated using RNeasy Mini Kit (Quiagen) with DNase I treatment from three wells at each time point and from three untreated wells.


title: U3021


title: D_48hr_2

description: 48h after dox treatment, rep 2


title: Tumor-U3065-rep2

source_name: U3065, tumor

value: U3065, tumor


title: U3020


title: Tumor-U3047-rep1


title: U3035


title: Tumor-U3065-rep1


title: U3034


title: U3053


title: U3039


title: U3017


title: D_24hr_1

description: 24h after dox treatment, rep 1


title: Tumor-U3020-rep2

source_name: U3020, tumor

value: U3020, tumor


title: U3019


title: U3031


title: U3042


title: Tumor-U3020-rep1


title: D_24hr_3

description: 24h after dox treatment, rep 3


title: U3047


title: D_24hr_2

description: 24h after dox treatment, rep 2


title: U3028


title: U3024


title: D_8hr_1

description: 8h after dox treatment, rep 1


title: U3029


title: U3021


title: Explanted cells-U3065-rep2

source_name: U3065, explanted cells

value: U3065, explanted cells


title: U3009


title: Control_8hr_3

description: control 8h, rep 3


title: U3016


title: D_8hr_3

description: 8h after dox treatment, rep 3


title: U3027


title: U3020


title: U3008


title: U3019


title: U3033


title: D_8hr_2

description: 8h after dox treatment, rep 2


title: Explanted cells-U3047-rep1

source_name: U3047, explanted cells

value: U3047, explanted cells


title: U3013


title: U3017


title: U3004


title: U3002


title: Explanted cells-U3047-rep2


title: Control_8hr_2

description: control 8h, rep 2


title: U3024


title: U3016


title: U3005


title: Control_8hr_1

description: control 8h, rep 1


title: U3009


title: U3013


title: Explanted cells-U3065-rep1


title: Explanted cells-U3020-rep2

source_name: U3020, explanted cells

value: U3020, explanted cells


title: Explanted cells-U3020-rep1


title: U3008