title: BCN-PM1-FEB-R1

city: Barcelona

first: Sofia Raquel

middle: Soares

last: Mesquita

state: Cataluña

address: C/ Jordi Girona 18-26

department: Quimica Ambiental

country: Spain

institute: IDAEA-CSIC

description: Biological replicate 1 of 3. Embryos treated with BCN PM1 extracts from February  vs DMSO control embryos

hyb_protocol: These following components were added in this order: 825ng of Cy3 labeled cRNA, 825 of Cy5 labeled cRNA, 11ul of 10x blocking Reagent, a volume of nuclease free water up to 52.8ul and 2.2ul of 25x fragmentation buffer. Samples were then incubated at 60ºC for exactly 30 minutes. After cooling on ice, the reaction was stopped by adding 55ul of 2x GEx Hybridization Buffer.  100ml of hybridization cocktail was used for each array. The Agilent hybridization oven was set at 65ºC and rotation speed to 10rpm, during 17hours. After hybridization, slides were washed. One last Acetonitrile wash was perform, followed by a stabilization and dry solution wash. Arrays were scanned immediately.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2505C, and data were acquired using Agilent's Feature Extraction Software version 10.5.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.5.1.1 (Agilent) using default parameters (protocol GE2_105_jan09 and Grid: 026437_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities

organism: Danio rerio

label_protocol: Cyanine 3-CTP samples and Cyanine 5-CTP samples were prepare from 200ng of total RNA using the Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent), followed by the purification of the labelled/amplified RNA using Qiagen RNeasy mini kit.

growth_protocol: Zebrafish (Danio rerio) embryos and eleutheroembryos were obtained by natural mating and raised at 28.5 ◦C with a 12L:12D photoperiod in embryo water [90  g/mL of Instant Ocean (Aquarium Systems, Sarrebourg, France; http://zfin.org/), 0.58 mM CaSO4•2H2O, dissolved in reverse osmosis purified water]. Animal stages were recorded as days (dpf).

extract_protocol: Total RNA was isolated from 20 embryos per replicate using Trizol reagent protocol (Invitrogen). RNA concentration was measured by spectrophotometric absorption at 260nm in Nanodrop ND-800 (nanodrop technologies, Wilmington, DE) and their integrity checked by Agilent 2100 bioanalyzer (agilent technologies, Santa Clara CA).

treatment_protocol: Zebrafish embryos were exposed to organic content of atmospheric PM, from urban (PM 10 and PM1) and rural environments (PM1). The solvent used was DMSO 0.2%, therefore organic extracts were diluted 500times. Three biological replicates were done. All the solutions were prepared on the same day of the experiment and renewal every day. Each biological replicate corresponds to 20 fertilized embryos exposed to PM samples.

value: BCN PM1 extracts from February

source_name: pooled embryos control solvent

tag: developmental stage

value: DMSO control


title: LaPOBLA-PM1-NOV-R2

status: Public on Oct 26 2015

type: RNA

description: Biological replicate 2 of 3. Embryos treated with LaPobla PM1 extracts from November vs DMSO control embryos

molecule: total RNA

tag: agent

value: LaPobla PM1 extracts from November


title: COLO205_CPD_1_2H_A

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: Cy 3 labelled cRNA was co-hybridized with Cy5 labelled Universal Human Reference RNA

scan_protocol: The arrays were scanned using an Agilent Technologies Scanner G2505C US94400327, using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.7.3.1 and extraction protocol GE2_107_Sep09 and grid file 039494_D_F_20120628

data_processing: Background subtracted data for sample and reference were entered in the Genespring analysis software (Agilent). Lowess normalization was applied to the samples.

organism: Homo sapiens

source_name: Colo205 colon cancer cells were treated with CPD 1 for 2H

label_protocol: Quick Amp Labeling protocol

growth_protocol: All cell lines were purchased from the American Type Culture Collection and grown in their recommended culture medium, which was supplemented with 10% fetal bovine serum (FBS) at 37°C in an atmosphere of 5% CO2 and passaged for less than six months

extract_protocol: RNA was extracted using the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer’s instructions

treatment_protocol: The Colo205 colon cancer cell line was treated for 2 or  6 hours with vehicle control (DMSO) or treated with Compound 1

tag: cell line

tag: treatment

value: Compound 1

tag: time

value: 2 hr

source_name: Stratagene Universal Human Reference RNA

tag: sample type

value: Reference


title: LaPOBLA-PM1-DEC-R3

description: Biological replicate 3 of 3. Embryos treated with LaPobla PM1 extracts from December vs DMSO control embryos

value: LaPobla PM1 extracts from December


title: LaPOBLA-PM1-NOV-R3

description: Biological replicate 3 of 3. Embryos treated with LaPobla PM1 extracts from November vs DMSO control embryos


title: LaPOBLA-PM1-NOV-R1

description: Biological replicate 1 of 3. Embryos treated with LaPobla PM1 extracts from November vs DMSO control embryos


title: BCN-PM10-FEB-R1

description: Biological replicate 1 of 3. Embryos treated with BCN PM10 extracts from February vs DMSO control embryos

value: BCN PM10 extracts from February


title: Liver, intermittent diet regimen, replicate 7

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

label: biotin

organism: Mus musculus

source_name: Liver, intermittent diet regimen

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received a semi-synthetic diet (AIN-93G) for a 2-week acclimatization period. At the age of 9 weeks, dietary intervention was started and the mice were sacrificed at the age of 12 months.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 0.5% carboxymethyl cellulose (CMC), after which they were fasted again for another 6 hours. Mice belonging to the INT group were sacrificed in their ad libitum MF feeding week. After sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

tag: gender

value: male

tag: age

value: 12 months

value: intermittent diet (INT)


title: LaPOBLA-PM1-DEC-R2

description: Biological replicate 2 of 3. Embryos treated with LaPobla PM1 extracts from December vs DMSO control embryos


title: COLO205_CPD_1_2H_C


title: Self-to-self

description: BCN PM10 extracts from February vs BCN PM10 extracts from February - self-to-self

source_name: Embryos treated with BCN PM10 extracts from February


title: LaPOBLA-PM1-DEC-R1

description: Biological replicate 1 of 3. Embryos treated with LaPobla PM1 extracts from December vs DMSO control embryos


title: COLO205_CPD_1_2H_B


title: BCN-PM1-FEB-R2

description: Biological replicate 2 of 3. Embryos treated with BCN PM1 extracts from February  vs DMSO control embryos


title: Liver, intermittent diet regimen, replicate 6


title: Liver, intermittent diet regimen, replicate 4


title: BCN-PM10-FEB-R2

description: Biological replicate 2 of 3. Embryos treated with BCN PM10 extracts from February vs DMSO control embryos


title: Technical replicate

source_name: Embryos treated with LaPobla PM1 extracts from November


title: Liver, intermittent diet regimen, replicate 5


title: Liver, intermittent diet regimen, replicate 1


title: BCN-PM1-FEB-R3

description: Biological replicate 3 of 3. Embryos treated with BCN PM1 extracts from February  vs DMSO control embryos


title: BCN-PM10-FEB-R3

description: Biological replicate 3 of 3. Embryos treated with BCN PM10 extracts from February vs DMSO control embryos


title: Liver, intermittent diet regimen, replicate 2


title: BCN-PM10-MAY-R2

description: Biological replicate 2 of 3. Embryos treated with BCN PM10 extracts from May vs DMSO control embryos

value: BCN PM10 extracts from May


title: BCN-PM1-MAY-R3

description: Biological replicate 3 of 3. Embryos treated with BCN PM1 extracts from May vs DMSO control embryos

value: BCN PM1 extracts from May


title: BCN-PM1-MAY-R1

description: Biological replicate 1 of 3. Embryos treated with BCN PM1 extracts from May vs DMSO control embryos


title: BCN-PM10-MAY-R1

description: Biological replicate 1 of 3. Embryos treated with BCN PM10 extracts from May vs DMSO control embryos


title: Liver, intermittent diet regimen, replicate 3


title: BCN-PM10-MAY-R3

description: Biological replicate 3 of 3. Embryos treated with BCN PM10 extracts from May vs DMSO control embryos


title: BCN-PM1-MAY-R2

description: Biological replicate 2 of 3. Embryos treated with BCN PM1 extracts from May vs DMSO control embryos


title: genomic DNA from 2014ccRCC44N

type: genomic

city: Guangzhou

first: jinhuan

last: wei

address: No.58 zhongshan 2rd Road

country: China

institute: SYSU

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybrdised to Illumina Infinium HumanMethyaltion450 bead chip using standard Illumina protocol

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

data_processing: RnBeads version 0.99.12 packages in R software 3.02; Raw data is available on sample records in the idat files and on the series record in the file Unmethylated_and_methylated_signal_intensities.csv.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using QIAmp DNA mini kit 50 (Qiagen) according to manufacturer's instructions

tag: tissue

value: kidney

value: female

value: Normal

tag: disease state

value: ccRCC


title: R144- siN1 1

city: Los Angeles

first: Anais

last: Briot

state: CA

address: 621 Charles E. Young Drive, South

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

description: replicate 1

hyb_protocol: cRNA was quantified and normalized and 850ng was hybridzed to Beadchips

scan_protocol: The hybridized Beadchips were scanned by Illumina Beadscan confocal scanner. cRNA synthesis, hybridization and scanning was performed at the UCLA Neuroscience Genomics Core (UNGC)

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value > 0.05 in all samples and normalizing neqc using the control probes

source_name: human aortic endothelial cells

label_protocol: biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX)

extract_protocol: RNA was isolated using Rneasy Mini kit (Qiagen)

treatment_protocol: HAEC were treated with siRNA targeting NOTCH1 using siPORT Amine (Ambion) transfection reagent or with Ox-PAPC (50ug/ml; 6 hours) in Medium 199 supplemented with 1% heat-inactivated fetal bovine serum and 1% antibiotics

tag: cell type

value: Human Aortic Endothelial Cells (HAEC)

value: NOTCH1 siRNA


title: R144- oxP 3

description: replicate 3

value: oxPAPC treatment


title: R144- oxP 2

description: replicate 2


title: R144- oxP 1

description: replicate 1


title: R144- siSC 3

description: replicate 3

value: Scrambled Control siRNA


title: R144- siN1 2

description: replicate 2


title: R144- siSC 2

description: replicate 2


title: R144- siN1 3

description: replicate 3


title: genomic DNA from 2014ccRCC43N


title: genomic DNA from 2014ccRCC46N


title: genomic DNA from 2014ccRCC44T

value: Tumor


title: genomic DNA from 2014ccRCC38N


title: genomic DNA from 2014ccRCC45N


title: genomic DNA from 2014ccRCC42T


title: genomic DNA from 2014ccRCC41T


title: genomic DNA from 2014ccRCC39N


title: genomic DNA from 2014ccRCC39T


title: genomic DNA from 2014ccRCC42N


title: genomic DNA from 2014ccRCC40N


title: genomic DNA from 2014ccRCC46T


title: genomic DNA from 2014ccRCC43T


title: genomic DNA from 2014ccRCC40T


title: genomic DNA from 2014ccRCC38T


title: HFK 2 24h L-CD40L 1

city: Leiden

first: Bart

last: Tummers

address: Albinusdreef 2

department: Clinical Oncology

institute: Leiden University Medical Center

description:
Replicate 1
7196843038_K
101880.71

hyb_protocol: 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 (Illumina, Inc., San Diego, CA, U.S.A.). Each BeadChip contains twelve arrays. Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”.

scan_protocol: The samples were scanned using the Illumina iScan array scanner (Illumina, Inc., San Diego, CA, U.S.A.). There were no deviations from the Illumina protocol and all experiments were performed in compliance with ServiceXS Standard Operating Procedures (SOPs).

data_processing: The expression array data was analyzed using R2.14.1 and Bioconductor. The data were normalized using the Bioconductor package lumi version 2.6.0. Quality control plots were generated using limma version 3.10.2 and mpm version 1.0-22. Differentially expressed genes were identified using maanova version 1.24.0.

label: Biotin

source_name: HFK 2 24h L-CD40L 1

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin,TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: Primary cultures of human epithelial keratinocytes (KCs) were established from foreskin, vaginal and cervical tissues as previously described (Karim et al., 2011) and grown in keratinocyte serum-free medium (K-SFM; Medium 154 supplemented with HKGS kit, Invitrogen, Breda, The Netherlands). Keratinocyte lines stably maintaining the full episomal HPV genome following electroporation (HPV-positive KCs) were grown in monolayer culture using E medium in the presence of mitomycin C treated J2 3T3 feeder cells for two passages and were then adapted to K-SFM for one passage before experimentation. J2 3T3 mouse fibroblasts and L-cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 8% fetal bovine serum, 2mM l-glutamine and 1% penicillin-streptomycin (complete DMEM medium) (Gibco-BRL, Invitrogen, Breda, The Netherlands).

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II kit (Machery-Nagel, Leiden, The Netherlands) according to the manufacturer’s instructions. Total RNA was analyzed by Lab-on-a-Chip. All RNA showed a RIN score of >9.5.

treatment_protocol: Uninfected KCs or HPV-positive KCs were seeded at 1.5x105 cells/well in 6-wells plates in K-SFM and allowed to attach for 24 hours, after which the cells received fresh K-SFM containing 50 IU/ml IFNγ (Immunotools, Friesoythe, Germany) for 72 hours. Control or CD40L-expressing L-cells were harvested, irradiated (4800 – 5200 rad) and resuspended in K-SFM containing 50 IU/ml IFNγ. L-cells were co-cultured with KCs in a 1:1 ratio for indicated time points, after which the supernatant was collected, the L-cells were removed and the RNA of the KCs was harvested. CD40L expression and functionality of the L-cells were validated as was the percentage of residual L-cells after co-culture (<1%).

tag: culture

value: HFK 2

tag: virus

value: uninfected

tag: stimulation time

tag: stimulus

tag: group

tag: sample


title: genomic DNA from 2014ccRCC36N


title: genomic DNA from 2014ccRCC41N


title: genomic DNA from 2014ccRCC37T


title: genomic DNA from 2014ccRCC37N


title: HFK 2 2h L-Control 1

description:
Replicate 1
7196843038_I
101880.69

source_name: HFK 2 2h L-Control 1

value: L-Control


title: genomic DNA from 2014ccRCC45T

value: male


title: HVK16 2h L-CD40L 1

description:
Replicate 1
7196843038_J
101880.70

source_name: HVK16 2h L-CD40L 1

value: HPV-positive


title: genomic DNA from 2014ccRCC35N


title: genomic DNA from 2014ccRCC36T


title: HCK 24h L-Control 1

description:
Replicate 1
7196843038_F
101880.66

source_name: HCK 24h L-Control 1

value: HCK


title: HFK16 24h L-CD40L 1

description:
Replicate 1
7196843038_H
101880.68

source_name: HFK16 24h L-CD40L 1


title: HFK 1 2h L-Control 1

description:
Replicate 1
7196843038_L
101880.72

source_name: HFK 1 2h L-Control 1

value: HFK 1


title: HFK 1 2h L-CD40L 2

description:
Replicate 2
7196843038_D
101880.64

source_name: HFK 1 2h L-CD40L 2


title: HVK18 2h L-Control 2

description:
Replicate 2
7196843038_B
101880.62

source_name: HVK18 2h L-Control 2


title: HVK18 0h IFNy

description:
Replicate 1
7196843038_E
101880.65

source_name: HVK18 0h IFNy

value: IFNy


title: HCK18  2h L-Control 2

description:
Replicate 2
7196843038_G
101880.67

source_name: HCK18  2h L-Control 2


title: genomic DNA from 2014ccRCC32N

value: kidney


title: HVK16 2h L-CD40L 2

description:
Replicate 2
7196843027_K
101880.59

source_name: HVK16 2h L-CD40L 2


title: R144- siSC 1

description: replicate 1


title: HFK 2 0h IFNy

description:
Replicate 1
7196843027_L
101880.60

source_name: HFK 2 0h IFNy


title: genomic DNA from 2014ccRCC33N


title: genomic DNA from 2014ccRCC35T

value: female


title: HVK18 24h L-CD40L 2

description:
Replicate 2
7196843027_J
101880.58

source_name: HVK18 24h L-CD40L 2


title: genomic DNA from 2014ccRCC34N

value: Normal


title: HVK 2h L-CD40L 1

description:
Replicate 1
7196843038_C
101880.63

source_name: HVK 2h L-CD40L 1

value: HVK


title: genomic DNA from 2014ccRCC33T

value: ccRCC


title: genomic DNA from 2014ccRCC30T


title: genomic DNA from 2014ccRCC34T


title: HFK16 24h L-CD40L 2

description:
Replicate 2
7196843038_A
101880.61

source_name: HFK16 24h L-CD40L 2


title: genomic DNA from 2014ccRCC32T


title: HFK 1 0h IFNy

description:
Replicate 1
7196843027_I
101880.57

source_name: HFK 1 0h IFNy


title: genomic DNA from 2014ccRCC31T


title: genomic DNA from 2014ccRCC30N


title: HVK 2h L-CD40L 2

description:
Replicate 2
7196843027_G
101880.55

source_name: HVK 2h L-CD40L 2


title: genomic DNA from 2014ccRCC31N


title: HCK18  2h L-CD40L 2

description:
Replicate 2
7196843027_H
101880.56

source_name: HCK18  2h L-CD40L 2


title: HCK 24h L-CD40L 2

description:
Replicate 2
7196843027_F
101880.54

source_name: HCK 24h L-CD40L 2


title: genomic DNA from 2014ccRCC29N


title: genomic DNA from 2014ccRCC29T


title: ctr_NP_4

city: Indianapolis

first: Jiangang

last: Liu

state: IN

address: 893 S Delaware St

department: Tailored Therapeutics

institute: Eli Lilly and Company

hyb_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneGhip® Human Genome U133 Plus 2 (Affymetrix, Santa Clara, CA) according to the company's standard operating procedures as described previously in detail

data_processing: A summary of the image signal data, detection calls and gene annotations for every gene interrogated on the arrays was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) (scaling factor = 1500) .

source_name: hiPSC-derived neural progenitor

growth_protocol: Selected iPSCs were expanded and cultured on irradiated mouse embryonic fibroblasts (MEF) (GlobalStem) in ES media, which contains DMEM/F12 (1:1) (HyClone) with 20% Knockout serum replacement (Invitrogen), 1X penicillin/Streptomycin (10U/ml/10µg/ml, Hyclone), 1X GlutaMax (Invitrogen), 1X Non-essential amino acids (Hyclone), 55 µM 2-mercaptoethanol (Gibco) and 10ng/ml human bFGF (R&D Systems) with daily media replacement

extract_protocol: Undifferentiated iPSCs, iPSC-derived NPs or neurons at E and L stage of differentiation were rinsed with 1X DPBS followed by RNA extraction using RNeasy Mini kit (Qiagen) using the manufacturer’s protocol. RNA was quantitated using a Nanodrop Spectrometer ND-1000 (Thermo Scientific)

value: Control

value: iPSC-derived NP


title: ctr_L_4

scan_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneGhip® Human Genome U133 Plus 2 (Affymetrix, Santa Clara, CA) according to the company's standard operating procedures as described previously in detail

source_name: hiPSC-derived neuron - late

value: iPSC-derived neuron (late)


title: HVK16 2h L-Control 2

description:
Replicate 2
7196843027_E
101880.53

source_name: HVK16 2h L-Control 2


title: BPD_NP_4

label_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneGhip® Human Genome U133 Plus 2 (Affymetrix, Santa Clara, CA) according to the company's standard operating procedures as described previously in detail

value: Bipolar


title: iPSC_d0_4

source_name: iPSCs

value: iPSC


title: BPD_L_4


title: HCK 2h L-CD40L 2

description:
Replicate 2
7196843027_D
101880.52

source_name: HCK 2h L-CD40L 2

value: uninfected


title: genomic DNA from 2014ccRCC28T

value: Tumor


title: HVK18 2h L-CD40L 1

description:
Replicate 1
7196843027_C
101880.51

source_name: HVK18 2h L-CD40L 1


title: genomic DNA from 2014ccRCC28N

value: male


title: genomic DNA from 2014ccRCC27N


title: ctr_E_4

source_name: hiPSC-derived neuron - early

value: iPSC-derived neuron (early)


title: HFK 2 2h L-CD40L 2

description:
Replicate 2
7196843027_B
101880.50

source_name: HFK 2 2h L-CD40L 2

value: HFK 2


title: genomic DNA from 2014ccRCC27T


title: iPSC_d0_3


title: BPD_E_4


title: genomic DNA from 2014ccRCC26N


title: genomic DNA from 2014ccRCC26T


title: HVK 24h L-Control 2

description:
Replicate 2
7196843027_A
101880.49

source_name: HVK 24h L-Control 2

value: L-Control


title: genomic DNA from 2014ccRCC25T


title: HVK18 24h L-Control 2

description:
Replicate 2
7509299139_K
101880.47

source_name: HVK18 24h L-Control 2

value: HPV-positive


title: ctr_NP_3


title: HCK 24h L-CD40L 1

description:
Replicate 1
7509299139_I
101880.45

source_name: HCK 24h L-CD40L 1

value: HCK


title: HCK18  0h IFNy

description:
Replicate 1
7509299139_L
101880.48

source_name: HCK18  0h IFNy

value: IFNy


title: ctr_L_3


title: HFK16 2h L-Control 1

description:
Replicate 1
7509299139_J
101880.46

source_name: HFK16 2h L-Control 1


title: ctr_E_3


title: BPD_L_3


title: ctr_L_2


title: ctr_NP_2


title: BPD_NP_3


title: genomic DNA from 2014ccRCC25N

value: kidney

value: female

value: Normal


title: HFK 1 24h L-Control 2

description:
Replicate 2
7509299139_H
101880.44

source_name: HFK 1 24h L-Control 2

value: HFK 1


title: HVK16 24h L-CD40L 2

description:
Replicate 2
7509299139_F
101880.42

source_name: HVK16 24h L-CD40L 2


title: genomic DNA from 2014ccRCC24N

value: ccRCC


title: HFK 2 2h L-CD40L 1

description:
Replicate 1
7509299139_G
101880.43

source_name: HFK 2 2h L-CD40L 1


title: genomic DNA from 2014ccRCC24T


title: genomic DNA from 2014ccRCC22N


title: BPD_E_3


title: genomic DNA from 2014ccRCC23N


title: HCK18  24h L-CD40L 1

description:
Replicate 1
7509299139_D
101880.40

source_name: HCK18  24h L-CD40L 1


title: genomic DNA from 2014ccRCC21N


title: genomic DNA from 2014ccRCC23T


title: HVK 2h L-Control 2

description:
Replicate 2
7509299139_E
101880.41

source_name: HVK 2h L-Control 2

value: HVK


title: genomic DNA from 2014ccRCC22T


title: BPD_L_2

source_name: hiPSC-derived neuron - late

value: Bipolar

value: iPSC-derived neuron (late)


title: HCK18  24h L-Control 1

description:
Replicate 1
7509299139_B
101880.38

source_name: HCK18  24h L-Control 1


title: iPSC_d0_2

source_name: iPSCs

value: Control

value: iPSC


title: HCK 2h L-CD40L 1

description:
Replicate 1
7509299139_A
101880.37

source_name: HCK 2h L-CD40L 1

value: uninfected


title: ctr_E_2

value: iPSC-derived neuron (early)


title: BPD_NP_2

source_name: hiPSC-derived neural progenitor

value: iPSC-derived NP


title: HCK 2h L-Control 2

description:
Replicate 2
7509299139_C
101880.39

source_name: HCK 2h L-Control 2

value: L-Control


title: genomic DNA from 2014ccRCC21T

value: Tumor


title: genomic DNA from 2014ccRCC20N


title: genomic DNA from 2014ccRCC19T


title: genomic DNA from 2014ccRCC19N


title: HVK16 24h L-CD40L 1

description:
Replicate 1
7509299161_L
101880.36

source_name: HVK16 24h L-CD40L 1

value: HPV-positive


title: BPD_E_2

source_name: hiPSC-derived neuron - early


title: HCK18  2h L-CD40L 1

description:
Replicate 1
7509299161_H
101880.32

source_name: HCK18  2h L-CD40L 1


title: ctr_L_1


title: ctr_E_1


title: HVK 24h L-CD40L 1

description:
Replicate 1
7509299161_K
101880.35

source_name: HVK 24h L-CD40L 1


title: iPSC_d0_1


title: BPD_NP_1


title: HFK 2 2h L-Control 2

description:
Replicate 2
7509299161_J
101880.34

source_name: HFK 2 2h L-Control 2

value: HFK 2


title: genomic DNA from 2014ccRCC18N

value: kidney


title: BPD_L_1


title: HVK18 2h L-CD40L 2

description:
Replicate 2
7509299161_G
101880.31

source_name: HVK18 2h L-CD40L 2


title: ctr_NP_1


title: BPD_E_1


title: HFK 2 24h L-Control 2

description:
Replicate 2
7509299161_F
101880.30

source_name: HFK 2 24h L-Control 2


title: HFK16 2h L-CD40L 2

description:
Replicate 2
7509299161_I
101880.33

source_name: HFK16 2h L-CD40L 2


title: HFK 1 2h L-Control 2

description:
Replicate 2
7509299161_E
101880.29

source_name: HFK 1 2h L-Control 2


title: HFK 1 24h L-Control 1

description:
Replicate 1
7509299161_D
101880.28

source_name: HFK 1 24h L-Control 1


title: genomic DNA from 2014ccRCC18T

value: female


title: genomic DNA from 2014ccRCC17T

value: male


title: genomic DNA from 2014ccRCC15N

value: Normal


title: HVK18 2h L-Control 1

description:
Replicate 1
7509299161_C
101880.27

source_name: HVK18 2h L-Control 1


title: genomic DNA from 2014ccRCC16N

value: ccRCC


title: genomic DNA from 2014ccRCC14T


title: HFK16 24h L-Control 1

description:
Replicate 1
7509299161_B
101880.26

source_name: HFK16 24h L-Control 1


title: genomic DNA from 2014ccRCC15T


title: HVK 0h IFNy

description:
Replicate 1
7509299161_A
101880.25

source_name: HVK 0h IFNy

value: HVK

value: IFNy


title: genomic DNA from 2014ccRCC16T


title: genomic DNA from 2014ccRCC17N


title: genomic DNA from 2014ccRCC14N


title: genomic DNA from 2014ccRCC20T


title: genomic DNA from 2014ccRCC13N


title: HVK16 0h IFNy

description:
Replicate 1
7509301069_I
101880.21

source_name: HVK16 0h IFNy


title: HVK18 24h L-CD40L 1

description:
Replicate 1
7509301069_K
101880.23

source_name: HVK18 24h L-CD40L 1


title: HVK 2h L-Control 1

description:
Replicate 1
7509301069_G
101880.19

source_name: HVK 2h L-Control 1


title: genomic DNA from 2014ccRCC12N


title: HCK18  24h L-CD40L 2

description:
Replicate 2
7509301069_E
101880.17

source_name: HCK18  24h L-CD40L 2


title: genomic DNA from 2014ccRCC13T


title: HVK16 24h L-Control 2

description:
Replicate 2
7509301069_F
101880.18

source_name: HVK16 24h L-Control 2


title: HFK16 0h IFNy

description:
Replicate 1
7509301069_D
101880.16

source_name: HFK16 0h IFNy


title: HFK 1 24h L-CD40L 2

description:
Replicate 2
7509301069_C
101880.15

source_name: HFK 1 24h L-CD40L 2

value: HFK 1


title: genomic DNA from 2014ccRCC12T


title: HFK 2 24h L-Control 1

description:
Replicate 1
7509301069_L
101880.24

source_name: HFK 2 24h L-Control 1


title: genomic DNA from 2014ccRCC08N


title: HFK16 24h L-Control 2

description:
Replicate 2
7509301069_B
101880.14

source_name: HFK16 24h L-Control 2


title: genomic DNA from 2014ccRCC10N


title: genomic DNA from 2014ccRCC11T


title: genomic DNA from 2014ccRCC09N


title: HVK16 24h L-Control 1

description:
Replicate 1
7509299156_J
101880.10

source_name: HVK16 24h L-Control 1


title: HFK 1 2h L-CD40L 1

description:
Replicate 1
7509301069_A
101880.13

source_name: HFK 1 2h L-CD40L 1


title: HVK 24h L-CD40L 2

description:
Replicate 2
7509299156_L
101880.12

source_name: HVK 24h L-CD40L 2


title: HCK 0h IFNy

description:
Replicate 1
7509299156_K
101880.11

source_name: HCK 0h IFNy

value: HCK


title: HCK 2h L-Control 1

description:
Replicate 1
7509301069_J
101880.22

source_name: HCK 2h L-Control 1


title: genomic DNA from 2014ccRCC11N


title: genomic DNA from 2014ccRCC08T


title: HVK 24h L-Control 1

description:
Replicate 1
7509299156_G
101880.07

source_name: HVK 24h L-Control 1


title: genomic DNA from 2014ccRCC09T


title: HVK18 24h L-Control 1

description:
Replicate 1
7509301069_H
101880.20

source_name: HVK18 24h L-Control 1


title: genomic DNA from 2014ccRCC07N


title: genomic DNA from 2014ccRCC06T


title: genomic DNA from 2014ccRCC06N


title: genomic DNA from 2014ccRCC04N


title: genomic DNA from 2014ccRCC05T


title: HCK18  24h L-Control 2

description:
Replicate 2
7509299156_H
101880.08

source_name: HCK18  24h L-Control 2


title: HCK 24h L-Control 2

description:
Replicate 2
7509299156_C
101880.03

source_name: HCK 24h L-Control 2


title: HCK18  2h L-Control 1

description:
Replicate 1
7509299156_E
101880.05

source_name: HCK18  2h L-Control 1


title: CaSm 03.22

status: Public on Oct 24 2015

city: Charleston

first: Elizabeth

last: Little

state: SC

address: 86 Jonathan Lucas St

department: Surgery

institute: Medical University of South Carolina

description: Tet-on CaSm Panc1 cells without doxycycline

scan_protocol: the Roche 480 Lightcycler

data_processing: Analysis was performed using SABioscience’s Free PCR Array Data Analysis Software (ΔΔCt method) with B2M, HPRT1, and GAPDH as pooled housekeeping genes.

label: SYBR Green I / HRM Dye (465-510)

source_name: Human Panc1 cells transfected with inducible full-length human CaSm and grown for 4 weeks without doxycycline

label_protocol: RT2  SYBR Green qPCR master mix was used for the microarray master mix reagent according to the manufacturer’s manual (SABiosciences).

growth_protocol: Tet-on driver and tet-on CaSm Panc-1 cells were grown with and without doxycycline (1 μg/mL) for 4 weeks

extract_protocol: RNA isolation was performed using RNeasy Plus kit (Qiagen, Valencia, CA) following the manufacturer’s protocols. The Hollings Cancer Center Tissue Biorepository core facility confirmed RNA quality using the 18S/28S Ratio Integrity Number using Agilent 2100 Bioanalyzer  (Agilent Technologies, Santa Clara, CA); RNA with a RIN of 10 was used for further analysis.  Complement DNA synthesis was performed using RT2 First Strand kit.

tag: construct

value: inducible full-length human CaSm


title: CaSm+Doxy 03.24

description: Tet-on CaSm Panc1 cells with doxycycline

source_name: Human Panc1 cells transfected with inducible full-length human CaSm and grown for 4 weeks with 1ug/mL doxycycline

tag: cell line


title: Driver+Doxy 03.24

description: Tet-on Driver Panc1 cells with doxycycline

source_name: Human Panc1 cells transfected with tet-on plasmid (driver) and grown for 4 weeks with 1ug/mL doxycycline

value: tet-on plasmid (driver)


title: CaSm+Doxy 03.22


title: CaSm 03.24


title: genomic DNA from 2014ccRCC03T


title: genomic DNA from 2014ccRCC10T


title: HFK 1 24h L-CD40L 1

description:
Replicate 1
7509299156_B
101880.02

source_name: HFK 1 24h L-CD40L 1

value: uninfected


title: Leaf 11 8mm primordium

city: Iowa City

first: Erin

last: Irish

state: IA

address: 129 E. Jefferson St.

department: Biology

institute: University of Iowa

hyb_protocol: Hybridization was performed according to the manufacturer's protocol, see www.nimblegen.com.

scan_protocol: Scanning was performed according to the manufacturer's protocol, see www.nimblegen.com.

data_processing: Array data were scaled in Array Star 4 (www.dnastar.com) using Robust Multi-array Average (RMA) analysis with quantile normalization.

organism: Zea mays

source_name: Leaf 11 8mm primordium

label_protocol: Labeling was performed according to the manufacturer's protocol, see www.nimblegen.com.

growth_protocol: B73 and Mo17 were crossed to generate hybrid seeds, which were planted and grown in a temperature-controlled greenhouse and illuminated for 14 hours daily under 1kW metal halide and sodium lights (www.osram.com). Plants were grown in Compost Plus growing mix (www.beautifullandproducts.com).

extract_protocol: Leaf primordia were isolated by dissection of shoot tips and flash-frozen in liquid nitrogen. Total RNA was extracted by Trizol (www.lifetechnologies.com) and purified on RNeasy columns (www.qiagen.com) using the manufacturer’s protocols.

treatment_protocol: Emerging seedlings of sample 5JA (first leaf partially expanded) received a single application of 100µl of varying concentrations of jasmonic acid to the apical whorl, other samples untreated

value: leaf


title: Leaf 12 8mm primordium

source_name: Leaf 12 8mm primordium


title: HFK16 2h L-Control 2

description:
Replicate 2
7509299156_I
101880.09

source_name: HFK16 2h L-Control 2

value: L-Control


title: HVK16 2h L-Control 1

description:
Replicate 1
7509299156_A
101880.01

source_name: HVK16 2h L-Control 1


title: Leaf 9 8mm primordium

source_name: Leaf 9 8mm primordium


title: genomic DNA from 2014ccRCC02T

value: Tumor


title: HFK 2 24h L-CD40L 2

description:
Replicate 2
7509299156_F
101880.06

source_name: HFK 2 24h L-CD40L 2


title: genomic DNA from 2014ccRCC04T


title: Driver+Doxy 04.06


title: genomic DNA from 2014ccRCC01N


title: genomic DNA from 2014ccRCC03N


title: genomic DNA from 2014ccRCC01T


title: Leaf 7 8mm primordium

source_name: Leaf 7 8mm primordium


title: Leaf 8 8mm primordium

source_name: Leaf 8 8mm primordium


title: Leaf 6 8mm primordium

source_name: Leaf 6 8mm primordium


title: Leaf 5 8mm primordium

source_name: Leaf 5 8mm primordium


title: Leaf 10 8mm primordium

source_name: Leaf 10 8mm primordium


title: Leaf 5 8mm primordium, Jasmonic Acid treated


title: Leaf 1 8mm primordium

source_name: Leaf 1 8mm primordium


title: genomic DNA from 2014ccRCC02N


title: genomic DNA from 2014ccRCC07T


title: genomic DNA from 2014ccRCC05N


title: Leaf 4 8mm primordium

source_name: Leaf 4 8mm primordium


title: SIRS_024

city: Seattle

first: Leo

middle: Charles

last: McHugh

state: Washington

address: 425 pontius ave N, Suite 430

department: Bioinformatics

institute: Immunexpress Inc

description: RMA normalized transcripts

hyb_protocol: Following fragmentation and labeling, 5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix Human Exon 1.0 ST Array. GeneChips were washed and stained with streptavidin-conjugated phycoerythrin in the Affymetrix Fluidics Station 450 following Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G using Affymetrix’ GeneChip Operating Software to generate raw and averaged image files (.DAT and .CEL).

data_processing: Affymetrix Power Tools used to generate transcript level data using DABG method.  Bioconductor ‘Affy’ package used for RMA summarization followed by quantile normalization.

source_name: peripheral blood

label_protocol: Biotin-labeled sense strand cDNA were prepared using Affymetrix’ GeneChip Whole Transcript Sense Target Labeling Assay under manufacturer’s recommendations from 300ng total RNA.

extract_protocol: Total RNA was extracted from PAXgene blood tubes using a KingFisher automated magnetic particle processor. 340uL of white blood cell lysate was used for purification.

value: post-surgical


title: SIRS_028

description: RMA normalized transcripts


title: SIRS_031

description: RMA normalized transcripts


title: SIRS_026

description: RMA normalized transcripts


title: SIRS_030

description: RMA normalized transcripts


title: SIRS_025

description: RMA normalized transcripts


title: HFK16 2h L-CD40L 1

description:
Replicate 1
7509299156_D
101880.04

source_name: HFK16 2h L-CD40L 1

value: HPV-positive


title: SIRS_021

description: RMA normalized transcripts


title: SIRS_023

description: RMA normalized transcripts


title: SIRS_019

description: RMA normalized transcripts


title: SIRS_016

description: RMA normalized transcripts


title: SIRS_018

description: RMA normalized transcripts


title: SIRS_029

description: RMA normalized transcripts


title: SIRS_022

description: RMA normalized transcripts


title: SIRS_014

description: RMA normalized transcripts


title: SIRS_020

description: RMA normalized transcripts


title: SIRS_015

description: RMA normalized transcripts


title: SIRS_017

description: RMA normalized transcripts


title: SIRS_011

description: RMA normalized transcripts


title: Leaf 3 8mm primordium

source_name: Leaf 3 8mm primordium


title: SIRS_013

description: RMA normalized transcripts


title: SIRS_012

description: RMA normalized transcripts


title: SIRS_008

description: RMA normalized transcripts


title: SIRS_009

description: RMA normalized transcripts


title: SIRS_005

description: RMA normalized transcripts


title: SIRS_004

description: RMA normalized transcripts


title: SIRS_006

description: RMA normalized transcripts


title: SIRS_002

description: RMA normalized transcripts


title: Sepsis_074

description: RMA normalized transcripts

value: Sepsis


title: SIRS_001

description: RMA normalized transcripts


title: Sepsis_070

description: RMA normalized transcripts


title: Sepsis_073

description: RMA normalized transcripts


title: Sepsis_072

description: RMA normalized transcripts


title: SIRS_010

description: RMA normalized transcripts


title: Sepsis_071

description: RMA normalized transcripts


title: Sepsis_068

description: RMA normalized transcripts


title: SIRS_027

description: RMA normalized transcripts


title: Sepsis_064

description: RMA normalized transcripts


title: Sepsis_061

description: RMA normalized transcripts


title: Sepsis_067

description: RMA normalized transcripts


title: Sepsis_062

description: RMA normalized transcripts


title: Sepsis_066

description: RMA normalized transcripts


title: Sepsis_065

description: RMA normalized transcripts


title: Sepsis_069

description: RMA normalized transcripts


title: SIRS_003

description: RMA normalized transcripts


title: Leaf 2 8mm primordium

source_name: Leaf 2 8mm primordium


title: Sepsis_059

description: RMA normalized transcripts


title: Sepsis_060

description: RMA normalized transcripts


title: Sepsis_058

description: RMA normalized transcripts


title: Sepsis_056

description: RMA normalized transcripts


title: Sepsis_049

description: RMA normalized transcripts


title: Sepsis_052

description: RMA normalized transcripts


title: Sepsis_053

description: RMA normalized transcripts


title: Sepsis_054

description: RMA normalized transcripts


title: Sepsis_055

description: RMA normalized transcripts


title: Sepsis_050

description: RMA normalized transcripts


title: Sepsis_048

description: RMA normalized transcripts


title: Sepsis_051

description: RMA normalized transcripts


title: Sepsis_045

description: RMA normalized transcripts


title: Sepsis_046

description: RMA normalized transcripts


title: Sepsis_047

description: RMA normalized transcripts


title: Sepsis_040

description: RMA normalized transcripts


title: Sepsis_057

description: RMA normalized transcripts


title: Sepsis_042

description: RMA normalized transcripts


title: Sepsis_044

description: RMA normalized transcripts


title: Sepsis_043

description: RMA normalized transcripts


title: Sepsis_041

description: RMA normalized transcripts


title: Sepsis_039

description: RMA normalized transcripts


title: Sepsis_038

description: RMA normalized transcripts


title: Sepsis_037

description: RMA normalized transcripts


title: SAHA biological rep 2

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

description: Gene expression data from mouse dendritic cells treated with SAHA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Affymetrix microarray data were published and analyzed using R statistical environment ( version 2.7) (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The probesets were selected based on a two-fold difference with the added constraint that at least one sample had to have an expression value of 26 or greater. This protects us from choosing probesets with a large fold change that is based on two small numbers.

source_name: Mouse dendritic cells treated with SAHA

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

growth_protocol: To obtain mouse dendritic cells, bone marrows were extracted from at least 3 mice for each experiment, and were cultured with murine recombinant GM-CSF (10 ng/ml; BDPharmingen) and IL-4 (10 ng/ml; Peprotech) for 7 days, then harvested and positively selected by the autoMACS® Pro Separator (Miltenyi Biotec) for CD11C+ cells. The purity was confirmed by FACS staining ( 95%).

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

treatment_protocol: Mouse DCs were  treated with SAHA (500 nm) or diluent for 12 hours

tag: strain

tag: treatment

value: SAHA (500 nm)


title: Sepsis_036

description: RMA normalized transcripts


title: Sepsis_035

description: RMA normalized transcripts


title: SAHA biological rep 1


title: control biological rep 2

description: Gene expression data from mouse dendritic cells treated with control diluent

source_name: Mouse dendritic cells treated with diluent

value: control


title: Sepsis_034

description: RMA normalized transcripts


title: control biological rep 1


title: SIRS_007

description: RMA normalized transcripts


title: Sepsis_033

description: RMA normalized transcripts


title: Sepsis_030

description: RMA normalized transcripts


title: Sepsis_032

description: RMA normalized transcripts


title: Sepsis_031

description: RMA normalized transcripts


title: Sepsis_028

description: RMA normalized transcripts


title: Sepsis_029

description: RMA normalized transcripts


title: Sepsis_022

description: RMA normalized transcripts


title: Sepsis_025

description: RMA normalized transcripts


title: Sepsis_024

description: RMA normalized transcripts


title: Sepsis_023

description: RMA normalized transcripts


title: Sepsis_027

description: RMA normalized transcripts


title: Sepsis_026

description: RMA normalized transcripts


title: Sepsis_019

description: RMA normalized transcripts


title: Sepsis_021

description: RMA normalized transcripts


title: Sepsis_015

description: RMA normalized transcripts


title: Sepsis_016

description: RMA normalized transcripts


title: Sepsis_020

description: RMA normalized transcripts


title: MSU_M86R

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 2104H McGavran-Greenberg 135 Dauer Drive Campus Box 7435 27599-7435

department: Center for Environmental Health Sciences Integrated Sciences Facility Corencer Center

institute: University of North Carolina at Chapel Hill

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

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: LFD-HFD; Early

label_protocol: Labelled by following Agilent's Low Input Quick Amp Standard Protocol.

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

tag: diet group

value: LFD to HFD switch

tag: tumor occurrence

value: Early

tag: morphology

value: p53 spindle-like

tag: location

value: Mammary

source_name: Universal Mouse Reference RNA (stratagene)

tag: reference

value: 11 mouse cell lines


title: MSU_M63L

source_name: HFD; Late

value: HFD

value: Late

tag: tissue


title: Sepsis_014

description: RMA normalized transcripts


title: MSU_M56LA


title: MSU_M76R

source_name: LFD-HFD; Late


title: MSU_M54R


title: MSU_M32L

source_name: LFD; Late

value: LFD


title: Sepsis_018

description: RMA normalized transcripts


title: Sepsis_011

description: RMA normalized transcripts


title: Sepsis_013

description: RMA normalized transcripts


title: MSU_M33R


title: Sepsis_012

description: RMA normalized transcripts


title: MSU_M128L

source_name: HFD-LFD; Late

value: HFD to LFD switch


title: MSU_M18L


title: Sepsis_017

description: RMA normalized transcripts


title: Sepsis_009

description: RMA normalized transcripts


title: Sepsis_010

description: RMA normalized transcripts


title: Sepsis_007

description: RMA normalized transcripts


title: MSU_M118R


title: Sepsis_008

description: RMA normalized transcripts


title: Sepsis_006

description: RMA normalized transcripts


title: MSU_M129L

source_name: HFD-LFD; Early


title: MSU_90R

value: p53 variable


title: MSU_92R


title: MSU_82L


title: Sepsis_002

description: RMA normalized transcripts


title: Sepsis_003

description: RMA normalized transcripts


title: Sepsis_004

description: RMA normalized transcripts


title: Sepsis_005

description: RMA normalized transcripts


title: Sepsis_001

description: RMA normalized transcripts


title: MSU_66L


title: MSU_71L


title: MSU_62L


title: MSU_65R

source_name: HFD; Early


title: MSU_60L


title: MSU_57R


title: MSU_80L


title: MSU_40R4A


title: MSU_42L4B


title: MSU_56R


title: GBM157 day0-2

city: Ariake, Koto-ku

first: Rie

last: Ouchi

state: Tokyo

country: Japan

institute: Japanese Foundation for Cancer Research

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: GSC of GBM157

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: GSC was cultured in free serum medium including growth factors (generally called sphere medium). GSC was induced to NSGC by added serum (10% FBS).

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: source id

tag: tissue type

value: glioblastoma

tag: cell type

value: glioma stem cells (GSCs)

tag: time point

value: day 0


title: GBM157 day30 after serum exposure

source_name: GSC of GBM157 at day30 after serum exposure

value: senescent non-stem glioma cells (NSGCs)

value: day 30 after serum exposure


title: GBM157 day7 after serum exposure-1

source_name: GSC of GBM157 at day7 after serum exposure

value: differentiated non-stem glioma cells (NSGCs)

value: day 7 after serum exposure


title: GBM157 day7 after serum exposure-2


title: GBM157 day0-1


title: MSU_19R

value: Tumor


title: MSU_22R

source_name: LFD; Early

value: Early


title: GBM146 day7 after serum exposure-2

source_name: GSC of GBM146 at day7 after serum exposure


title: GBM146 day7 after serum exposure-1


title: Sepsis_063

description: RMA normalized transcripts

source_name: peripheral blood

value: Sepsis


title: GBM146 day0-2

source_name: GSC of GBM146


title: GBM146 day30 after serum exposure

source_name: GSC of GBM146 at day30 after serum exposure


title: MSU_27L4A

value: Mammary


title: MSU_31R

value: 11 mouse cell lines


title: MSU_17R


title: LMH_2 dpi_ILTV_rep3

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

description: Gene expression 2 days after ILTV infection in LMH cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a 4×44K Agilent Chicken Gene Expression Microarray (Design ID 026441)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis.

organism: Gallus gallus

source_name: LMH, 2 dpi, ILTV, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.

treatment_protocol: LMH cells were infected with LJS09 at a multiplicity of infection (MOI) of 0.1.

value: LMH

tag: infection

value: infected


title: MSU_13L

value: LFD

value: Late


title: LMH_2 dpi_ILTV_rep2

source_name: LMH, 2 dpi, ILTV, replicate 2


title: GBM146 day0-1


title: LMH_2 dpi_ILTV_rep1

source_name: LMH, 2 dpi, ILTV, replicate 1


title: LMH_2 dpi_ILTV_rep4

source_name: LMH, 2 dpi, ILTV, replicate 4


title: pDC_Untreated_3hrs_donor_4 (62_4_3)

city: Nutley

first: Kai

last: Lau

address: 340 Kingsland St

institute: Hoffmann-La Roche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to the manufacturer's instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 18,935 out of 54,675 probesets passed the QC and curation processes, corresponding to 10,260 unique genes.

source_name: pDC from donor 4, untreated, 3 hrs

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3'IVT Express Kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer's instructions on a GCAS (GeneChip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA Isolation Kit (Ambion, Inc., Austin, TX, USA) according to the manufacturer's protocol. RNA was quantified using a ND-1000 spectrophotometer (NanoDrop Technology®, Cambridge, UK), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The 260/280 ratios were between 1.7 and 2.1, and the RINs (RNA Integrity Numbers) were greater than 6 for all samples.

value: plasmacytoid dendritic cells (pDCs)

value: untreated

tag: timepoint

value: 3 hrs

tag: subject


title: MSU_122Rb

value: HFD to LFD switch

value: p53 variable

source_name: Universal Mouse Reference RNA (stratagene)


title: LMH_2 dpi_Control_rep4

description: Gene expression of control LMH cells

source_name: LMH, 2 dpi, Control, replicate 4


title: pDC_Untreated_3hrs_donor_4 (60_4_3)


title: LMH_2 dpi_Control_rep3

description: Gene expression of control LMH cells

source_name: LMH, 2 dpi, Control, replicate 3


title: MSU_11R


title: LMH_2 dpi_Control_rep1

description: Gene expression of control LMH cells

source_name: LMH, 2 dpi, Control, replicate 1


title: MSU_11L

source_name: LFD; Late


title: pDC_Gard_Btki_3hrs_donor_4 (59_4_3)

source_name: pDC from donor 4, gardiquimod_Btki, 3 hrs

value: gardiquimod and BTK inhibitor


title: Gills_HD_Troutlodge_rep1

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

description: Pool of 5 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

source_name: gill filaments

label_protocol: Five individual RNA samples from the same tissue (liver, gills, kidney), strain (Born or Troutlodge) and stocking density (MD, ED, HD) were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Tank (0.74 m length × 0.58 m width × 0.72 m height) with a volume of ~310 L water received a continuous supply of running brackish water from the Baltic sea (2.5–6 practical salinity units) with a flow rate of 100–150 L/h. Water quality was monitored in all of the tanks throughout the trial. Light:dark period was 17.5:6.5. The water quality parameters were maintained as follows: temperature 16.4–19.8 °C, dissolved oxygen 9.8–10.5 mg/l, and pH 7.4–7.8. Trout were fed commercial dry pellets by automatic feeders located centrally above each tank distributing the food 12 h/d.

extract_protocol: Entire liver; gill filaments; and head and trunk kidney were taken from ten Born and ten Troutlodge trout kept at MD, ED, and HD. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and quantitative real-time PCR (qPCR) assays.

treatment_protocol: Rainbow trout were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.

value: gill filaments

tag: gender

value: female

tag: age

value: 11 months

value: Troutlodge

tag: density

value: high


title: Gills_HD_Troutlodge_rep2

description: Pool of 5 individual RNAs

tag: strain


title: MSU_M84R

source_name: LFD-HFD; Early

tag: diet group

value: LFD to HFD switch

value: Early

value: p53 spindle-like

value: Mammary

value: Tumor


title: pDC_ODN2216_3hrs_donor_4 (57_4_3)

source_name: pDC from donor 4, ODN 2216, 3 hrs

tag: treatment


title: MSU_117R

source_name: HFD-LFD; Early

tag: tumor occurrence

tag: morphology

value: 11 mouse cell lines


title: MSU_117L

tag: location

tag: reference


title: Gills_HD_Born_rep2

description: Pool of 5 individual RNAs

tag: tissue

value: mixed

value: 10 months

value: Born


title: pDC_Gard_3hrs_donor_4 (53_4_3)

source_name: pDC from donor 4, gardiquimod, 3 hrs

value: plasmacytoid dendritic cells (pDCs)

value: gardiquimod

value: 3 hrs


title: LMH_2 dpi_Control_rep2

description: Gene expression of control LMH cells

source_name: LMH, 2 dpi, Control, replicate 2

tag: cell line

value: LMH


title: MSU_110R

source_name: HFD-LFD; Late

value: HFD to LFD switch

value: Late

value: p53 variable


title: P5-35-24h

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

country: Australia

institute: Children’s Cancer Institute Australia

description: xenograft cells Injected at 6-10 weeks

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The matrix non-normalized was generated using IlluminaExpressionFileCreator module in GenePattern. The data were then normalised using quantile normalisation with NormalizeColumns module in Genepattern

source_name: ALL-19 sample3 - 24h in vitro

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA kit for Illumina arrays

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly.

extract_protocol: RNA was extracted with a combination of Trizol reagent and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

value: Patient-derived xenograft cells (>95% hCD45+ cells) from mouse spleens

tag: host strain

value: NOD/SCID

tag: dexamethasone response

value: Resistant


title: P5-18-24h

description: xenograft cells Injected at 6-10 weeks

source_name: ALL-19 sample2 - 24h in vitro


title: pDC_Gard_Btki_3hrs_donor_3 (44_3_3)

source_name: pDC from donor 3, gardiquimod_Btki, 3 hrs

tag: cell type

value: gardiquimod and BTK inhibitor


title: pDC_Gard_3hrs_donor_3 (52_3_3)

source_name: pDC from donor 3, gardiquimod, 3 hrs

tag: timepoint


title: MSU_109L

value: Mammary

source_name: Universal Mouse Reference RNA (stratagene)


title: pDC_ODN2216_3hrs_donor_3 (50_3_3)

source_name: pDC from donor 3, ODN 2216, 3 hrs

tag: subject


title: Gills_MD_Troutlodge_rep2

description: Pool of 5 individual RNAs

value: gill filaments

tag: gender

value: female

value: 11 months

value: Troutlodge

value: moderate


title: Gills_HD_Born_rep1

description: Pool of 5 individual RNAs

value: mixed

tag: age

value: 10 months

value: Born

value: high


title: pDC_Untreated_3hrs_donor_3 (41_3_3)

source_name: pDC from donor 3, untreated, 3 hrs

value: plasmacytoid dendritic cells (pDCs)

value: untreated

value: 3 hrs


title: P5-35

description: xenograft cells Injected at 6-10 weeks

source_name: ALL-19 sample3

value: Patient-derived xenograft cells (>95% hCD45+ cells) from mouse spleens


title: P5-18

description: xenograft cells Injected at 6-10 weeks

source_name: ALL-19 sample2

value: NOD/SCID


title: Gills_MD_Born_rep2

description: Pool of 5 individual RNAs

tag: density


title: pDC_ODN2216_3hrs_donor_3 (38_3_3)


title: pDC_ODN2216_Btki_3hrs_donor_3 (39_3_3)

source_name: pDC from donor 3, ODN 2216_Btki, 3 hrs

value: ODN 2216 and BTK inhibitor


title: MSU_107R

value: HFD to LFD switch

value: Early

value: p53 variable

value: Tumor

value: 11 mouse cell lines


title: Gills_MD_Troutlodge_rep1

description: Pool of 5 individual RNAs

source_name: gill filaments

value: gill filaments

value: female

value: 11 months

tag: strain

value: Troutlodge


title: pDC_Gard_3hrs_donor_3 (37_3_3)

value: gardiquimod


title: P5-17-24h

description: xenograft cells Injected at 6-10 weeks

source_name: ALL-19 sample1 - 24h in vitro

value: Resistant


title: Gills_MD_Born_rep1

description: Pool of 5 individual RNAs

value: mixed

value: 10 months

value: Born

value: moderate


title: P5-17

description: xenograft cells Injected at 6-10 weeks

source_name: ALL-19 sample1

value: Patient-derived xenograft cells (>95% hCD45+ cells) from mouse spleens

value: NOD/SCID


title: Kidney_HD_Troutlodge_rep2

description: Pool of 5 individual RNAs

source_name: head and trunk kidney

value: head and trunk kidney

value: high


title: Kidney_HD_Born_rep2

description: Pool of 5 individual RNAs


title: NIH3T3-Kras at 72h+FSK biological replicate 3

city: Milan

first: Ferdinando

last: Chiaradonna

address: Piazza della scienza, 2

department: Biotechnology and Biosciences

country: Italy

institute: University of Milano-Bicocca

description: Gene expression data from NIH3T3-Kras at 72h of growth in imM glucose+FSK

hyb_protocol: 15ug of total RNA Biotinylated cRNA was hybridized to the Mouse MOE430 2.0 Genome Arrays (Affymetrix), following the manufacturer protocol.

scan_protocol: Chips were washed and scanned on the Affymetrix Complete GeneChip System, generating digitized image data files.

data_processing: The data were analyzed with R/Bioconductor package 'oligo' using the RMA method targeted at “core” probesets, and normalization and background correction turned on.

source_name: NIH3T3-Kras at 72h+FSK

label_protocol: cRNA was generated by using the Affymetrix One-Cycle target Labeling and Control Reagent kit (Affymetrix Inc), following the manufacturer protocol.

growth_protocol: Both cell lines are plated in 25 mM glucose. After 16h, the medium is changed with a new at in 1mM glucose andthe cells growth for further 72h.

treatment_protocol: Both cell lines are treated at 24h and 48h of growth in 1mM glucose with 10 uM Forskolin.

tag: cell line type

value: Transformed cell line


title: Placenta_WT2

city: Cardiff

first: Rosalind

middle: M

last: John

address: Museum Avenue

department: Biosciences

institute: Cardiff University

description: Phlda2 WT E16.5 Placenta, Biological Rep2

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

scan_protocol: 1-5 micro grams of good quality total RNA. Affymetrix genechip platform hybridication, washing and scanning of chip, along with QC of all samples and data on a CD-R.

data_processing: Data was initially analysed at the genome wide level using the Bioconductor packages such as Limma (Linear Model for Microarray data Analysis) written in R statistical software to identify differentially expressed genes between all pair-wise comparisons of the groups. Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to generate molecular function and biological processes pathway data on the unselected dataset highlighting significant changes in genes.

source_name: E16.5 Phlda2 WT Fetal Placenta

extract_protocol: Sigma GenElute™ Mammalian Total RNA Miniprep Kit.

value: Placenta

tag: Stage

tag: genotype/variation

value: E16.5 Phlda2+/+(129) (non-transgenic; 1X)


title: MSU_108R

source_name: HFD-LFD; Late

tag: diet group

value: HFD to LFD switch

tag: tumor occurrence

value: Late

tag: morphology

value: p53 variable

value: Mammary

value: Tumor

value: 11 mouse cell lines


title: Placenta_WT3

description: Phlda2 WT E16.5 Placenta, Biological Rep3

tag: tissue


title: pDC_ODN2216_Btki_3hrs_donor_3 (33_3_3)

value: plasmacytoid dendritic cells (pDCs)

tag: treatment

value: ODN 2216 and BTK inhibitor

value: 3 hrs


title: pDC_ODN2216_3hrs_donor_2 (30_2_3)

source_name: pDC from donor 2, ODN 2216, 3 hrs


title: pDC_Untreated_3hrs_donor_3 (36_3_3)

value: untreated


title: MSU_101L4A

source_name: LFD-HFD; Late

value: LFD to HFD switch

tag: location

tag: reference


title: Placenta_WT4

description: Phlda2 WT E16.5 Placenta, Biological Rep4


title: NIH3T3-Kras at 72h+FSK biological replicate 1

tag: cell line


title: Placenta_TG3

description: Phlda2 TG E16.5 Placenta, Biological Rep3

source_name: E16.5 Phlda2 TG Fetal Placenta

value: Phlda2+/+BACx1(129) (single copy Phlda2 transgene; 2X)


title: Kidney_HD_Troutlodge_rep1

description: Pool of 5 individual RNAs

value: head and trunk kidney

value: female

value: 11 months

value: Troutlodge


title: Placenta_WT1

description: Phlda2 WT E16.5 Placenta, Biological Rep1

value: Placenta

value: E16.5 Phlda2+/+(129) (non-transgenic; 1X)


title: Kidney_HD_Born_rep1

description: Pool of 5 individual RNAs

value: mixed

value: 10 months

value: Born

value: high


title: NIH3T3 at 72h+FSK biological replicate 3

description: Gene expression data from NIH3T3 at 72h of growth in imM glucose+FSK

source_name: NIH3T3 at 72h+FSK

value: Immortalized cell line


title: Kidney_MD_Troutlodge_rep2

description: Pool of 5 individual RNAs

value: moderate


title: Kidney_MD_Troutlodge_rep1

description: Pool of 5 individual RNAs


title: Placenta_TG2

description: Phlda2 TG E16.5 Placenta, Biological Rep2


title: pDC_Untreated_3hrs_donor_2 (28_2_3)

source_name: pDC from donor 2, untreated, 3 hrs

tag: cell type

value: plasmacytoid dendritic cells (pDCs)

tag: timepoint


title: pDC_Gard_3hrs_donor_2 (27_2_3)

source_name: pDC from donor 2, gardiquimod, 3 hrs

value: gardiquimod

value: 3 hrs

tag: subject


title: Kidney_MD_Born_rep2

description: Pool of 5 individual RNAs

tag: gender

tag: age


title: NIH3T3 at 72h+FSK biological replicate 2


title: pDC_ODN2216_3hrs_donor_2 (26_2_3)


title: NIH3T3-Kras at 72h no FSK biological replicate 3

description: Gene expression data from NIH3T3-Kras at 72h of growth in imM glucose

source_name: NIH3T3-Kras cells at 72h

value: Transformed cell line


title: NIH3T3 at 72h+FSK biological replicate 1


title: Placenta_TG1

description: Phlda2 TG E16.5 Placenta, Biological Rep1

tag: strain

value: Phlda2+/+BACx1(129) (single copy Phlda2 transgene; 2X)


title: pDC_Untreated_3hrs_donor_2 (22_2_3)

value: untreated


title: Placenta_KO3

description: Phlda2 KO E16.5 Placenta, Biological Rep3

source_name: E16.5 Phlda2 KO Fetal Placenta

value: Phlda2-/+(129) (maternal KO; 0X)


title: NIH3T3-Kras at 72h no FSK biological replicate 2

tag: cell line type


title: Liver_HD_Troutlodge_rep2

description: Pool of 5 individual RNAs

source_name: liver

value: liver

value: female

value: 11 months

tag: density


title: pDC_Gard_Btki_3hrs_donor_2 (25_2_3)

source_name: pDC from donor 2, gardiquimod_Btki, 3 hrs

value: gardiquimod and BTK inhibitor


title: NIH3T3-Kras at 72h+FSK biological replicate 2


title: pDC_Gard_3hrs_donor_2 (21_2_3)


title: Placenta_KO2

description: Phlda2 KO E16.5 Placenta, Biological Rep2

value: Placenta

tag: Stage

tag: genotype/variation


title: Placenta_KO4

description: Phlda2 KO E16.5 Placenta, Biological Rep4


title: Kidney_MD_Born_rep1

description: Pool of 5 individual RNAs

value: head and trunk kidney

value: mixed

value: 10 months


title: NIH3T3-Kras at 72h no FSK biological replicate 1


title: Liver_HD_Troutlodge_rep1

description: Pool of 5 individual RNAs

value: Troutlodge

value: high


title: pDC_ODN2216_Btki_3hrs_donor_1 (13_1_3)

source_name: pDC from donor 1, ODN 2216_Btki, 3 hrs

value: plasmacytoid dendritic cells (pDCs)

value: ODN 2216 and BTK inhibitor


title: pDC_Untreated_3hrs_donor_1 (15_1_3)

source_name: pDC from donor 1, untreated, 3 hrs

value: 3 hrs


title: PMA/Ionomycin+MALT1 Inhibitor, biol. rep. 1

city: Tübingen

first: Günter

last: Jäger

address: Calwerstr. 7

institute: Institute of Medical Genetics Tübingen

description: 80 ng/ml PMA and 1 µM ionomycin, 5µM LVSR-fmk, 8h

hyb_protocol: Following fragmentation, 5 ug cRNA were hybridized for 16 h at 45°C on GeneChip HuGene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using Affymetrix Expression Console with RMA as normalization method

source_name: Human primary keratinocytes, passage 2

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip WT Kit protocol from 5.5 ug total RNA (GeneChip WT Terminal Labeling and Hybridisation, Rev. 7).

growth_protocol: Primary keratinocytes from at least 3 donors were pooled and cultivated in CnT-BM.1 medium supplemented with the CnT-07 Supplement Pack and Gentamycin (all from CELLnTEC, Bern, Switzerland).

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: DMSO 1/1000, 8 h or 80 ng/ml PMA and 1 µM ionomycin, 8 h or pre-treatment with LVSR-fmk 5 µM for 30 min and  80 ng/ml PMA and 1 µM ionomycin, 8 h

value: PMA/Ionomycin+MALT1 Inhibitor


title: PMA/Ionomycin+MALT1 Inhibitor, biol. rep. 3


title: NIH3T3 at 72h no FSK biological replicate 3

description: Gene expression data from NIH3T3 at 72h of growth in imM glucose

source_name: NIH3T3 cells at 72h

value: Immortalized cell line


title: pDC_ODN2216_Btki_3hrs_donor_2 (17_2_3)

source_name: pDC from donor 2, ODN 2216_Btki, 3 hrs


title: NIH3T3 at 72h no FSK biological replicate 1


title: NIH3T3 at 72h no FSK biological replicate 2


title: PMA/Ionomycin, biol. rep. 3

description: 80 ng/ml PMA and 1 µM ionomycin, 8h

value: PMA/Ionomycin


title: pDC_ODN2216_3hrs_donor_1 (10_1_3)

source_name: pDC from donor 1, ODN 2216, 3 hrs


title: Liver_ED_Troutlodge_rep2

description: Pool of 5 individual RNAs

value: elevated


title: Liver_HD_Born_rep1

description: Pool of 5 individual RNAs

value: liver

value: Born


title: Liver_HD_Born_rep2

description: Pool of 5 individual RNAs


title: PMA/Ionomycin+MALT1 Inhibitor, biol. rep. 2


title: Liver_ED_Born_rep2

description: Pool of 5 individual RNAs


title: pDC_Gard_Btki_3hrs_donor_1 (7_1_3)

source_name: pDC from donor 1, gardiquimod_Btki, 3 hrs


title: pDC_Untreated_3hrs_donor_1 (5_1_3)

value: untreated


title: pDC_Gard_3hrs_donor_1 (8_1_3)

source_name: pDC from donor 1, gardiquimod, 3 hrs

value: gardiquimod


title: Liver_ED_Troutlodge_rep1

description: Pool of 5 individual RNAs

value: female

value: 11 months


title: Transgenic_biological replicate 2

city: Philadelphia

first: Christopher

last: Lengner

state: PA

address: 3800 Spruce Street, Room 390EA

department: Biomedical Sciences

institute: University of Pennsylvania

description:
Gene expression data from transgenic
tg3

hyb_protocol: 5.5ug of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA).The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Cel files were imported into Partek Genomics Suite v6.5 where RMA normalization was applied

source_name: Intestinal epthelial cells

label_protocol: All protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: No in vitro growth- primary murine intestinal epithelial cells were isolated.

extract_protocol: Total RNA was extracted using a 5-Prime PerfectPure RNA Tissue Kit

treatment_protocol: Mice were treated with doxycycline in the drinking water for 24 hours prior to isolation

value: TRE-MSI2::R26-M2rtTA (transgenic)

value: jejunum

value: intestinal epithelial cell


title: Control_biological replicate 3

description:
Gene expression data from control
ctr4

value: R26-M2rtTA (control)


title: PMA/Ionomycin, biol. rep. 2

description: 80 ng/ml PMA and 1 µM ionomycin, 8h


title: PMA/Ionomycin, biol. rep. 1

description: 80 ng/ml PMA and 1 µM ionomycin, 8h


title: DMSO, biol. rep. 3

description: DMSO 1/1000, 8h

value: DMSO


title: Liver_MD_Troutlodge_rep2

description: Pool of 5 individual RNAs

value: Troutlodge

value: moderate


title: Transgenic_biological replicate 3

description:
Gene expression data from transgenic
tg4


title: Liver_ED_Born_rep1

description: Pool of 5 individual RNAs

value: mixed

value: 10 months


title: Control_biological replicate 2

description:
Gene expression data from control
ctrl3


title: DMSO, biol. rep. 2

description: DMSO 1/1000, 8h


title: Control_biological replicate 1

description:
Gene expression data from control
ctrl2


title: Transgenic_biological replicate 1

description:
Gene expression data from transgenic
tg1


title: pDC_Gard_3hrs_donor_1 (3_1_3)

value: plasmacytoid dendritic cells (pDCs)

value: 3 hrs


title: Liver_MD_Troutlodge_rep1

description: Pool of 5 individual RNAs

value: liver


title: DMSO, biol. rep. 1

description: DMSO 1/1000, 8h


title: pDC_ODN2216_3hrs_donor_1 (1_1_3)


title: Liver_MD_Born_rep2

description: Pool of 5 individual RNAs

value: Born


title: DMSO treated 5 day

status: Public on Oct 23 2015

first: Joseph

last: ZHOU

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: replicate 1

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

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

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

value: Breast


title: drug14 treated 1 day

description: replicate 1


title: drug14 treated 5 day

description: replicate 1


title: DMSO treated 3 day

description: replicate 1


title: drug12 treated 3 day

description: replicate 1


title: drug15 treated 5 day

description: replicate 1


title: drug12 treated 1 day

description: replicate 1


title: drug16 treated 5 day

description: replicate 1


title: Untreated

description: replicate 1


title: drug15 treated 3 day

description: replicate 1


title: drug16 treated 1 day

description: replicate 1


title: drug13 treated 5 day

description: replicate 1


title: Liver_MD_Born_rep1

description: Pool of 5 individual RNAs


title: drug12 treated 5 day

description: replicate 1


title: drug16 treated 3 day

description: replicate 1


title: drug13 treated 3 day

description: replicate 1


title: drug11 treated 5 day

description: replicate 1


title: drug13 treated 1 day

description: replicate 1


title: drug14 treated 3 day

description: replicate 1


title: drug15 treated 1 day

description: replicate 1


title: drug11 treated 3 day

description: replicate 1


title: drug11 treated 1 day

description: replicate 1


title: drug9 treated 5 day

description: replicate 1


title: drug9 treated 3 day

description: replicate 1


title: drug10 treated 3 day

description: replicate 1


title: drug9 treated 1 day

description: replicate 1


title: drug7 treated 5 day

description: replicate 1


title: drug8 treated 1 day

description: replicate 1


title: drug7 treated 3 day

description: replicate 1


title: drug3 treated 1 day

description: replicate 1


title: drug8 treated 5 day

description: replicate 1


title: drug8 treated 3 day

description: replicate 1


title: drug10 treated 1 day

description: replicate 1


title: drug6 treated 3 day

description: replicate 1


title: drug5 treated 5 day

description: replicate 1


title: drug4 treated 1 day

description: replicate 1


title: Sputum_R145

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.

source_name: Sputum sample from R145 (group:Asthma)

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: Sex

value: Male

tag: disease

value: Asthma

value: Sputum

tag: subtype

value: pauci


title: drug1 treated 5 day

description: replicate 1

tag: tissue


title: drug1 treated 1 day rep1

description: replicate 2


title: drug7 treated 1 day

description: replicate 1


title: drug1 treated 3 day

description: replicate 1


title: drug6 treated 1 day

description: replicate 1


title: drug6 treated 5 day

description: replicate 1


title: drug3 treated 5 day

description: replicate 1


title: drug2 treated 5 day

description: replicate 1


title: drug4 treated 3 day

description: replicate 1


title: drug5 treated 1 day

description: replicate 1


title: drug5 treated 3 day

description: replicate 1


title: drug1 treated 1 day rep2

description: replicate 3


title: drug1 treated 1 day

description: replicate 1


title: Sputum_R132

source_name: Sputum sample from R132 (group:Control)

value: Control

value: neutro


title: Sputum_R137

source_name: Sputum sample from R137 (group:Asthma)


title: Sputum_R130

source_name: Sputum sample from R130 (group:Control)

value: Female


title: Sputum_R139

source_name: Sputum sample from R139 (group:Asthma)


title: Sputum_R127

source_name: Sputum sample from R127 (group:Asthma)

value: eosino


title: Sputum_R126

source_name: Sputum sample from R126 (group:Asthma)


title: Sputum_R120

source_name: Sputum sample from R120 (group:Asthma)


title: Sputum_R112

source_name: Sputum sample from R112 (group:Asthma)


title: Placenta_KO1

description: Phlda2 KO E16.5 Placenta, Biological Rep1

source_name: E16.5 Phlda2 KO Fetal Placenta

value: Placenta

value: Phlda2-/+(129) (maternal KO; 0X)


title: Sputum_R119

source_name: Sputum sample from R119 (group:Asthma)


title: Sputum_R123

source_name: Sputum sample from R123 (group:Asthma)

value: mixed


title: Sputum_R102

source_name: Sputum sample from R102 (group:Asthma)


title: Sputum_R104

source_name: Sputum sample from R104 (group:Asthma)


title: Sputum_R107

source_name: Sputum sample from R107 (group:Asthma)


title: Sputum_R100

source_name: Sputum sample from R100 (group:Asthma)


title: Sputum_R109

source_name: Sputum sample from R109 (group:Control)


title: Sputum_R88

source_name: Sputum sample from R88 (group:Asthma)


title: Sputum_R93

source_name: Sputum sample from R93 (group:Asthma)


title: Sputum_R86

source_name: Sputum sample from R86 (group:Asthma)


title: Sputum_R76

source_name: Sputum sample from R76 (group:Asthma)


title: Sputum_R92

source_name: Sputum sample from R92 (group:Asthma)


title: Sputum_R78

source_name: Sputum sample from R78 (group:Asthma)


title: Sputum_R90

source_name: Sputum sample from R90 (group:Asthma)


title: Sputum_R71

source_name: Sputum sample from R71 (group:Asthma)


title: Sputum_R87

source_name: Sputum sample from R87 (group:Asthma)


title: Sputum_R72

source_name: Sputum sample from R72 (group:Asthma)


title: Sputum_R68

source_name: Sputum sample from R68 (group:Asthma)


title: Sputum_R82

source_name: Sputum sample from R82 (group:)


title: Sputum_R64

source_name: Sputum sample from R64 (group:Control)


title: Sputum_R69

source_name: Sputum sample from R69 (group:Asthma)


title: Sputum_R60

source_name: Sputum sample from R60 (group:Asthma)


title: Sputum_R97

source_name: Sputum sample from R97 (group:Asthma)


title: Sputum_R80

source_name: Sputum sample from R80 (group:Asthma)


title: Sputum_R39

source_name: Sputum sample from R39 (group:Asthma)


title: Sputum_R53

source_name: Sputum sample from R53 (group:Asthma)


title: Sputum_R49

source_name: Sputum sample from R49 (group:Asthma)


title: Sputum_R41

source_name: Sputum sample from R41 (group:Asthma)


title: Sputum_R44

source_name: Sputum sample from R44 (group:Asthma)


title: Sputum_R50

source_name: Sputum sample from R50 (group:Control)


title: Sputum_R56

source_name: Sputum sample from R56 (group:Control)


title: Sputum_R67

source_name: Sputum sample from R67 (group:Asthma)


title: Sputum_R37

source_name: Sputum sample from R37 (group:Asthma)


title: Sputum_R36

source_name: Sputum sample from R36 (group:Asthma)


title: Sputum_R40

source_name: Sputum sample from R40 (group:Asthma)


title: Sputum_R33

source_name: Sputum sample from R33 (group:Asthma)


title: Sputum_R19

source_name: Sputum sample from R19 (group:Asthma)


title: Sputum_R26

source_name: Sputum sample from R26 (group:Control)


title: Sputum_R21

source_name: Sputum sample from R21 (group:Asthma)


title: Sputum_R31

source_name: Sputum sample from R31 (group:Control)


title: Sputum_R29

source_name: Sputum sample from R29 (group:Asthma)


title: Sputum_R14

source_name: Sputum sample from R14 (group:Asthma)


title: Sputum_R27

source_name: Sputum sample from R27 (group:Control)


title: Sputum_R9

source_name: Sputum sample from R9 (group:Asthma)


title: Sputum_R5

source_name: Sputum sample from R5 (group:Asthma)


title: NS_R145

source_name: Nasal Scrape sample from R145 (group:Asthma)

value: Nasal Scrape


title: Sputum_R17

source_name: Sputum sample from R17 (group:Asthma)


title: NS_R144

source_name: Nasal Scrape sample from R144 (group:Asthma)


title: NS_R141

source_name: Nasal Scrape sample from R141 (group:Asthma)


title: NS_R140

source_name: Nasal Scrape sample from R140 (group:Asthma)


title: Sputum_R63

source_name: Sputum sample from R63 (group:Asthma)


title: NS_R134

source_name: Nasal Scrape sample from R134 (group:Control)


title: NS_R129

source_name: Nasal Scrape sample from R129 (group:Asthma)


title: NS_R137

source_name: Nasal Scrape sample from R137 (group:Asthma)


title: NS_R127

source_name: Nasal Scrape sample from R127 (group:Asthma)


title: NS_R136

source_name: Nasal Scrape sample from R136 (group:Asthma)


title: NS_R128

source_name: Nasal Scrape sample from R128 (group:Asthma)


title: NS_R139

source_name: Nasal Scrape sample from R139 (group:Asthma)


title: NS_R138

source_name: Nasal Scrape sample from R138 (group:Asthma)


title: NS_R126

source_name: Nasal Scrape sample from R126 (group:Asthma)


title: NS_R130

source_name: Nasal Scrape sample from R130 (group:Control)


title: NS_R131

source_name: Nasal Scrape sample from R131 (group:Asthma)


title: NS_R123

source_name: Nasal Scrape sample from R123 (group:Asthma)


title: NS_R125

source_name: Nasal Scrape sample from R125 (group:Asthma)


title: NS_R122

source_name: Nasal Scrape sample from R122 (group:Asthma)


title: NS_R132

source_name: Nasal Scrape sample from R132 (group:Control)


title: NS_R121

source_name: Nasal Scrape sample from R121 (group:Asthma)


title: NS_R120

source_name: Nasal Scrape sample from R120 (group:Asthma)


title: NS_R119

source_name: Nasal Scrape sample from R119 (group:Asthma)


title: NS_R115

source_name: Nasal Scrape sample from R115 (group:Asthma)


title: NS_R114

source_name: Nasal Scrape sample from R114 (group:Control)


title: NS_R117

source_name: Nasal Scrape sample from R117 (group:Asthma)


title: drug10 treated 5 day

description: replicate 1


title: NS_R116

source_name: Nasal Scrape sample from R116 (group:Asthma)


title: NS_R112

source_name: Nasal Scrape sample from R112 (group:Asthma)


title: NS_R101

source_name: Nasal Scrape sample from R101 (group:Asthma)


title: NS_R104

source_name: Nasal Scrape sample from R104 (group:Asthma)


title: NS_R107

source_name: Nasal Scrape sample from R107 (group:Asthma)


title: NS_R97

source_name: Nasal Scrape sample from R97 (group:Asthma)


title: NS_R109

source_name: Nasal Scrape sample from R109 (group:Control)


title: NS_R102

source_name: Nasal Scrape sample from R102 (group:Asthma)


title: NS_R95

source_name: Nasal Scrape sample from R95 (group:Asthma)


title: NS_R113

source_name: Nasal Scrape sample from R113 (group:Asthma)


title: NS_R99

source_name: Nasal Scrape sample from R99 (group:Asthma)


title: NS_R108

source_name: Nasal Scrape sample from R108 (group:Control)


title: NS_R96

source_name: Nasal Scrape sample from R96 (group:Asthma)


title: NS_R98

source_name: Nasal Scrape sample from R98 (group:Control)


title: NS_R100

source_name: Nasal Scrape sample from R100 (group:Asthma)


title: NS_R94

source_name: Nasal Scrape sample from R94 (group:Asthma)


title: NS_R89

source_name: Nasal Scrape sample from R89 (group:Asthma)


title: NS_R91

source_name: Nasal Scrape sample from R91 (group:Asthma)


title: NS_R93

source_name: Nasal Scrape sample from R93 (group:Asthma)


title: NS_R105

source_name: Nasal Scrape sample from R105 (group:Asthma)


title: NS_R87

source_name: Nasal Scrape sample from R87 (group:Asthma)


title: NS_R88

source_name: Nasal Scrape sample from R88 (group:Asthma)


title: NS_R82

source_name: Nasal Scrape sample from R82 (group:)


title: NS_R92

source_name: Nasal Scrape sample from R92 (group:Asthma)


title: NS_R86

source_name: Nasal Scrape sample from R86 (group:Asthma)


title: NS_R83

source_name: Nasal Scrape sample from R83 (group:Asthma)


title: NS_R81

source_name: Nasal Scrape sample from R81 (group:Control)


title: NS_R76

source_name: Nasal Scrape sample from R76 (group:Asthma)


title: NS_R85

source_name: Nasal Scrape sample from R85 (group:Control)


title: NS_R79

source_name: Nasal Scrape sample from R79 (group:Asthma)


title: NS_R90

source_name: Nasal Scrape sample from R90 (group:Asthma)


title: NS_R77

source_name: Nasal Scrape sample from R77 (group:Asthma)


title: NS_R67

source_name: Nasal Scrape sample from R67 (group:Asthma)


title: NS_R84

source_name: Nasal Scrape sample from R84 (group:Asthma)


title: NS_R74

source_name: Nasal Scrape sample from R74 (group:Asthma)


title: NS_R68

source_name: Nasal Scrape sample from R68 (group:Asthma)


title: NS_R78

source_name: Nasal Scrape sample from R78 (group:Asthma)


title: NS_R69

source_name: Nasal Scrape sample from R69 (group:Asthma)


title: NS_R73

source_name: Nasal Scrape sample from R73 (group:Asthma)


title: NS_R75

source_name: Nasal Scrape sample from R75 (group:Asthma)


title: NS_R65

source_name: Nasal Scrape sample from R65 (group:Asthma)


title: NS_R80

source_name: Nasal Scrape sample from R80 (group:Asthma)


title: NS_R72

source_name: Nasal Scrape sample from R72 (group:Asthma)


title: NS_R70

source_name: Nasal Scrape sample from R70 (group:Control)


title: NS_R63

source_name: Nasal Scrape sample from R63 (group:Asthma)


title: NS_R64

source_name: Nasal Scrape sample from R64 (group:Control)


title: NS_R71

source_name: Nasal Scrape sample from R71 (group:Asthma)


title: NS_R58

source_name: Nasal Scrape sample from R58 (group:Asthma)


title: NS_R61

source_name: Nasal Scrape sample from R61 (group:Asthma)


title: NS_R57

source_name: Nasal Scrape sample from R57 (group:Asthma)


title: NS_R60

source_name: Nasal Scrape sample from R60 (group:Asthma)


title: NS_R55

source_name: Nasal Scrape sample from R55 (group:Asthma)


title: NS_R56

source_name: Nasal Scrape sample from R56 (group:Control)


title: NS_R62

source_name: Nasal Scrape sample from R62 (group:Asthma)


title: NS_R53

source_name: Nasal Scrape sample from R53 (group:Asthma)


title: NS_R51

source_name: Nasal Scrape sample from R51 (group:Asthma)


title: NS_R50

source_name: Nasal Scrape sample from R50 (group:Control)


title: NS_R49

source_name: Nasal Scrape sample from R49 (group:Asthma)


title: NS_R59

source_name: Nasal Scrape sample from R59 (group:Asthma)


title: NS_R44

source_name: Nasal Scrape sample from R44 (group:Asthma)


title: NS_R52

source_name: Nasal Scrape sample from R52 (group:Asthma)


title: NS_R46

source_name: Nasal Scrape sample from R46 (group:Asthma)


title: NS_R43

source_name: Nasal Scrape sample from R43 (group:Asthma)


title: NS_R40

source_name: Nasal Scrape sample from R40 (group:Asthma)


title: NS_R54

source_name: Nasal Scrape sample from R54 (group:Asthma)


title: NS_R45

source_name: Nasal Scrape sample from R45 (group:Control)


title: NS_R33

source_name: Nasal Scrape sample from R33 (group:Asthma)


title: NS_R32

source_name: Nasal Scrape sample from R32 (group:Control)


title: NS_R39

source_name: Nasal Scrape sample from R39 (group:Asthma)


title: NS_R36

source_name: Nasal Scrape sample from R36 (group:Asthma)


title: NS_R31

source_name: Nasal Scrape sample from R31 (group:Control)


title: NS_R37

source_name: Nasal Scrape sample from R37 (group:Asthma)


title: NS_R48

source_name: Nasal Scrape sample from R48 (group:Asthma)


title: NS_R30

source_name: Nasal Scrape sample from R30 (group:Control)


title: NS_R47

source_name: Nasal Scrape sample from R47 (group:Asthma)


title: NS_R42

source_name: Nasal Scrape sample from R42 (group:Asthma)


title: NS_R29

source_name: Nasal Scrape sample from R29 (group:Asthma)


title: NS_R27

source_name: Nasal Scrape sample from R27 (group:Control)


title: NS_R28

source_name: Nasal Scrape sample from R28 (group:Control)


title: NS_R34

source_name: Nasal Scrape sample from R34 (group:Asthma)


title: NS_R25

source_name: Nasal Scrape sample from R25 (group:Asthma)


title: NS_R26

source_name: Nasal Scrape sample from R26 (group:Control)


title: NS_R24

source_name: Nasal Scrape sample from R24 (group:Asthma)


title: NS_R22

source_name: Nasal Scrape sample from R22 (group:Asthma)


title: NS_R41

source_name: Nasal Scrape sample from R41 (group:Asthma)


title: NS_R21

source_name: Nasal Scrape sample from R21 (group:Asthma)


title: NS_R20

source_name: Nasal Scrape sample from R20 (group:Asthma)


title: NS_R19

source_name: Nasal Scrape sample from R19 (group:Asthma)


title: LAE_AA-094

source_name: Bronchial epithelial brushing sample from AA-094 (Moderate Asthma)

value: F

tag: severity

value: Moderate

value: Lower airway (bronchial)


title: LAE_AA-095

source_name: Bronchial epithelial brushing sample from AA-095 (Moderate Asthma)

value: M


title: LAE_AA-088

source_name: Bronchial epithelial brushing sample from AA-088 (Moderate Asthma)


title: LAE_AA-090

source_name: Bronchial epithelial brushing sample from AA-090 (Moderate Asthma)


title: LAE_AA-082

source_name: Bronchial epithelial brushing sample from AA-082 (Mild Asthma)

value: Mild


title: LAE_AA-093

source_name: Bronchial epithelial brushing sample from AA-093 (Moderate Asthma)


title: LAE_AA-091

source_name: Bronchial epithelial brushing sample from AA-091 (Moderate Asthma)


title: LAE_AA-080

source_name: Bronchial epithelial brushing sample from AA-080 (Mild Asthma)


title: LAE_AA-079

source_name: Bronchial epithelial brushing sample from AA-079 (Mild Asthma)


title: NS_R18

source_name: Nasal Scrape sample from R18 (group:Asthma)

value: Male


title: CTL-HSPC-replicate2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
sh_CTL_12052010
Gene expression data from HSPC control samples.
Hematopoietic immature cells.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: HSPCs, control

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit).

growth_protocol: HSPCs from cord blood were isolated using MACS and cell sorting. Cells were thereafter incubated with lentiviral vectors allowing to either increase or reduce TAL1 expression. Control cells were transduced with a GFP-encoding lentivector.

treatment_protocol: We have used lentiviral vector transduction of human cord blood HSPCs to overexpress (O/E) or knock down (KD) SCL/TAL1. Cells were lysed 24 hours after the end of transduction.

value: CD34+CD38-lowCD34RA-CD90+ HSPCs from cord blood

tag: tal1 expression

value: control


title: CTL-HSPC-replicate1

description:
sh_CTL_02102010
Gene expression data from HSPC control samples.
Hematopoietic immature cells.


title: LAE_AA-077

source_name: Bronchial epithelial brushing sample from AA-077 (Moderate Asthma)

value: Asthma


title: O/E TAL1_HSPC_replicate3

description:
pV81/TAL1_18032010
Gene expression data from HSPC O/E TAL1.
Hematopoietic immature cells.

source_name: HSPCs, TAL1 overexpression

value: overexpression


title: O/E TAL1_HSPC_replicate2

description:
pV81/TAL1_12052010
Gene expression data from HSPC O/E TAL1.
Hematopoietic immature cells.


title: CTL-HSPC-replicate3

description:
sh_CTLl_18032010
Gene expression data from HSPC control samples.
Hematopoietic immature cells.


title: LAE_AA-073

source_name: Bronchial epithelial brushing sample from AA-073 (Healthy Control)

value: Control

value: Healthy


title: LAE_AA-074

source_name: Bronchial epithelial brushing sample from AA-074 (Mild Asthma)


title: LAE_AA-070

source_name: Bronchial epithelial brushing sample from AA-070 (Mild Asthma)


title: scramble_3 days_ischemic_G21

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

description: sample 13 (scramble-ischemic replicate 2)

data_processing: Summarized signal intensities were generated in BRB ArrayTools using justRMA

source_name: scramble_3 days_ischemic

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

treatment_protocol: In vivo down-modulation of miR-210 was carried out by tail vein injection of Locked Nucleic Acid (LNA) oligonucleotides against miR-210 (anti-miR-210) or scrambled (SCR) control sequence (In vivo LNAmicroRNA Inhibitors, Exiqon).The following 15mers LNA-enhanced sequences with complete phosphothioate backbone were used: anti-miR-210, GCTGTCACACGCACA; SCR, CGTCTAGCCACCTAG. Twelve mg/Kg of anti-miR-210 LNA or scrambled LNA were diluted in 200 µl of saline and injected in the tail vein of 2 different groups of CD1mice, 2 days before femoral artery dissection. Mice were sacrified 3 days later and gastrocnemius muscles were harvested

value: 2 months

tag: injected with

value: scrambled control sequence (SCR)

value: gastrocnemius


title: anti-miR-210_3 days_control_G11

description: sample 11 (anti-miR-210-non ischemic replicate 4)

source_name: anti-miR-210_3 days_control

value: miR-210 complementary LNA-oligonucleotide (anti-miR-210)


title: anti-miR-210_3 days_control_G10

description: sample 10 (anti-miR-210-non ischemic replicate 3)


title: scramble_3 days_ischemic_G22

description: sample 14 (scramble-ischemic replicate 3)


title: LAE_AA-069

source_name: Bronchial epithelial brushing sample from AA-069 (Healthy Control)


title: anti-miR-210_3 days_control_G9

description: sample 9 (anti-miR-210-non ischemic replicate 2)


title: LAE_AA-097

source_name: Bronchial epithelial brushing sample from AA-097 (Moderate Asthma)


title: anti-miR-210_3 days_control_G8

description: sample 8 (anti-miR-210-non ischemic replicate 1)


title: LAE_AA-085

source_name: Bronchial epithelial brushing sample from AA-085 (Moderate Asthma)


title: LAE_AA-086

source_name: Bronchial epithelial brushing sample from AA-086 (Moderate Asthma)


title: scramble_3 days_control_G7

description: sample 7 (scramble-non ischemic replicate 4)

source_name: scramble_3 days_control