title: Activated Neutrophils (MRL/MpJ), biological replicate 3

value: Neutrophils activated using immune complex


title: Activated Neutrophils (C57Bl/6J), biological replicate 3

status: Public on Jun 24 2015

type: RNA

city: Lübeck

first: Saleh

middle: M.

last: Ibrahim

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Dermatology

country: Germany

institute: Universität zu Lübeck

description: Neutrophils activated using immune complex

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data was processed using oligo R package. The data was normalized using RMA method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Neutrophils

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: Neutrophils were derived from bone marrow of MRL/MpJ and C57Bl/6J mice.

extract_protocol: Total RNA was isolated from neutrophils using TRIzol (Invitrogen, Germany). Total RNA was digested with DNase, and cDNA synthesis from 500 ng of RNA was carried out using a SuperScript first-strand synthesis system for RT-PCR (Invitrogen).

treatment_protocol: The derived neutrophils were stimulated from immune complexes (IC) and Phorbol myristate acetate (PMA).

tag: strain

tag: sample type


title: Activated Neutrophils (C57Bl/6J), biological replicate 2


title: GW_010 Head and neck squamous cell carcinoma Illumina HT12v4

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

hyb_protocol: 750 ng of cRNA were hybridized to Human HT12 v4 Expression BeadChips (Illumina, San Diego, CA, USA)

scan_protocol: and scanned on the Illumina HiScan instrument according to the manufacturer’s specifications

data_processing: Raw data of all 47,323 probes was extracted by Illumina GenomeStudio without additional background correction. Data was further processed within R / Bioconductor. Expression values were log2-transformed and normalized using RSN. Batch effects of expression BeadChips were corrected using ComBat. Two criteria were used to remove arrays of low quality. First, the number of detected features with P<0.01 on an array was required to be within 3 interquartile ranges from the median of all arrays. 9 samples did not pass this criterion. Second, the Mahalanobis distance of several quality characteristics was computed for each array. These quality characteristics included signals from perfect-match and miss-match control probes, control probes present at different concentrations, mean of negative control probes, mean of house-keeping genes, number of expressed genes, mean signal strength of biotin-control-probes, and Euclidean distances of expression values. Thereby, Euclidean distances of expression values of each sample were based on their distances to the center, which was defined as the average of all samples after removing 10% samples farthest away from the center. The Mahalanobis distances of 4 arrays were more than 3 interquartile ranges away from the median of all arrays and were therefore excluded. Overall, of the assayed 300 samples 13 samples were excluded for quality reasons. Features detected by Illumina GenomeStudio with P<0.05 in less than 1% of the samples were excluded resulting in 31,347 features. Additionally, 17 feature were removed as their expression levels were still found to be significantly associated after Bonferroni-correction with batches of BeadChips. Finally, the preprocessing resulted in 31,330 features.  There were 12 paired measurements in the data including 10 pairs of samples taken from the same patients at short intervals, 1 pair of a primary and relapse tumor and 1 pair of biopsies from a first and second relapse. To remove the duplicates, the array with more detected features at P<0.01 was selected from each pair. Among the remaining 275 samples, 3 were taken from lymph node metastases and 2 were cell lines and 270 (included here) were tumor samples.

organism: Homo sapiens

label_protocol: Before microarray analysis RNA integrity and concentration was examined on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6.000 LabChip Kit (Agilent Technologies) according to the manufacturer’s instructions. Of the available 307 tumor samples 298 samples fulfilled criteria of good RNA-quality and together with 2 additional tumor cell lines were selected for further analysis conducted at the microarray core facility of the Interdisciplinary Center for Clinical Research Leipzig (Faculty of Medicine, University of Leipzig). 250 ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 100 – 150 ng/µl prior to probe synthesis using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

extract_protocol: Biopsy samples of HNSCC taken during panendoscopy or definitive surgery. They were immediately transfered into TRIzol™ (Invitrogen, Darmstadt, Germany) and then stored at -80°C until mechanical disintegration of the frozen sample for 80 sec at 4000 rpm in a Peqlab MiniLys (Peqlab, Erlangen, Germany) followed by isolation of DNA, RNA, and protein according to the method of Chomczynski (1) as specified in the standard TRIzol® protocol provided by the manufacturer (Invitrogen). The aqueous phase was used for RNA preparation by use of the Ambion Pure Link™ RNA Mini Kit (Life technologies, Carlsbad) including the on-column DNase I digestion (Qiagen, Hilden, Germany) according the manufacturer’s instructions. After ethanol precipitation of the interphase, DNA was resolved in water and used without further cleanup. Quantity and quality of DNA and RNA were determined by measuring optical density (OD) at λ1=260 nm and λ2=280 nm using the Take3 plate (BioTek, Bad Friedrichshall, Germany) in the Synergy2 spectrophotometer (BioTek), and a quotient of (OD1/OD2)>1.8 and >1.95 were regarded as sufficient quality of DNA and RNA, respectively.

tag: ID

tag: gender

value: F

tag: age

tag: smoking

value: Yes

tag: packyears

tag: alcohol

value: no

value: Primary

value: Cavum Oris

value: IVA

tag: treatment

value: multi

value: Negative

value: DNA-

tag: os

value: FALSE

tag: pfs

value: Basal 4

value: WT


title: GW_069 Head and neck squamous cell carcinoma Illumina HT12v4

value: M


title: Un-activated Neutrophils (C57Bl/6J), biological replicate 1

description: Neutrophils unactivated

value: Neutrophils unactivated


title: GW_012 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: II

value: Mesenchymal 3


title: GW_018 Head and neck squamous cell carcinoma Illumina HT12v4

value: Other HPV

value: TRUE

value: Disruptive


title: adipo-d3_siMEST_vs_siC_rep2

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

description: Biological replicate 1, cells harvested at day 3 after induction of adipocye differentiation

hyb_protocol: Shortly before hybridization, microarrays were washed in 0.2% SDS (3 times, 2 min each) and ddH2O (4 times, 1 min each), then incubated in prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 45 min, again washed with ddH2O (five times, 30 sec each), finally dipped in isopropanol, and dried by immediate centrifugation. Immediately before applying the labeled cDNA samples to the microarray, the samples were heated at 95°C for 3 min, snap cooled on ice for 30 sec and centrifuged for 1 min at maximum speed. The sample was pipetted onto the microarray surface, and a rectangular coverslip was gradually lowered, distributing the sample across the spotted area of the microarray. Hybridization was performed by incubation at 42°C for 16-20 h. Subsequently, microarrays were submerged in wash buffer I (2x SSC, 0.1% SDS, preheated to 42°C) for 2 min, leading to separation of the microarray and the coverslip. Three washing steps (each 5 min at room temperature with gentle rotation) were performed using wash buffer I (2x SSC, 0.1% SDS, preheated to 30°C), wash buffer II (1x SSC), and wash buffer III (0.5xSSC). Finally, the microarray was dipped into ddH2O and dried by immediate centrifugation.

scan_protocol: Scanning of microarrays was performed with a GenePix 4000B microarray scanner (Axon Instruments) at 10 µm resolution using GenePix Pro 4.1 software (Axon Instruments).

data_processing: GenePix Pro 4.1 was used to filter out low intensity, saturated and inhomogenous spots. Further, the raw data was background corrected, normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026), and then exported as text-file containing log2 transformed ratios of gene expression.

source_name: hMADS cells, transfected with siRNA targeting MEST

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 15 µg total RNA in 16.5 µL RNase-free H2O were prepared. For reverse transcription (RT), 2 µL random primers (3 mg/ml, lifetechnologies # 48190-011) were added to the RNA sample, followed by incubation at 70°C for 10 min and snap-freezing on ice for 30 sec. Subsequently, the following agents were added to complete the RT reactions: 0.6 µL aminoallyl-dNTP mix (25 mM dATP, 25 mM dCTP, 25 mM dGTP, 15mM dTTP (all lifetechnologies #10297-018), 10mM aminoallyl-dUTP (Sigma #A0410)), 6 µL 5x first strand buffer, 3 µL 0.1 M DTT, 2 µL SuperScript II Reverse Transcriptase (all lifetechnologies #18064-014). After mixing, RT reactions were incubated at 42°C for ~18 h. RNA was then hydrolyzed by adding 10 µL 1  M NaOH and 10 µL 0.5 M EDTA, followed by incubation at 65°C for 15 min. Subsequently, pH was neutralized by adding 10 µL 1 M HCl. To remove unincorporated aminoallyl-dUTP, reactions were purified based on the QIAquick PCR purification kit (QIAGEN #28106). Briefly, 300 µL of buffer PB were added to each sample before transfer to a QIAquick column and centrifugation (13000 x rcf, 1 min). Flowthrough was discarded and the cDNA (captured in the column matrix) was washed twice by addition of 750 µL phosphate wash buffer (5 mM potassium phosphate (prepared from 1M potassium phosphate buffer, pH 8.5), 80% EtOH) and subsequent centrifugation and discarding of flowthrough as above. Finally, the column matrix was dried by additional centrifugation for 1 min at maximum speed, and elution of purified cDNA was performed with 60 µL 4 mM potassium phosphate (diluted from 1M potassium phosphate buffer, pH 8.5). Samples were dried completely in a SpeedVac for 45 min and then resuspended in 4.5 µL of 0.1 M Na2CO3 buffer. To label the samples with fluorescent dyes, 4.5 µL of Cy5 or Cy3 NHS-ester (GE healthcare #PA25001 and #PA23001, one aliquot dissolved in 73 µL DMSO and stored at -80°C) were added and the samples were mixed and incubated at room temperature in the dark for 1 h. To remove uncoupled NHS-ester dyes, labeled cDNA samples were purified using the QIAquick PCR purification kit (QIAGEN #28106) according to the manufacturer’s instructions. After elution of the purified labeled cDNA in 60 µL Buffer EB, samples were again completely dried in a SpeedVac for 45 min. Subsequently, samples were resuspended in 24 µL hybridization buffer (50% N,N-Dimethylformamide (Sigma #D4551), 5xSSC, 0.1% SDS) and 1 µL human COT-1 DNA (lifetechnologies #15279-011, 20µg/µL, prepared according to the manufacturer’s instructions) as well as 1 µL poly(A)-DNA (20µg/µL, lifetechnologies primer service) were added to block nonspecific hybridization.

growth_protocol: For experiments, hMADS cells (Rodriguez et al., 2005, PMID: 15867092) were used between passage (P) 19 and P21. Medium for proliferation of hMADS cells was termed Medium I and consisted of (DMEM 1 g/l Glc (Lonza #BE12-707F), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100ug/ml Normocin (InVivogen #ant-nr-2), 10% FBS (Lonza, #14-801F, Lot.no. 9SB031), supplemented with 2.5 ng/mL human Fibroblast Growth Factor 2 (hFGF2, Sigma #F0291). In this medium, hMADS cells had population doubling times of 48-96 h (depending on the passage number, i.e. the replicative age of cells). At densities in the range of 50–80% of optical confluence, passaging of cells was performed at passaging ratios between 1:2 and 1:4, depending on the actual population doubling time. Cells were cultivated in 100 mm dishes (Greiner Bio-One #664160), with 10 ml Medium I per dish, at 37°C in a humidified atmosphere with 5% CO2. For passaging, old medium was aspirated and cells were washed with Phosphate Buffered Saline (PBS, Invitrogen / Gibco #10010015) before incubation with 0.05% Trypsin with EDTA in PBS (Invitrogen / Gibco #15400054; 1mL per 100 mm dish) for 3–5 min at 37°C. Subsequently, Trypsin was inactivated by addition of Medium I (prewarmed to 37°C), and the cell suspension was transferred to new culture dishes according to the desired passaging ratio.

extract_protocol: At day 3 after induction of adipocyte differentiation, cells were harvested with TRIzol reagent (lifetechnologies, Catalog number 15596-026). Total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: Transient transfection of hMADS cells (when cells had reached confluence, designated day –2) with oligonucleotides (siRNAs, purchased from Dharmacon) was performed using HiPerFect transfection Reagent (QIAGEN #301707). Briefly, Medium I was changed 1 h before transfection (12 ml per 100 mm dish). The final oligonucleotide concentration was 10 nM. Therefore, previously established stock solutions of oligonucleotides (20 µm in sterile PBS, stored at -80°C) were thawed on ice. Subsequently, transfection mixtures were generatedby mixing 6.8 uL oligonucleotide stock solution, 1162 uL DMEM (without any additives) and 137 uL HiPerFect transfection reagent (for one 100 mm dish). The reactions were incubated at room temperature for 10 min and finally added dropwise onto the cells while gently swaying the dish. Adipocyte differentiation was induced two days later (designated day 0) by changing the medium to Medium II, consisting of DMEM(1 g/L Glc, Lonza Lonza #BE12-707F)/ Ham’s F12 (Lonza # BE12-615F) (50:50), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100 µg/mL Normocin (InVivogen #ant-nr-2), 10 nM human insulin (Sigma #I9278), 10 µg/mL apo-transferrin (Sigma #T2252), 0.2 nM T3 (Sigma #T6397), 100 nM rosiglitazone (Cayman Chemicals / BRL49653), 100 µM IBMX (Sigma #I7018) and 1 µm Dexamethasone (Sigma #D4902). 12 ml Medium II were used for 1 100mm dish.

tag: differentiation stage

value: early adipocyte differentiation

source_name: hMADS cells, transfected with control siRNA


title: adipo-d3_siMEST_vs_siC_rep3


title: GW_009 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Primary

value: III

value: Classical 2


title: GW_008 Head and neck squamous cell carcinoma Illumina HT12v4

value: Yes

value: multi

value: Atypical IR 1


title: GW_007 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: no

value: IVA

value: Basal 4

value: WT


title: GW_006 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: IVB

value: DNA+RNA+


title: GW_004 Head and neck squamous cell carcinoma Illumina HT12v4

value: M

value: mono

value: TRUE

value: Disruptive


title: adipo-d3_siMEST_vs_siC_rep1

value: early adipocyte differentiation


title: Activated Neutrophils (C57Bl/6J), biological replicate 1

value: Neutrophils activated using immune complex


title: GW_005 Head and neck squamous cell carcinoma Illumina HT12v4

value: No

value: Primary

value: FALSE


title: Un-activated Neutrophils (MRL/MpJ), biological replicate 1

description: Neutrophils unactivated

value: MRL/MpJ

value: Neutrophils unactivated


title: HSC3 TCF12

city: Taipei

first: Yi-Fen

last: Chen

address: No. 155, Li-Nong St., Section 2,

department: Institute of Oral Biology

country: Taiwan

institute: National Yang-Ming University

hyb_protocol: standard Affymetrix protocol. Qualified RNA was submitted to National Yang-Ming University VGH Genome Research Center (VYMGC) for GeneChip analysis.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: GeneSpring

source_name: HSC3 TCF12 cell line

growth_protocol: Cells were grown in an 37C. 5% CO2 incubator. OECM1 growth in RPMI 1640 with 10% FBS and 1% 3 in 1; HSC3 growth in DMEM-F12 with 10% FBS and 1% 3 in 1.

extract_protocol:
1. Pellet cells by centrifugation.
2. Add TRIzol to the cell pellet (1 ml of TRIzol Reagent per 5-10x106 of cells) and repeat pipetting.
3. Incubate the homogenized sample for 5-10 min at room temperature.
4. Add 0.2 ml chloroform to the TRIzol-treated cell lysate (per 1 ml), and shake vigorously by hand. Incubate the mixed solution at room temperature for 5-10 min.
5. Centrifuge the tube at 12,000 rpm for 15 min at 4?.
6. Obtain the upper phase of the solution carefully (about 0.6 ml), and transfer the solution to a fresh 1.5 ml eppendrof tube.
7. Add 0.5 ml isopropyl alcohol to the tube (per 1 ml initial TRIzol cell lysate).  Mix thoroughly and incubate at room temperature for 10 min.
8. Centrifuge the tube at 12,000 rpm for 10 min at 4?.
9. Discard the supernatant. Wash the pellet (containing total RNA) twice with 1 ml 75% pre-chilled (-20?) ethanol.
10. Remove the supernatant ethanol completely.
11. Spin down the tube and remove the ethanol adhered to the tube wall.
12. Dry the RNA pellet (air-dry) for 5-10 min. Prevent over drying the RNA pellet.
13. Re-suspend the RNA in RNase-free DEPC water.
14. Measure the 260/280 ratio (indicating protein contamination) and quantify the RNA concentration.

treatment_protocol:
1. The coding sequence (CDS) of TCF12 was cloned into the pBabe-puro vector (VA) to produce constructs. Cell subclones with stable TCF12 expression (TCF12 CDS) and the control (VA) were established by viral infection and puromycin selection.
2. Short hairpin shTCF12 constructs packed in lentiviruses were purchased from the RNA interference consortium (Academia Sinica, Taipei, Taiwan). Cell subclones exhibiting the knockdown of TCF12 together with shLuc (control) were achieved after viral infection and puromycin selection.

tag: cell type

value: HNSCC cell line

tag: cell line


title: HSC3 VA

source_name: HSC3 VA cell line

label_protocol: standard Affymetrix protocol. Qualified RNA was submitted to National Yang-Ming University VGH Genome Research Center (VYMGC) for GeneChip analysis.


title: Cell_6hr_10ppmZnONP & 50ppmTiO2NP_replicate 2

status: Public on Jun 23 2015

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

country: China

institute: Southeast University

description: Gene expression after 6h exposure to nanoparticles

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent N. europaea ATCC 19718 Microarrays (8x15K, Agilent Technologies) 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 at 37 °C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software ( version 11.0.1.1, Agilent). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 12 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance (P≤0.05) were identified through Volcano Plot filtering.

organism: Nitrosomonas europaea ATCC 19718

source_name: Cell, 6hr, 10ppm ZnONP & 50ppm TiO2NP, replicate 2

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, USA) on the Agilent Array platform. Fluorescent cRNA was produced and labeled with Cy3-UTP using Quick Amp Labeling Kit, One-Color (Agilent Technologies, Inc., Palo Alto, CA, USA). The labeled cRNAs were then purified with RNeasy Mini Kit. The concentrations of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) before hybridization onto the N. europaea ATCC 19718 Microarray (8x15K, Agilent Technologies).

growth_protocol: The studied N. europaea (ATCC 19718) was cultured  in a constantly stirred (100~150 rpm) chemostat bioreactor (3L working volume, 2.2 d hydraulic residence time (HRT)) in the dark at 25℃~28℃with the dissolved oxygen (DO) concentration in the reactor maintained at 2.0±0.10 mg/L by air aeration. The chemical composition of the cultivation medium was the same as we reported before (Yu and Chandran, 2010), and the medium pH in the reactor was controlled at 7.45±0.05 with a 40 % NaHCO3 solution as buffer automatically titrated with a pH controller (Meller, Taiwang, China).

extract_protocol: The cells were collected by centrifuging 40 mL sample at 9300 rpmm for 10 min. The pellet was immediately re-suspended in 1 mL Trizol solution (Invitrogen, Carlsbad, CA, USA) and stored at -80 °C. The total RNA was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality control was accessed by electrophoresis on a denaturing agarose gel before microarray hybridization.

treatment_protocol: (NH4)2SO4 was added into a series of sterile 500 mL media bottles containing 300 mL chemostat growing N. europaea cultures to reach a final concentration of 50 mg NH3-N/L. One bottle was used as control with no nanoparticle added. The other two bottles were added with the freshly prepared sterile NP stock solution to a final concentration of 10 mg/L n-ZnO and 50 mg/L n-TiO2, respectively. The another bottle contained 10 mg/L n-ZnO and 50 mg/L n-TiO2. The cultures were incubated on the incubator shaker (120rpm and 28 °C ) for 6 hrs (the typical HRT in the aerobic zone of biological nitrogen removal system) in the dark before analysis. The independent triplicates were performed for each experiment.

tag: tag

value: 10ppm ZnONP & 50ppm TiO2NP


title: OECM1 shTCF12

source_name: OECM1 shTCF12 cell line


title: Cell_6hr_10ppmZnONP & 50ppmTiO2NP_replicate 3

source_name: Cell, 6hr, 10ppm ZnONP & 50ppm TiO2NP, replicate 3


title: Cell_6hr_10ppmZnONP & 50ppmTiO2NP_replicate 1

source_name: Cell, 6hr, 10ppm ZnONP & 50ppm TiO2NP, replicate 1


title: Cell_6hr_10ppm_ZnONP_replicate 3

source_name: Cell, 6hr, 10ppm, ZnONP, replicate 3

value: 10ppm, ZnONP


title: Cell_6hr_50ppm_TiO2NP_replicate 1

source_name: Cell, 6hr, 50ppm, TiO2NP, replicate 1

value: 50ppm, TiO2NP


title: Cell_6hr_50ppm_TiO2NP_replicate 3

source_name: Cell, 6hr, 50ppm, TiO2NP, replicate 3


title: OECM1 shluc

source_name: OECM1 shluc cell line


title: GW_003 Head and neck squamous cell carcinoma Illumina HT12v4

value: Oropharynx

value: IVA

value: Atypical IR 1

value: Non-disruptive


title: Cell_6hr_10ppm_ZnONP_replicate 2

source_name: Cell, 6hr, 10ppm, ZnONP, replicate 2


title: Cell_6hr_0ppm_con_replicate 2

source_name: Cell, 6hr, 0ppm, con, replicate 2

value: 0ppm, con


title: Cell_6hr_0ppm_con_replicate 3

source_name: Cell, 6hr, 0ppm, con, replicate 3


title: Cell_6hr_10ppm_ZnONP_replicate 1

source_name: Cell, 6hr, 10ppm, ZnONP, replicate 1


title: GW_001 Head and neck squamous cell carcinoma Illumina HT12v4

value: F

value: multi

value: DNA+RNA+


title: mESCs cultured without LIF #1

first: Chen-Yun

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

institute: Acdemia Sinica

description: Gene expression data from mESCs cultured without LIF

hyb_protocol: Hybridize fragmented cRNA to GeneChip array for 16.5 hours. Wash/stain protocol of Fluidic Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  Filtered on Expression (50.0 - 50488.008) in the Raw Data.

source_name: embryonic stem cells

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA using T7 RNA polymerase (IVT).

growth_protocol: CGR8 mouse embryonic stem cells were cultured on 0.1% gelatin (Sigma) coated dishes in maintenance medium; Glasgow Minimum Essential Medium (Sigma) supplemented with 15% knock-out serum replacement (Invitrogen), 1x non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 1x penicillin/streptomycin (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen) and 1000 U/ml leukemia inhibitory factor (Millipore).

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

treatment_protocol: One day after subpassage, culture medium were replaced with conventional medium or medium without LIF.

value: embryonic stem cells


title: mESCs cultured without LIF #2


title: II-MSF-a2

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

country: USA

institute: Drexel University College of Medicine

description:
raw data file: IIMSF_415500A02_42020_532.pair
This sample is of Haemophilus influenzae PittIIΔmsf::Kanr grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This strain is a four gene deletion mutant in which msfA1, msfA2, msfA3 and msfA4 are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw data (.pair file) was edited to remove subclusters(genes) that are not present in Haemophilus influenzae PittII by merging it with a list of subclusters known to be present in PittII. These modified data (.pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae PittII

source_name: Haemophilus influenzae PittII Δmsf::Kanr

label_protocol: Labeling of cDNA was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Haemophilus influenzae PittII and Haemophilus influenzae PittIIΔmsf::Kanr were grown in CDM (Coleman et al. J Clin Microbiol. 41 (9), 4408-10.) early stationary phase using an inoculum from an overnight culture grown in BHI. 40 mL cultures were incubated at 37°C with shaking at 200 rpm.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Plus kit with the standard protocol with gDNA eliminator columns. Eluted RNA (~85 µL) was DNased by adding 10 µL 10X TurboDNase buffer and 5 µL TurboDNase (2 units/µL) (Ambion) and incubating at 37 °C for 1.5 hours. 2 µL more TurboDNase was added and incubation continued for an additional 1.5 hours. DNased RNA samples were cleaned by passing the samples through the RNeasy protocol a second time (with gDNA eliminator steps). Samples were eluted in nuclease free (n.f.) water, quantitated on a Nanodrop 1000 spectrophotometer and stored at -80 °C. First and second-strand cDNA synthesis was performed using a SuperScript® One-Cycle cDNA Kit (Invitrogen) as outlined in the NimbleGen Microarray Experienced User’s Guide including RNaseA and cDNA precipitation steps.

treatment_protocol: 1 mL of culture was diluted in 2 mL RNAProtect (Qiagen) and stored at RT for 10 minutes, then 4 °C overnight. Samples were pelleted, the supernatant removed and the cell pellets resuspended in 100 µL of 1X Tris-EDTA (TE) + 1 mg/mL lysozyme (Worthington Biochemical) and 1 mg/mL proteinase K (Qiagen).

tag: genotype

tag: growth medium

value: chemically-defined media (CDM)

tag: biological replicate

tag: technical replicate


title: II-MSF-b1

description:
raw data file: IIMSF_415504A02_44020_532.pair
This sample is of Haemophilus influenzae PittIIΔmsf::Kanr grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This strain is a four gene deletion mutant in which msfA1, msfA2, msfA3 and msfA4 are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets.


title: II-MSF-b2

description:
raw data file: IIMSF_415504A02_44020_532.pair
This sample is of Haemophilus influenzae PittIIΔmsf::Kanr grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This strain is a four gene deletion mutant in which msfA1, msfA2, msfA3 and msfA4 are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets.


title: Cell_6hr_50ppm_TiO2NP_replicate 2

source_name: Cell, 6hr, 50ppm, TiO2NP, replicate 2


title: Cell_6hr_0ppm_con_replicate 1

source_name: Cell, 6hr, 0ppm, con, replicate 1


title: II-MSF-a1

description:
raw data file: IIMSF_415500A02_42020_532.pair
This sample is of Haemophilus influenzae PittIIΔmsf::Kanr grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This strain is a four gene deletion mutant in which msfA1, msfA2, msfA3 and msfA4 are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets.


title: II-WT-b1

description:
raw data file: IIWT_415504A01_44020_532.pair
This sample is of Haemophilus influenzae PittII grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This an otorrheic WT clinical isolate. It is the second of two biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets.

source_name: Haemophilus influenzae PittII

value: wild-type


title: mESCs cultured with LIF #2

description: Gene expression data from mESCs cultured with LIF


title: mESCs cultured with LIF #1


title: Sorted MSC MCF7 Rep1

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

description: Gene expression in MSCs sorted from seven days co-culture with BT-20 breast cancer cell line replica 1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2× Hi-RPM Hybridization Buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome GE 4x44K v2 Microarray chip 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were analyzed using Agilent GeneSpring X software

source_name: Sorted MSC MCF7 Rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (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-2000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM 4.5g/l glucose supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: Total RNA were isolated from transfected hMSC-TERT cells using Total RNA Purification Kit (Norgen-Biotek Corp., Canada) according to the manufacturer’s instructions. The concentrations of total RNA were measured using NanoDrop 2000 (Thermo-Scientific).

treatment_protocol: hMSC cells were co-cultured with the indicated cancer cell lines in 24 well plate in complete DMEM medium

value: bone marrow mesenchymal stem cells

value: hMSC-TERT

tag: co-culture cell line


title: II-WT-a2

description:
raw data file: IIWT_415500A01_42020_532.pair
This sample is of Haemophilus influenzae PittII grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This an otorrheic WT clinical isolate. It is the first of two biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets.


title: OSCC_T4_8

city: Ribeirao Preto

first: Joao Paulo

last: Oliveira-Costa

state: SP

address: Av Bandeirantes, 3900

department: Pathology

country: Brazil

institute: University of Sao Paulo

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 G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: OSCC

label_protocol: Labeled using Low Input Quick Amp kit following manufacturer's instructions

extract_protocol: Total RNA extracted using Rneasy Mini Kit following manufacturer's instructions

tag: disease state

value: oral squamous cell carcinoma

tag: t stage

source_name: Pool of 15 human cell lines

tag: sample type

value: Universal Control


title: Sorted MSC MCF7 Rep2

description: Gene expression in MSCs sorted from seven days co-culture with BT-20 breast cancer cell line replica 2

source_name: Sorted MSC MCF7 Rep2


title: Sorted MSC BT20 Rep2

description: Gene expression in MSCs sorted from seven days co-culture with MCF7 breast cancer cell line replica 2

source_name: Sorted MSC BT20 Rep2


title: II-WT-a1

description:
raw data file: IIWT_415500A01_42020_532.pair
This sample is of Haemophilus influenzae PittII grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This an otorrheic WT clinical isolate. It is the first of two biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets.


title: EPEMB-1 iPS3 at passage 10

type: genomic

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description:
Genomic DNA extracted from cells was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).
Genomic DNA extracted from cells was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing: Data were processed using GenomeStudio V2011.1

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: iPS cell derived from XPEMB-1

label_protocol: Illumina's standard protocol

growth_protocol: The cell lines were maintained at 37°C in a humidified atmosphere containing 95% air and 5% CO2. When the cultures reached subconfluence, the cells were harvested with Trypsin-EDTA Solution (cat# 23315, IBL CO., Ltd, Gunma, Japan), and re-plated at a density of 5 x 105 cells in a 100-mm dish. Medium changes were carried out twice a week thereafter.

extract_protocol: Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).

value: iPS cell

value: xeroderma pigmentosum


title: Euploid MFI, biological replicate 3

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

description: gene expression data

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: RMA

source_name: human placenta

label_protocol: Double-stranded cDNAs were generated from total RNA samples by using SuperScript II reverse transcriptase (Invitrogen) and a T7-oligo primer (QIAGEN). Biotin-labeled cRNA was synthesized by in vitro transcription using an Enzo Bioassay RNA labeling kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus.

tag: tissue

value: maternal fetal interface

value: euploid


title: OSCC_T3_9


title: OSCC_T3_8


title: XPEMB-1

source_name: fibroblast from a xeroderma pigmentosum embryo

value: embryo fibroblast


title: OSCC_T2_8


title: MSC Control Rep2

description: Gene expression in control MSCs replica 2

source_name: MSC Control Rep2


title: Sorted MSC BT20 Rep1

description: Gene expression in MSCs sorted from seven days co-culture with MCF7 breast cancer cell line replica 1

source_name: Sorted MSC BT20 Rep1


title: Euploid MFI, biological replicate 4

description: gene expression data


title: OSCC_T3_10


title: MSC Control Rep1

description: Gene expression in control MSCs replica 1

source_name: MSC Control Rep1


title: XP3OS iPS1 at passage 25

source_name: iPS cell derived from XP3OS


title: OSCC_T3_7


title: Euploid MFI, biological replicate 2

description: gene expression data


title: OSCC_T4_7


title: OSCC_T4_6


title: OSCC_T2_7


title: OSCC_T1_9


title: OSCC_T2_9


title: OSCC_T1_8


title: XP40OS iPS2 at passage 15

source_name: iPS cell derived from XP40OS


title: Euploid MFI, biological replicate 1

description: gene expression data


title: Trisomy 21 MFI, biological replicate 8

description: gene expression data

value: trisomy 21


title: OSCC_T4_5


title: OSCC_T2_5


title: OSCC_T3_6


title: OSCC_T2_6


title: OSCC_T2_4


title: OSCC_T4_4


title: Trisomy 21 MFI, biological replicate 6

description: gene expression data


title: OSCC_T1_7


title: OSCC_T1_6


title: Trisomy 21 MFI, biological replicate 5

description: gene expression data


title: OSCC_T4_3


title: OSCC_T3_3


title: Trisomy 21 MFI, biological replicate 4

description: gene expression data


title: OSCC_T2_3


title: Trisomy 21 MFI, biological replicate 3

description: gene expression data


title: OSCC_T2_1


title: Trisomy 21 MFI, biological replicate 1

description: gene expression data


title: Trisomy 21 MFI, biological replicate 2

description: gene expression data


title: OSCC_T3_2


title: OSCC_T1_5


title: OSCC_T4_2


title: Trisomy 21 MFI, biological replicate 7

description: gene expression data


title: OSCC_T2_2


title: OSCC_T3_4


title: XP40OS

source_name: fibroblast from a xeroderma pigmentosum patient

value: fibroblast


title: OSCC_T3_5


title: OSCC_T4_1


title: Trisomy 18 MFI, biological replicate 3

description: gene expression data

value: trisomy 18


title: Trisomy 18 MFI, biological replicate 4

description: gene expression data


title: OSCC_T1_4


title: OSCC_T1_2


title: OSCC_T1_3


title: OSCC_T3_1


title: Trisomy 13 MFI, biological replicate 2

description: gene expression data

value: trisomy 13


title: Trisomy 13 MFI, biological replicate 1

description: gene expression data


title: Trisomy 18 MFI, biological replicate 2

description: gene expression data


title: XP3OS


title: II-WT-b2

description:
raw data file: IIWT_415504A01_44020_532.pair
This sample is of Haemophilus influenzae PittII grown in chemically defined media and sampled in early stationary phase (OD ~1.0). This an otorrheic WT clinical isolate. It is the second of two biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets.


title: Trisomy 13 MFI, biological replicate 3

description: gene expression data


title: Non_responder_6

city: Kyoto

first: Naoki

last: Horikawa

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University

description: 3 courses of CPT11/NDP

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip U133 Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneArray Scanner System 3000.

data_processing: The data were analyzed using R Console 2.15.1 as normalization method using RMA.

source_name: squamous cell carcinoma tissues from uterine cervix after NAC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: SCC tissues were obtained from uterine cervix surgically resected after receiving neoadjuvant chemotherapy.

treatment_protocol: All samples were obtained from patients who underwent chemotherapy using irinotecan and nedaplatin

value: cervical cancer

tag: phenotype

value: non responder


title: E11.5_dorsal cortex_litter3_mt3

city: Zurich

first: Lukas

last: Sommer

address: Winterthurerstr 190

country: Switzerland

institute: University of Zurich

description: Gene expression on E11.5 dorsal forebrain, directly dissected

hyb_protocol: Described in One-Color Microarray-Based Gene OneColor Microarray-Based Gene Expression Analysis, Agilent Technologies

scan_protocol: Raw data processing was performed using the Agilent Scan Control and the Agilent Feature Extraction Software Version 10

data_processing: Spot intensities were loaded into R/Bioconductor and further processed with the limma package.

source_name: dorsal forebrain,E11.5

growth_protocol: Time-mated mice

extract_protocol: Mothers were sacrificed and embryos isolated. Dorsal forebrain was dissected in  ice-cold HBSS without Ca/Mg and snap-frozen before RNA isolation with RNAeasy kit with on-column DNase digestion (Qiagen).

value: dorsal forebrain

tag: dev stage

tag: genotype/variation

value: mutant


title: Non_responder_4

description: 2 courses of CPT11/NDP


title: Non_responder_1

description: 2 courses of CPT11/NDP


title: responder_3

description: 3 courses of CPT11/NDP

value: responder


title: OSCC_T1_1


title: responder_2

description: 2 courses of CPT11/NDP


title: responder_6

description: 2 courses of CPT11/NDP


title: Non_responder_3

description: 2 courses of CPT11/NDP


title: E11.5_dorsal cortex_litter3_co3

label_protocol: One-Color  Microarray-Based Gene  OneColor Microarray-Based Gene Expression Analysis, Agilent Technologies

value: control


title: Trisomy 13 MFI, biological replicate 4

description: gene expression data


title: responder_4

description: 2 courses of CPT11/NDP


title: E11.5_dorsal cortex_litter2_co2


title: E11.5_dorsal cortex_litter2_mt2


title: Non_responder_5

description: 2 courses of CPT11/NDP


title: Trisomy 18 MFI, biological replicate 1

description: gene expression data


title: responder_5

description: 2 courses of CPT11/NDP


title: E11.5_dorsal cortex_litter1_mt1


title: E11.5_dorsal cortex_litter1_co1


title: SPL_warm_Treg#1_9482914037_D

city: Mainz

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description: SAMPLE 16

hyb_protocol: 1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray

scan_protocol: Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner

data_processing:
Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are than quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads.
[1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001
[2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289-300.

source_name: Warm-conditioned Spleen

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of 2.5 ng RNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.

extract_protocol: Spleen and BAT were harvested directly after euthanasia of mice

treatment_protocol: Mice were housed in a control environment using TSE phenomaster systems

tag: strain background

value: Spleen

tag: temp.

tag: replicate

value: Replicate 1

value: CD4+CD25+Foxp3+ Treg


title: responder_1

description: 2 courses of CPT11/NDP


title: SPL_warm_Treg#3_9482914037_F

description: SAMPLE 18

value: Replicate 3

tag: cell type


title: Non_responder_2

description: 2 courses of CPT11/NDP


title: SPL_warm_Treg#2_9482914037_E

description: SAMPLE 17

value: Replicate 2


title: SPL_warm_Tconv#2_9482914037_B

description: SAMPLE 14

value: CD4+Foxp3- Tconv


title: SPL_warm_Tconv#3_9482914037_C

description: SAMPLE 15


title: Liver from wild type mouse, fed regular chow diet Replicate 2

city: Seoul

first: Je Kyung

last: Seong

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

hyb_protocol: The resultant labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST arrays.

scan_protocol: Arrays were scanned following manufacturers instructions

data_processing: All data preprocessing was performed R. CEL file was processed and normalized by 'oligo' package  package.

source_name: Mouse liver_wildtype_regular_chow

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: Mice were maintained in temperature-controlled (24±2C) facility with a 12h light/dark cycle, and fed regular chow diet (Lab Diets, IN, USA) ad libitum with tap water.

extract_protocol: Total RNA was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer's instruction

treatment_protocol: Male mice were established in weight-matched groups fed either regular chow diet and high fat diet (20% carbohydrate, 60% fat, 20% protein : D12492: Research Diets Inc., New Brunswick, NJ) for 8 weeks.

tag: diet

value: regular chow diet

tag: period

value: 8 weeks

value: liver

tag: gender

value: male

tag: strain

value: wildtype


title: Liver from wild type mouse, fed regular chow diet Replicate 3

tag: genotype


title: BAT_cold_Treg#2_9482914035_E

description: SAMPLE 11

source_name: Cold-conditioned Brown Adipose Tissue

value: Brown Adipose Tissue (BAT)


title: SPL_warm_Tconv#1_9482914037_A

description: SAMPLE 13


title: Liver from wild type mouse, fed high fat diet(60%) Replicate 1

source_name: Mouse liver_wildtype_high_fat_diet

value: high fat diet


title: BAT_cold_Tconv#1_9482914035_A

description: SAMPLE 7


title: BAT_cold_Treg#1_9482914035_D

description: SAMPLE 10


title: BAT_warm_Treg#3_9482914022_F

description: SAMPLE 6

source_name: Warm-conditioned Brown Adipose Tissue


title: DC4 6h Ca WT

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

institute: University Hospital of Würzburg

hyb_protocol: Standard Affymetrix GeneTitan Hyb protocol

scan_protocol: Standard Affymetrix GeneTitan Scan protocol

data_processing: RMA normalisation using Agilent Genespring version 13.1

source_name: DC 6h + C. albicans wild type

label_protocol: Standard 3´-Assay Labeling for Affymetrix Plates

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from leucocyte concentrate blood of healthy donors (Univeristy Hospital Würzburg, transfusion medicine, Germany) by Ficoll-Hypaque density gradient centrifugation (Biochrom AG, Berlin, Germany). Human monocytes were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany). Wild-type C. albicans SC5314 was maintained on YPD agar. For experiments, colonies were transferred to M199 medium (PAA), pH 4 and cultured at 30°C to stationary phase. Germ tubes were induced by culturing in M199 medium, pH 8 for one hour at 37°C. Germ tubes were inactivated by washing them in phosphate-buffered saline (PBS) and followed by incubation in PBS containing 0.1% thimerosal (Sigma-Aldrich) for one hour at 37°C with shaking. Afterwards, germ tubes were washed 5 times and then re-suspended in RPMI-1640. Killing was confirmed by plating potential CFU on YPD (2% D-glucose, 1% peptone, 5% yeast extract, Roth) agar plates. A. fumigatus was cultivated on beer mesh plates at 37°C. After 3 days, conidia were detached by adding sterile water and singularized by a 40 µm cell strainer. swelling and germination was achieved by incubation in RPMI 1640 medium with refocabin at room temperature and 37°C, respectively. Germ tubes and conidia were inactivated by incubation in 100% Ethanol for 45°min.

extract_protocol: Qiagen RNA-Isolation Kit (miRNeasy Mini)

treatment_protocol: Differentiation of monocytes into immature DCs (moDCs) was achieved by cultivating cells in RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 100 mg/ml Refobacin (Merck, Darmstadt, Germany), 10% fetal calf serum (FCS, Sigma-Aldrich, Taufkirchen, Germany), 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (Leukine, Novartis, Basel, Switzerland) and 10 ng/ml interleukin-4 (Miltenyi Biotec, Germany). Cultures were fed with fresh medium and cytokines every other day. After culturing for 6 days at 37°C and 5% CO2, moDCs were collected and 1x 106 cells were resuspended in 1 ml complete medium. If moDCs were stimulated 1 x 10^6 Aspergillus fumigatus germ tubes,  1 x 10^6 Aspergillus conidia,  1 x 10^6 Candida albicans wild type,  1 x 10^6 Candida albicans mutant or LPS (1 µg/ml)  were added for 0,6 and 12h.

tag: donor id

value: donor 4

value: dendritic cells

tag: co-cultivated with

value: C. albicans SC5314 (MOI1) WT


title: BAT_cold_Tconv#2_9482914035_B

description: SAMPLE 8


title: DC3 6h

source_name: DC 6h negative control

value: donor 3

value: none (negative control)


title: DC4 6h LPS

source_name: DC 6h + LPS

value: LPS (1µg/ml) for 6hrs


title: BAT_cold_Treg#3_9482914035_F

description: SAMPLE 12

value: CD4+CD25+Foxp3+ Treg


title: DC4 6h


title: Liver from wild type mouse, fed regular chow diet Replicate 1


title: Liver from wild type mouse, fed high fat diet(60%) Replicate 2


title: BAT_warm_Treg#2_9482914022_E

description: SAMPLE 5


title: DC3 6h LPS


title: DC2 6h Af GT

source_name: DC 6h + A. fumigatus germ tubes

value: donor 2

value: A. fumigatus 46645 germ tubes


title: DC4 6h Af GT


title: Liver from Ahnak deficient mouse, fed regular chow diet Replicate 3

source_name: Mouse liver_Ahnak_regular_chow

value: AHNAK KO


title: DC3 6h Af GT


title: Liver from wild type mouse, fed high fat diet(60%) Replicate 3


title: BAT_cold_Tconv#3_9482914035_C

description: SAMPLE 9

value: Replicate 3

value: CD4+Foxp3- Tconv


title: DC2 6h


title: DC3 6h Ca WT


title: platelets_CTRL_after_medication_rep26

status: Public on Jun 22 2015

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Labeled samples were hybridized on Human 8x15k miRNA microarrays based on Sanger miRbase release 12.0 containing 866 human and 89 human viral miRNAs (G4470C, Agilent Technologies) at 55°C and 20 rpm for 20 hours.

scan_protocol: After washing, the arrays were scanned using the Agilent DNA microarray scanner (G2565CA, Agilent Technologies). Data was extracted with Feature Extraction (v10.7.3.1, Agilent Technologies) with the miRNA_107_Sep09 protocol for miRNA microarrays

data_processing: A two-step normalization approach was taken. In the first step, we corrected for systematic technical effects starting from the raw probe-level data as extracted via the Agilent Feature Extraction software. For this purpose, we fitted a linear mixed-effects model to the raw data including coefficients for three technical effects (hybridization block, slide, slide position (upper/lower half)), and patient status using the R/MAANOVA package.  Residuals after correcting for the three technical effects were further pre-processed and summarized using a modified version of the robust multi-array average (RMA) method with background correction, as implemented in version 1.4.0 of the AgiMicroRna R/Bioconductor package. Quality control was performed using the R/Bioconductor package arrayQualityMetrics. Based on arrayQualityMetics outlier detection and visual inspection of heatmaps, MA-plots, and intensity distributions, 11 arrays were excluded from further analysis. Data from the 96 remaining arrays (33 CAD, 37 control without medication and 26 control after medication) was renormalized using the two-stage procedure described above. MiRNAs detected in none of the samples were filtered out.

label_protocol: The integrity of total RNA including microRNAs from platelets was investigated with the BioAnalyzer (Agilent Technologies) using the RNA 6000 Pico kit (Agilent Technologies) and Small RNA kit (Agilent Technologies) according to the manufacturer’s instructions.  100 ng of total RNA including microRNAs was dried down in a Centrivap concentrator (Labconco) and dissolved in 2 µl RNase-free water. Sample labeling with Cy3 was performed as described in the miRNA Microarray System with miRNA Complete Labeling and Hyb Kit manual version 2.2 (Agilent Technologies) with the inclusion of spike-ins and the optional desalting step with spin columns (Micro Bio-Spin 6, Bio-Rad).

extract_protocol: Total RNA from platelets was extracted using the mirVana miRNA Isolation kit (Ambion, Inc.) essentially according to the manufacturer’s protocols. The protocol was modified such that the column was air-dried for 3 minutes after the last washing step and before elution.

treatment_protocol: In short, blood was collected in 10 ml CTAD tubes (BD Vacutainer). Immediately after blood withdrawal, the samples were centrifuged (160g, 20 min, room temperature) to obtain platelet-rich plasma (PRP). PRP was carefully transferred to a plastic tube leaving at least 1 cm above the interface of the PRP to avoid leukocyte contamination. The number of platelets was determined in a Beckman Coulter counter. To deplete leukocytes, 30 µl Dynabeads CD45 coated beads (4 x 10^8 beads/ml, Invitrogen) were added in phosphate buffered saline (PBS). The PRP samples and the beads were mixed gently on rotary mixer (30 min, room temperature). Mixed PRP and CD45 coated beads were placed on the Magnetic Particle Separator (MPC) for 2 minutes to obtain leukocyte depleted PRP. Leukocyte depleted PRP was transferred to a fresh tube. The number of platelets in leukocyte depleted PRP was determined. The remaining leukocyte depleted PRP was centrifuged (1500g, 20 min, room temperature). The platelet-poor plasma was discarded. The platelet pellet was snap-frozen and stored at -80oC before RNA isolation.

value: platelets

tag: condition

tag: age


title: platelets_CAD_rep33

source_name: platelets,CAD

tag: tissue

value: CAD


title: platelets_CTRL_without_medication_rep36


title: 168_wt_1

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

description:
wild-type strain replicate 1
168_wt_1.530779A02

hyb_protocol: Hybridization was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).

scan_protocol: Scanning was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347). Data were quantile normalized using LIMMA package.
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: B. subtilis strains (wild-type and mutants) were grown in LB medium and harvested by centrifigution during the exponential phase of growth.

extract_protocol: Total RNA was extracted as described in Nicolas et al (2012) (PMID:22383849)

value: wild-type

tag: growth phase

value: exponential phase


title: platelets_CTRL_without_medication_rep34


title: platelets_CTRL_without_medication_rep35


title: platelets_CAD_rep29


title: platelets_CAD_rep30


title: platelets_CAD_rep28


title: platelets_CAD_rep31


title: 168_Dhfq_1

description:
hfq mutant replicate 1
168_ymaH_1.530779A03

value: hfq deletion mutant


title: DC2 6h Ca WT


title: DC1 6h Af GT

value: donor 1


title: 168_wt_2

description:
wild-type strain replicate 2
168_wt_2.415689


title: platelets_CAD_rep32


title: platelets_CTRL_without_medication_rep37


title: 168_Dhfq_2

description:
hfq mutant replicate 2
168_ymaH_2.415690


title: BAT_warm_Tconv#3_9482914022_C

description: SAMPLE 3

value: Brown Adipose Tissue (BAT)


title: DC1 6h

value: dendritic cells


title: BAT_warm_Tconv#1_9482914022_A

description: SAMPLE 1

value: Replicate 1


title: platelets_CTRL_without_medication_rep33


title: platelets_CTRL_without_medication_rep32


title: platelets_CTRL_without_medication_rep31


title: Liver from Ahnak deficient mouse, fed high fat diet(60%) Replicate 1

source_name: Mouse liver_Ahnak_high_fat_diet

value: high fat diet

value: 8 weeks

value: liver

value: male


title: platelets_CAD_rep26


title: BAT_warm_Treg#1_9482914022_D

description: SAMPLE 4

value: CD4+CD25+Foxp3+ Treg


title: DC1 6h Ca WT

value: C. albicans SC5314 (MOI1) WT


title: Liver from Ahnak deficient mouse, fed regular chow diet Replicate 1

value: regular chow diet

value: AHNAK KO


title: platelets_CAD_rep24

value: platelets


title: platelets_CTRL_without_medication_rep30


title: platelets_CTRL_without_medication_rep29


title: DC1 6h LPS

value: LPS (1µg/ml) for 6hrs


title: Liver from Ahnak deficient mouse, fed high fat diet(60%) Replicate 2


title: BAT_warm_Tconv#2_9482914022_B

description: SAMPLE 2

value: Replicate 2

value: CD4+Foxp3- Tconv


title: platelets_CTRL_after_medication_rep25


title: platelets_CAD_rep23

value: CAD


title: Liver from Ahnak deficient mouse, fed high fat diet(60%) Replicate 3


title: platelets_CTRL_without_medication_rep28


title: platelets_CAD_rep27


title: platelets_CTRL_without_medication_rep25


title: platelets_CAD_rep22


title: platelets_CTRL_without_medication_rep27


title: platelets_CTRL_without_medication_rep26


title: platelets_CAD_rep20


title: platelets_CAD_rep21


title: platelets_CAD_rep18


title: platelets_CAD_rep19


title: platelets_CAD_rep25


title: platelets_CAD_rep17


title: platelets_CTRL_after_medication_rep24


title: platelets_CTRL_without_medication_rep24


title: platelets_CTRL_without_medication_rep23


title: platelets_CAD_rep15


title: platelets_CTRL_after_medication_rep23


title: platelets_CTRL_without_medication_rep20


title: platelets_CTRL_after_medication_rep20


title: platelets_CAD_rep14


title: platelets_CTRL_without_medication_rep19


title: platelets_CAD_rep13


title: platelets_CTRL_without_medication_rep21


title: platelets_CTRL_after_medication_rep21


title: platelets_CTRL_after_medication_rep22


title: platelets_CTRL_without_medication_rep22


title: platelets_CTRL_after_medication_rep19


title: platelets_CTRL_without_medication_rep18


title: platelets_CAD_rep16


title: DC2 6h LPS

value: donor 2


title: platelets_CTRL_after_medication_rep18


title: platelets_CAD_rep11


title: platelets_CTRL_without_medication_rep16


title: platelets_CTRL_after_medication_rep16


title: platelets_CAD_rep9


title: platelets_CAD_rep12


title: platelets_CAD_rep10


title: platelets_CTRL_without_medication_rep15


title: platelets_CTRL_after_medication_rep17


title: platelets_CAD_rep8


title: platelets_CTRL_after_medication_rep15


title: platelets_CTRL_without_medication_rep17


title: platelets_CTRL_after_medication_rep14


title: platelets_CTRL_without_medication_rep14


title: platelets_CAD_rep7


title: platelets_CTRL_after_medication_rep10


title: platelets_CTRL_after_medication_rep11


title: platelets_CTRL_after_medication_rep12


title: platelets_CAD_rep6


title: platelets_CTRL_without_medication_rep11


title: platelets_CTRL_after_medication_rep13


title: platelets_CTRL_after_medication_rep9


title: platelets_CTRL_without_medication_rep10


title: platelets_CTRL_without_medication_rep9


title: platelets_CTRL_without_medication_rep8


title: platelets_CTRL_after_medication_rep8


title: platelets_CTRL_after_medication_rep7


title: platelets_CTRL_without_medication_rep13


title: platelets_CAD_rep5


title: platelets_CTRL_without_medication_rep6


title: platelets_CAD_rep4


title: platelets_CTRL_after_medication_rep6


title: platelets_CTRL_without_medication_rep5


title: platelets_CTRL_without_medication_rep12


title: platelets_CAD_rep3


title: platelets_CTRL_without_medication_rep7


title: platelets_CTRL_after_medication_rep5


title: platelets_CTRL_after_medication_rep4


title: platelets_CTRL_after_medication_rep3


title: platelets_CTRL_after_medication_rep2


title: platelets_CTRL_without_medication_rep4


title: platelets_CTRL_without_medication_rep3


title: platelets_CTRL_after_medication_rep1


title: platelets_CTRL_without_medication_rep2


title: platelets_CAD_rep2


title: platelets_CTRL_without_medication_rep1


title: platelets_CAD_rep1


title: Skin_day28 (DC01759)

city: Gaithersburg

first: Xiang

last: Guo

state: MD

address: One MedImmune Way

department: Translational Sciences

institute: MedImmune

description:
CP180_BIO_DC01759
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Genome U133 Plus GeneChip@ arrays (Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned according to standard Affymetrix protocol.

data_processing: Probe-level summaries (fRMA) were calculated from the array cell intensity files (CEL).

source_name: SSc patients at day 28 after anifrolumab administration

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

extract_protocol: Total RNA was extracted using the PAXgene Blood RNA kit and Qiagen RNeasy Fibrous Tissue Mini kit (Hilden, Germany) respectively.

tag: disease state

value: SSc

value: Skin

tag: agent

value: anifrolumab

tag: dose

value: 5.0 mpk_Multi

tag: time


title: Skin_day0 (DC01629)

description:
CP180_BIO_DC01629
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

source_name: SSc patients at baseline


title: Liver from Ahnak deficient mouse, fed regular chow diet Replicate 2

value: 8 weeks


title: Skin_day28 (DC01701)

description:
CP180_BIO_DC01701
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day28 (DC01740)

description:
CP180_BIO_DC01740
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day0 (DC01658)

description:
CP180_BIO_DC01658
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 1.0 mpk_Multi


title: Skin_day28 (DC01731)

description:
CP180_BIO_DC01731
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day0 (DC01721)

description:
CP180_BIO_DC01721
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01166)

description:
CP180_WBR1_DC01166
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

source_name: SSc patients at day 56 after anifrolumab administration

value: Whole Blood

value: 5 mpk_Multi


title: Skin_day0 (DC01698)

description:
CP180_BIO_DC01698
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day0 (DC01705)

description:
CP180_BIO_DC01705
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day28 (DC01750A)

description:
CP180_BIO_DC01750A
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day28 (DC01755)

description:
CP180_BIO_DC01755
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day28 (DC01678)

description:
CP180_BIO_DC01678
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Day5-1

city: Edmonton

first: chi

last: zhou

state: Alberta

address: 114 street 90 ave NW.

department: Agriculture Food and Nutritional Science

country: Canada

institute: University of Alberta

hyb_protocol: 80 μl of hybridization mixture containing 8 ul 20X SSC, 3.2 ul 2% SDS, 4.8 ul Liquid Blocking reagent (Amersham, USA), 120pmol of samples labelled with each dye

scan_protocol: GenePix 4200 Autoloader by Molecular Devices. Software is GenePix Pro, Acuity 4.0

data_processing: background subtracted, data obtained from log2 of processed Red signal/processed Green signal

organism: Sus scrofa

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: developmental stage

value: Day5 blastocyst


title: Day5-2


title: Day5-4


title: Skin_day0 (DC01642)

description:
CP180_BIO_DC01642
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 0.3 mpk_Multi


title: Skin_day0 (DC01676)

description:
CP180_BIO_DC01676
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Day5-5


title: Skin_day0 (DC01684)

description:
CP180_BIO_DC01684
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01161)

description:
CP180_WBR1_DC01161
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Day5-6


title: Skin_day28 (DC01711)

description:
CP180_BIO_DC01711
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Day5-3


title: Skin_day28 (DC01752)

description:
CP180_BIO_DC01752
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day0 (DC01730)

description:
CP180_BIO_DC01730
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day28 (DC01720)

description:
CP180_BIO_DC01720
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Skin_day0 (DC01706)

description:
CP180_BIO_DC01706
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01247)

description:
CP180_WBR1_DC01247
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01133)

description:
CP180_WBR1_DC01133
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 1 mpk_Multi


title: Blood_day0 (DC01196)

description:
CP180_WBR1_DC01196
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01208)

description:
CP180_WBR1_DC01208
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Astro, biological replicate4

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 .

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: Astro, biological replicate4

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: Samples were grown in DMEM 10% FBS for 12 days

extract_protocol: Total RNAs were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: Induced astrocytes were obtained by infecting fibroblasts with the gliogenic transcription factors NFIA, NFIB and SOX9.

value: FVB

tag: cell type

value: primary astrocytes


title: Blood_day0 (DC01005)

description:
CP180_WBR1_DC01005
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: iAstro, biological replicate3

source_name: iAstro, biological replicate3

value: Induced astrocytes


title: Blood_day0 (DC01052)

description:
CP180_WBR1_DC01052
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01076)

description:
CP180_WBR1_DC01076
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Astro, biological replicate3

source_name: Astro, biological replicate3


title: iAstro, biological replicate4

source_name: iAstro, biological replicate4


title: Blood_day56 (DC01053)

description:
CP180_WBR1_DC01053
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01060_v2)

description:
CP180_WBR1_DC01060_v2
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Astro, biological replicate1

source_name: Astro, biological replicate1


title: Blood_day56 (DC01148)

description:
CP180_WBR1_DC01148
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01202)

description:
CP180_WBR1_DC01202
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01131)

description:
CP180_WBR1_DC01131
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01150)

description:
CP180_WBR1_DC01150
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Astro, biological replicate2

source_name: Astro, biological replicate2


title: Fibro, biological replicate 4

source_name: Fibro, biological replicate 4

value: Fibroblasts


title: iAstro, biological replicate2

source_name: iAstro, biological replicate2


title: Fibro, biological replicate 3

source_name: Fibro, biological replicate 3


title: Blood_day56 (DC01097)

description:
CP180_WBR1_DC01097
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01198)

description:
CP180_WBR1_DC01198
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01058_v2)

description:
CP180_WBR1_DC01058_v2
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC01110)

description:
CP180_WBR1_DC01110
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 20 mpk_Single


title: iAstro, biological replicate1

source_name: iAstro, biological replicate1


title: Blood_day0 (DC01073)

description:
CP180_WBR1_DC01073
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01102)

description:
CP180_WBR1_DC01102
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01111)

description:
CP180_WBR1_DC01111
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC01246)

description:
CP180_WBR1_DC01246
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00950)

description:
CP180_WBR1_DC00950
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 10 mpk_Single


title: Fibro, biological replicate 1

source_name: Fibro, biological replicate 1


title: Blood_day0 (DC00974)

description:
CP180_WBR1_DC00974
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: SSc


title: Blood_day56 (DC01195)

description:
CP180_WBR1_DC01195
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Fibro, biological replicate 2

source_name: Fibro, biological replicate 2


title: Blood_day0 (DC01233)

description:
CP180_WBR1_DC01233
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: PC-9_Adenocarcinoma

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)

tag: histology

value: Adenocarcinoma

value: M

tag: race

value: Asian

tag: smoker

value: N

tag: egfr

value: mutant

tag: kras

value: WT


title: HCC4019_Adenocarcinoma

tag: gender

value: White

value: Y

tag: pack-years


title: Blood_day56 (DC01003)

description:
CP180_WBR1_DC01003
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: Whole Blood

value: anifrolumab


title: Blood_day56 (DC01192)

description:
CP180_WBR1_DC01192
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00953)

description:
CP180_WBR1_DC00953
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00927)

description:
CP180_WBR1_DC00927
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 3 mpk_Single


title: Blood_day56 (DC00989)

description:
CP180_WBR1_DC00989
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: HCC4011_Adenocarcinoma

value: Ex-smoker


title: HCC2279_Adenocarcinoma

value: F


title: HCC2935_Adenocarcinoma


title: Blood_day56 (DC00857)

description:
CP180_WBR1_DC00857
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00870)

description:
CP180_WBR1_DC00870
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 1 mpk_Single


title: Blood_day0 (DC01088)

description:
CP180_WBR1_DC01088
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 20 mpk_Single


title: Blood_day0 (DC01178)

description:
CP180_WBR1_DC01178
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00869)

description:
CP180_WBR1_DC00869
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 10 mpk_Single


title: HCC4006_Adenocarcinoma


title: HCC4017_Large Cell

value: Large Cell


title: Blood_day56 (DC00975)

description:
CP180_WBR1_DC00975
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: SSc


title: HCC827_Adenocarcinoma

value: Adenocarcinoma


title: Blood_day0 (DC00859)

description:
CP180_WBR1_DC00859
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00959)

description:
CP180_WBR1_DC00959
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00971)

description:
CP180_WBR1_DC00971
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00866)

description:
CP180_WBR1_DC00866
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00865)

description:
CP180_WBR1_DC00865
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00867)

description:
CP180_WBR1_DC00867
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00877)

description:
CP180_WBR1_DC00877
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00926)

description:
CP180_WBR1_DC00926
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: H3255_Adenocarcinoma


title: H2291_Adenocarcinoma

value: M


title: H2405_Adenocarcinoma


title: H2228_Adenocarcinoma

value: N


title: Blood_day56 (DC00814)

description:
CP180_WBR1_DC00814
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 0.3 mpk_Single


title: H2030_Adenocarcinoma

value: WT

value: mutant


title: Blood_day0 (DC00880)

description:
CP180_WBR1_DC00880
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00844)

description:
CP180_WBR1_DC00844
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day0 (DC00808)

description:
CP180_WBR1_DC00808
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: H2122_Adenocarcinoma

value: White

value: Y


title: Blood_day56 (DC00856)

description:
CP180_WBR1_DC00856
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: Whole Blood

value: anifrolumab


title: Blood_day56 (DC00891)

description:
CP180_WBR1_DC00891
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Blood_day56 (DC00925)

description:
CP180_WBR1_DC00925
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: H1975_Adenocarcinoma


title: Blood_day56 (DC00888)

description:
CP180_WBR1_DC00888
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Positive_AI_1

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Labeled cRNA were hybridized to Affymetrix Mouse Gene 2.0 ST Array (Affymetrix, Inc) in blinded interleaved fashion.  Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate probe-level measurements for each hybridized cRNA.

scan_protocol: Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 41,345 RMA normalized gene fragment expression values for each hybridized cRNA.

label: Biotin

source_name: Brain

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse Gene 2.0 ST Array (Affymetrix, Inc).

growth_protocol: C57BL/6J (B6), B6.129S7-Ifngtm1Ts/J (IFNγ-/-), B6.129S-Tnftm1Gkl/J (TNFα-/-) and B6.129S4-Ifngtm3.1Lky/J (IFNγ-YFP) mice were purchased from The Jackson Laboratory (Bar Harbor, ME). Actin-OFP+, actin-TFP+, Thy1.1+ P14, OFP+ P14, TFP+ SMARTA, and CD11c-YFP+ mice (all on a pure B6 background) were bred and maintained under specific pathogen-free conditions at the National Institutes of Health (NIH). CD11c-YFP+ mice were generously provided by Dr. Michel Nussenzweig (Rockefeller University) (Lindquist et al., 2004). Actin-OFP+ and actin-TFP+ were generated as described at the NIH (Gossa et al., 2014). All animal experiments were conducted in accordance with the guidelines set forth by the National Institutes of Health Animal Care and Use Committee.

extract_protocol: Brain tissue was collected in TRIzol (Invitrogen), and total RNA was extracted using PureLink RNA Mini Kits (Life Technologies) per the manufacturer’s instructions. Purified RNA was then treated with amplification grade DNase I (Invitrogen) to remove contaminating DNA.

treatment_protocol: The Armstrong (Arm) 53b strain of lymphocytic choriomeningitis virus (LCMV) was propagated and maintained on BHK-21 cells. To generate an initial colony of LCMV carriers, newborn mice were infected intracranially (i.c.) with 1x103 plaque forming units (PFU) of LCMV Arm within 24 hours of birth. The carrier colony was then maintained by breeding adult persistently infected female mice with uninfected or persistently infected male mice. All offspring were confirmed to be persistently infected carriers by performing serum plaque assays on Vero cells. CD11c-YFP+ carriers were generated by mating B6 carrier females with uninfected homozygous male CD11c-YFP mice. All resultant F1 mice were used for experimentation. LCMV meningitis was induced by infecting adult (6-8 weeks old) B6 mice i.c. with 1x103 PFU of LCMV Arm.  Per adoptive transfer, memory donor mice for adoptive immunotherapy were generated by infecting mice intraperitoneally (i.p.) with 1x105 PFU of LCMV Arm, which is completely cleared from all tissues within 8-10 days. Splenocytes were harvested from LCMV immune mice at >45 days post-infection. To perform adoptive immunotherapy, 2x107 cells were injected i.p. into recipient LCMV carrier mice. For experiments involving tagged CD8+ P14 or CD4+ SMARTA T cells, the respective populations were purified from the spleens of naïve transgenic mice using negative selection kits (Stem Cell Technologies). Naïve donor mice were then seeded intravenously (i.v.) with 5,000 19 P14 or SMARTA T cells. In some experiments, mice were seeded with both populations simultaneously. One day later mice were infected i.p. with 1x105 PFU of LCMV Arm and considered memory donors at >45 days post-infeciton.

tag: class


title: Positive_AI_2


title: Blood_day0 (DC00837)

description:
CP180_WBR1_DC00837
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

value: 0.1 mpk_Single


title: Blood_day56 (DC00897)

description:
CP180_WBR1_DC00897
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: H1993_Adenocarcinoma

tag: age

value: F


title: Positive_AI_3


title: Blood_day0 (DC00847)

description:
CP180_WBR1_DC00847
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients

tag: tissue


title: H2009_Adenocarcinoma


title: Blood_day0 (DC00839)

description:
CP180_WBR1_DC00839
Gene expression data from phase 1 clinical trial of anifrolumab in SSc patients


title: Negative_AI_3


title: Bone.Marrow_OA_No_ST07

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Hybridization of Chips was performed as per manufacturers instructions.

scan_protocol: SData were scanned as per manufactureres instructions on a GeneArray Scanner.

data_processing: Data was processed and normalized using the RMA methodology. Probes that were called absent in 50% of samples have been removed.

source_name: Bone Marrow

label_protocol: 50ng of total RNA was amplified using Nugen Ovation Biotin RNA amplification

growth_protocol: Cells were seeded in duplicate at the required density using 10% FCS. Once attached, the medium was removed and the cells washed in serum free medium before replacing with fibroblast medium, which was identical but contained either 10% or 0.1% FCS.

extract_protocol: Fibroblasts were retrieved from culture by trypsin digestion and washed in fibroblast medium then PBS before resuspending in 200µl of RLT RNA protection buffer (Quiagen) followed by the manufacturer instructions of the RNeasy extraction kit.

value: Bone Marrow

tag: disease

value: OA

tag: serum

value: Low Serum


title: H1944_Adenocarcinoma


title: H1792_Adenocarcinoma


title: Bone.Marrow_OA_Yes_ST07

value: High Serum


title: Negative_AI_2


title: Bone.Marrow_OA_Yes_ST06


title: H1703_Adenosquamous

value: Adenosquamous


title: IL-1β stimulated cells with Lactobacillus acidophilus-conditioned media treatment, biological rep3

city: Charlestown

first: Kriston

last: Ganguli

state: MA

address: 114 16th street

institute: Mass General Hospital for Children

description: The cell line was isolated from a 20-wk-old normal fetal small intestine and used as a model of immature enterocytes.

hyb_protocol: Following fragmentation, 41 uL of cDNA were hybridized for 16 hr at 45 C on GeneChip Human 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing:
The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

source_name: nontransformed primary fetal intestinal epithelial cell line

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit WT PLUS, Lot # 4224182, followed by labeling 5.5 ug cDNA using kit WT PLUS, Lot # 4224182.

growth_protocol: The cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 1% nonessential amino acid, 1% glutamine, 1% antibiotic/antimycotic solution, 10 mM HEPES buffer, 1 mM sodium pyruvate and 0.2 units/mL human recombinant insulin.

extract_protocol: Cells were lysed in RLT buffer (containing guanidine isothiocyanate) from Qiagen. Total RNA was isolated using an RNeasy kit following the manufacturer’s instruction. As instructed by protocol, total RNA was treated with RNase-free DNase I to eliminate genomic DNA contamination.

treatment_protocol: The H4 cells (a human nontransformed primary intestinal epithelial cell line) were pretreated with BCM or LCM (15%) for 30 minutes, and then stimulated with or without IL-1β (10 ng/mL) for 4 h. Cell media and IL-1β stimulation were negative and positive control, respectively.

tag: cell line

value: passage 18

value: small intestine

tag: genotype

value: wild-type


title: Bone.Marrow_OA_No_ST06


title: Bone.Marrow_OA_Yes_ST04


title: H1819_Adenocarcinoma

value: Adenocarcinoma


title: Bone.Marrow_OA_Yes_ST02


title: Bone.Marrow_OA_No_ST03


title: Lactobacillus acidophilus-conditioned media treatment, biological rep3


title: Negative_AI_1


title: H1385_NSCLC

value: NSCLC

value: Black

value: WT


title: IL-1β stimulated cells with Lactobacillus acidophilus-conditioned media treatment, biological rep2


title: H1568_Adenocarcinoma

value: White

value: Y


title: Bone.Marrow_OA_Yes_ST03


title: IL-1β stimulated cells with Bifidobacterium infantis-conditioned media treatment, biological rep2


title: H1693_Adenocarcinoma


title: IL-1β stimulated cells with Lactobacillus acidophilus-conditioned media treatment, biological rep1


title: H1437_Adenocarcinoma

value: M


title: Lactobacillus acidophilus-conditioned media treatment, biological rep2


title: H1650_Adenocarcinoma

value: mutant


title: Lactobacillus acidophilus-conditioned media treatment, biological rep1


title: IL-1β stimulated cells with Bifidobacterium infantis-conditioned media treatment, biological rep1


title: Bifidobacterium infantis-conditioned media treatment, biological rep3


title: H1395_Adenocarcinoma

value: F


title: H1373_Adenocarcinoma


title: Bone.Marrow_OA_No_ST04

value: Bone Marrow


title: Liver_NEMO_f/f_repl3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
A186_18_964_WT
Replicate 3

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

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

source_name: liver, wild type (NEMO floxed/floxed)

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Mice carrying the loxP-site-flanked NEMO gene under the control of the Alb-cre promoter were generated as previously described (PMID: 19635861). From NEMOΔhepa mice, we generated double-knockout animals by crossing NEMOΔhepa with either constitutive Jnk1-/- or Jnk2-/- in a defined C57BL/6 background.

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: Mice had free acces to standard laboratory chow and water. Mice were killed at the age of 8 wks.

tag: strain/background

tag: genotype/variation

value: wild type (NEMO floxed/floxed)

tag: Sex

value: male

value: 8 wk

value: liver

tag: mouseid


title: Bone.Marrow_RA_Yes_RA17

value: RA

value: High Serum


title: H1355_Adenocarcinoma

tag: histology

tag: race


title: Bone.Marrow_OA_No_ST02

value: OA

value: Low Serum


title: Bone.Marrow_OA_Yes_ST01


title: H1573_Adenocarcinoma

value: Adenocarcinoma

tag: smoker

tag: egfr


title: Bifidobacterium infantis-conditioned media treatment, biological rep2

value: passage 18

value: small intestine

value: wild-type


title: Bifidobacterium infantis-conditioned media treatment, biological rep1


title: H969_Adenocarcinoma

tag: gender

value: White

value: N

value: WT

tag: kras


title: Liver_NEMO_f/f_repl1

description:
A186_16_938_WT
Replicate 1


title: Bone.Marrow_OA_No_ST01


title: Liver_NEMO_f/f_repl2

description:
A186_17_935_WT
Replicate 2


title: Bone.Marrow_RA_Yes_RA16


title: H838_Adenocarcinoma

value: M

value: Y

tag: pack-years


title: postive control, IL-1β stimulation alone, biological rep3

tag: age


title: Bone.Marrow_RA_No_RA17

tag: tissue

value: Bone Marrow


title: postive control, IL-1β stimulation alone, biological rep2


title: Liver_NEMO_/JNK2_DKO_repl3

description:
A186_12_189_NEMOJNK2
Replicate 3

source_name: liver, global JNK2 / hepatocyte-specific NEMO double-knockout

value: global Jnk2-/-/NEMOΔhepa

value: male


title: Liver_NEMO_/JNK2_DKO_repl2

description:
A186_11_139_NEMOJNK2
Replicate 2

value: 8 wk

value: liver


title: Bone.Marrow_RA_No_RA16

tag: disease

value: RA


title: H920_Adenocarcinoma


title: H820_Adenocarcinoma

value: mutant


title: H650_Adenocarcinoma


title: postive control, IL-1β stimulation alone, biological rep1


title: Liver_NEMO_/JNK2_DKO_repl1

description:
A186_10_119_NEMOJNK2
Replicate 1


title: Liver_NEMO_/JNK1_DKO_repl3

description:
A186_09_128_NEMOJNK1
Replicate 3

source_name: liver, global JNK1 / hepatocyte-specific NEMO double-knockout

value: global Jnk1-/-/NEMOΔhepa


title: Bone.Marrow_RA_Yes_RA14

tag: serum

value: High Serum


title: Bone.Marrow_RA_Yes_RA15


title: Bone.Marrow_RA_No_RA15

value: Low Serum


title: negative control, cell media alone, biological rep3

tag: cell line

value: passage 18

value: small intestine


title: Bone.Marrow_RA_No_RA14


title: Liver_NEMO_/JNK1_DKO_repl2

description:
A186_08_97_NEMOJNK1
Replicate 2


title: H647_Adenosquamous

value: Adenosquamous

value: White


title: H522_Adenocarcinoma

value: Adenocarcinoma

value: WT


title: negative control, cell media alone, biological rep1

tag: genotype

value: wild-type


title: Bone.Marrow_RA_Yes_RA12

value: Bone Marrow


title: H23_Adenocarcinoma

value: M

value: Black

value: Y


title: negative control, cell media alone, biological rep2


title: DFCI032_Adenocarcinoma

value: F

value: N


title: DFCI024_Adenocarcinoma

value: mutant


title: Liver_JNK2_KO_repl3

description:
A186_06_199_JNK2
Replicate 3

source_name: liver, global JNK2 knockout

tag: strain/background

value: global Jnk2-/-

value: male

value: 8 wk

value: liver


title: Liver_JNK2_KO_repl2

description:
A186_05A_198_JNK2
Replicate 2

tag: genotype/variation


title: Bone.Marrow_RA_Yes_RA08

value: RA

value: High Serum