title: IGG_control_WT_EMB_rep2

city: Berkeley

last: Meyer

address: 16 Barker Hall

institute: University of California Berkeley

hyb_protocol: Hybridization protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

scan_protocol: Sample scan protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: ChIP input DNA from wild type N2 XX embryo

label_protocol: 3 µg of amplified ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Embryo extracts were prepared as described previously (Jans et al. 2009) except FLAG-tagged SDC-2 (TY2095) ChIP extracts were pre-cleared with protein G sepharose. Briefly, embryos collected by bleaching were crosslinked in 2% formaldehyde in M9 for 30 min at 20oC and quenched with 100 mM Tris-HCl (pH 7.5). Samples were then washed twice with M9, once with Homogenization Buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF) and frozen in liquid nitrogen. 10mM N-Ethylmaleimide (NEM) was added to the Homogenization Buffer used to make extracts for sequential ChIP. Samples were sonicated to a range of 200 bp – 1 kb using a Heat System XL2020 Sonicator with a Misonix 419 tip for 10x30 sec at 10%, then centrifuged at 5,000 x g for 20 minutes at 4°C.  The supernatant was again sonicated for 10x30 sec at 10% and spun at 20,000 x g for 20 minutes at 4°C. The resulting supernatant was pre-cleared with protein A sepharose for 30 min and frozen in liquid nitrogen.  Immunoprecipitations were performed with the appropriate antibody (as displayed in the beginning of each sample name) and were washed and processed as described in Pferdehirt et al.

value: wild type N2 XX embryo

source_name: IGG control ChIP DNA from wild type N2 XX embryo


title: MS0357_miRNA

status: Public on Aug 30 2013

type: RNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MS0357

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55?C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as 'absent' (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

molecule: total RNA

organism: Homo sapiens

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37?C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: vh status [igvh mutational status (fais et al. j clin invest, 1998)

value: mut


title: Topotecan_1µM_vehicle_2

city: Carrboro

first: Chandri

last: Yandava

state: NC

address: 101 Renee Lynne Court

department: Carolina Institute for Developmental Disabilities

country: USA

institute: University of North Carolina at Chapel Hill

description:
MoGene-2_1-st
Gene Expression data for dose response to Topotecan  treatment of  mouse cultured cortical neurons

hyb_protocol: Arrays for experiments (1) and (3) were washed and stained using the Affymetrix Gene Fluidics station 450. Hybridization was performed at 48˚C for 17 hours. Arrays for other experiments were run using the Affymetrix GeneTitan system. Steps subsequent to hybridization were performed with the Beckman Coulter FXP Target Express Robot. Hybridization was performed at 45˚C for 16 hours with the Affymetrix GeneTitan instrument, controlled using AGCC software.

scan_protocol: GeneTitan arrays were scanned using the Affymetrix GeneTitan instrument, controlled by AGCC software. Individual arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus with autoloader.

data_processing: Arrays were normalized and expression values determined using Affymetrix Expression Console. Linear RMA normalization was used for all experiments.

label: biotin

organism: Mus musculus

source_name: cultured cortical neurons

label_protocol: RNA was labeled using the Affymetrix/Ambion WT Expression kit, combined with Affymetrix GeneChip WT terminal labeling kit.

growth_protocol: Mouse cortical neurons were cultured from E13-15 mouse embryos for 7 days in vitro.

extract_protocol: Total RNA was extracted from mouse cortical neurons using Trizol reagent.

treatment_protocol: After 7 days in vitro, mouse cortical neurons were treated with drug or vehicle. After 24 or 72 hrs drug treatement, total RNA was prepared.

tag: treatment

tag: cell type

value: cultured cortical neurons

tag: strain


title: MS0189_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MS0189


title: Topotecan_1µM_5


title: Topotecan_1µM_4


title: DPY-27_smo1RNAi_EMB_rep2

status: Public on Aug 31 2013

type: genomic

first: Barbara

state: CA

department: Molecular and Cellular Biology

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: ChIP input DNA from smo-1(RNAi) XX embryo

growth_protocol: Worms grown on NG agar with HT115 bacteria expressing smo-1 RNAi

treatment_protocol: Briefly, gravid hermaphrodites were bleached and embryos crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator.

value: smo-1(RNAi) XX embryo

source_name: DPY-27 ChIP DNA from smo-1(RNAi) XX embryo


title: Topotecan_1µM_1


title: Top2b_shRNA_3


title: Topotecan_1µM_vehicle_3


title: Top2b_shRNA_1


title: Topotecan_1µM_3


title: Topotecan_1µM_vehicle_1


title: Topotecan_1µM_2


title: Top2b_shRNA_2


title: Top1_shRNA_3


title: Top1_shRNA_2


title: MS0115_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MS0115

value: unmut


title: MM0097_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MM0097


title: MO0323_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MO0323


title: Topotecan_1µM_6


title: IGG_control_WT_EMB_rep1


title: Topotecan_washout_And_Irinotecan_10µM_vehicle_1


title: Top1_shRNA_1


title: Paraquat_10µM


title: Topotecan_washout_And_Irinotecan_10µM_vehicle_2


title: MG0248_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MG0248


title: MG0110_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MG0110


title: MM0330_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MM0330


title: MF0379_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MF0379


title: MN0167_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MN0167


title: MF0048_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MF0048


title: MC0105_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MC0105


title: MA0088_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MA0088


title: GS0343_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GS0343


title: IA0025_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient IA0025


title: H2O2_Paraquat_vehicle_1

description:
MoGene-2_1-st
Gene Expression data for Irinotecan treated mouse cultured cortical neurons


title: LR0247_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient LR0247


title: LI0133_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient LI0133


title: Irinotecan_10µM_2

description:
MoGene-2_1-st
Gene Expression data for dose response to Topotecan  treatment of  mouse cultured cortical neurons


title: GR0169_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GR0169


title: GP0278_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GP0278


title: GP0171_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GP0171


title: GL0368_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GL0368


title: GN0095_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GN0095


title: control_shRNA_2

description:
MoGene-2_1-st
Gene Expression data for ICRF-193 treated mouse cultured cortical neurons


title: pool 3

city: Tianjin

first: Lina

last: Zhang

address: HuanHuXi Road

department: Breast Oncology

country: China

institute: Tianjin Medical Univercity Cancer Institute and Hospital

description: Late-stage EOC

data_processing:
Data were analyzed using RQ Manager Software version 1.2 and 7900 Sequence Detection System 2.4 (Applied Biosystems).
For the normalization it uses MammU6 as endogenous control miRNA.

label: FAM

source_name: Plasma

label_protocol: The RNA was reverse transcribed using the TaqMan miRNA reverse transcription kit. The TaqMan PreAmp master mix kit (Applied Biosystems) is intended to increase the quantity of cDNA available for analysis before using the TLDA. PCR assays were performed using the TaqMan Human MicroRNA Array Set v2.0.

extract_protocol: Total RNA was extracted with miRNeasy Mini Kit.

tag: tumor stage

value: stage IIIc-IV


title: pool 2

description: Early-stage EOC

value: stage I


title: Irinotecan_10µM_1


title: GC0328_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GC0328


title: GE0125_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GE0125


title: GF0281_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GF0281


title: H2O2_Paraquat_vehicle_2


title: Irinotecan_10µM_3


title: control_shRNA_1


title: H2O2_100µM


title: DRB_100µM_vehicle


title: GC0015_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GC0015


title: DRB_100µM


title: GC0147_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GC0147


title: pool 1

description: Control

value: normal


title: GA0141_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GA0141


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 120 min anaerob

city: Braunschweig

first: Sebastian

middle: Walter Friedrich

last: Laaß

address: Spielmannstraße 7

department: Inst. f. Mikrobiologie

country: Germany

institute: Technische Universität Braunschweig

hyb_protocol: 300 ng of each labeled RNA were pooled, fragmented and hybridized according to the “two-colour microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing: Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). Only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.

organism: Dinoroseobacter shibae

source_name: Dinoroseobacter shibae, aerob

label_protocol: Two µg of isolated total cellular RNA was either labeled with Cy3 or Cy5, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: Continuous cultivation of Dinoroseobacter shibae DFL12T was performed in Salt-Water-minimal medium (SWM) in an Infors HT Multifor 2 reactor (Infors, Bottmingen, Switzerland) at 30 °C, pH 8.0, with aeration of 0.7 l per minute and a stirring speed of 150 r.p.m. The reactor working volume was 1 l. The pH was adjusted automatically with 0.5 M HPO3 and 0.5 M NaOH. In the steady state the oxygen saturation of the culture was stable at approximately 85 %. To avoid aerobic anoxygenic photosynthesis of D. shibae during the experiment, the chemostat was covered with aluminium foil. The bioreactor was inoculated to a starting optical density of OD578 0.02 with a pre-culture grown in erlenmeyer flask in SWM at 30 °C and 200 rpm. Continuous flow of fresh medium was started after the culture reached an OD578 of 0.5. The dilution rate was 0.1 h-1 corresponding to the half-maximum growth rate of D. shibae in the exponential phase.

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was qualified and quantified using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: An anaerobic shift was performed after two reactor residence time points (20 hours) by stopping the aeration. The investigated time points were 5 min, 10 min, 15 min, 20 min, 30 min, 60 min, 120 min after oxygen supply switched off.

tag: growth phase

value: exponential phase

source_name: Dinoroseobacter shibae, 120 min anaerob


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 120 min anaerob


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 120 min anaerob


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 120 min anaerob


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 120 min anaerob


title: FI0152_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FI0152


title: GB0293_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GB0293


title: FD0404_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FD0404


title: Technical replicate 2 of 2, Control D. shibae aerob, Sample D. shibae 60 min anaerob

source_name: Dinoroseobacter shibae, 60 min anaerob


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 120 min anaerob


title: control_shRNA_3


title: FC0075_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FC0075


title: Technical replicate 1 of 2, Control D. shibae aerob, Sample D. shibae 60 min anaerob


title: GA0398_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GA0398


title: FB0332_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FB0332


title: FA0294_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FA0294


title: DT0300_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DT0300


title: FP0153_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FP0153


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 30 min anaerob

source_name: Dinoroseobacter shibae, 30 min anaerob


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 30 min anaerob


title: Biological replicate 2 of 2. Control D. shibae aerob, Sample D. shibae 60 min anaerob


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 30 min anaerob


title: DD0280_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DD0280


title: DM0050_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DM0050


title: DA0215_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DA0215


title: DR0312_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DR0312


title: DA0029_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient DA0029


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 30 min anaerob


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 30 min anaerob


title: Biological replicate 1 of 2. Control D. shibae aerob, Sample D. shibae 60 min anaerob


title: CS0030_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CS0030


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 30 min anaerob


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 20 min anaerob

source_name: Dinoroseobacter shibae, 20 min anaerob


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 20 min anaerob


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 20 min anaerob


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 20 min anaerob


title: CS0290_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CS0290


title: Urothelial Carcinoma, Sample 67

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: Labeled sample and reference DNA was hybridized to arrays according to manufacturers specifications (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Raw data was filtered from control probes and probes that did not pass Agilent's default well above background condition. Remaining probes were corrected for background signal and log 2 ratios (log 2 (Signal sample/Signal reference)) were calculated from the adjusted signal intensities for each array. The log 2 ratios were normalized and centered using popLowess (Staaf, et al, BMC Genomics, 2007, 8:382). The log 2 values of replicate probes were merged to their median value.

source_name: Urothelial Carcinoma

label_protocol: Tumor sample and male reference DNA (Promega) were labeled according to manufacturers specifications (Agilent Technologies).

extract_protocol:
Sample collection: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resecrtions at hospitals within the southern healthcare region of Sweden.
Genomic DNA was extracted using the AllPrep (Qiagen) following manufacturer's instructions.

tag: gender

value: male

tag: tumor grade

source_name: promega male reference

extract_protocol: Promega pooled male genomic DNA (reference)

tag: sample type

value: Reference:Pooled genomic DNA (Promega)


title: Urothelial Carcinoma, Sample 68

value: Female


title: Urothelial Carcinoma, Sample 66

extract_protocol:
Sample collection: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resecrtions at hospitals within the southern healthcare region of Sweden.
Genomic DNA was extracted using the DNeasy Tissue kit (Qiagen) following manufacturer's instructions.


title: CP0104_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CP0104


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 20 min anaerob


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 20 min anaerob


title: Urothelial Carcinoma, Sample 63


title: Urothelial Carcinoma, Sample 64


title: Urothelial Carcinoma, Sample 65


title: CL0317_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CL0317


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 15 min anaerob

source_name: Dinoroseobacter shibae, 15 min anaerob


title: Urothelial Carcinoma, Sample 59


title: Urothelial Carcinoma, Sample 62


title: Urothelial Carcinoma, Sample 60


title: Urothelial Carcinoma, Sample 57


title: Urothelial Carcinoma, Sample 61


title: CI0005_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CI0005


title: CG0204_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CG0204


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 15 min anaerob


title: CG0166_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CG0166


title: Urothelial Carcinoma, Sample 56


title: Urothelial Carcinoma, Sample 55


title: Urothelial Carcinoma, Sample 54


title: Urothelial Carcinoma, Sample 58


title: CF0003_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CF0003


title: CE0399_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CE0399


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 15 min anaerob


title: CE0078_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CE0078


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 15 min anaerob


title: Urothelial Carcinoma, Sample 51


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 15 min anaerob


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 10 min anaerob

source_name: Dinoroseobacter shibae, 10 min anaerob


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 10 min anaerob


title: Urothelial Carcinoma, Sample 52


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 15 min anaerob


title: Urothelial Carcinoma, Sample 53


title: Urothelial Carcinoma, Sample 50


title: Urothelial Carcinoma, Sample 49


title: Urothelial Carcinoma, Sample 43


title: CC0311_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CC0311


title: CA0345_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CA0345


title: Urothelial Carcinoma, Sample 46


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 10 min anaerob


title: Urothelial Carcinoma, Sample 45


title: Urothelial Carcinoma, Sample 42


title: Urothelial Carcinoma, Sample 41


title: Urothelial Carcinoma, Sample 47


title: Urothelial Carcinoma, Sample 48


title: Urothelial Carcinoma, Sample 40


title: CA0160_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CA0160


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 10 min anaerob


title: BV0176_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BV0176


title: Urothelial Carcinoma, Sample 39


title: Technical replicate 2 of 3, Control D. shibae aerob, Sample D. shibae 5 min anaerob

source_name: Dinoroseobacter shibae, 5 min anaerob


title: BL0162_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BL0162


title: Urothelial Carcinoma, Sample 44


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 10 min anaerob


title: Urothelial Carcinoma, Sample 37


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 10 min anaerob


title: CC0244_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CC0244


title: Urothelial Carcinoma, Sample 33


title: Urothelial Carcinoma, Sample 34


title: Urothelial Carcinoma, Sample 36


title: Urothelial Carcinoma, Sample 38


title: Technical replicate 1 of 3, Control D. shibae aerob, Sample D. shibae 5 min anaerob


title: Urothelial Carcinoma, Sample 31


title: Urothelial Carcinoma, Sample 30


title: BE0192_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BE0192


title: BF0316_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BF0316


title: Urothelial Carcinoma, Sample 32


title: Biological replicate 2 of 3. Control D. shibae aerob, Sample D. shibae 5 min anaerob


title: BB0238_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BB0238


title: Urothelial Carcinoma, Sample 35


title: Urothelial Carcinoma, Sample 29


title: Urothelial Carcinoma, Sample 28


title: AS0012_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AS0012


title: AM0270_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AM0270


title: BB0245_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BB0245


title: AR0090_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AR0090


title: Biological replicate 1 of 3. Control D. shibae aerob, Sample D. shibae 5 min anaerob


title: Biological replicate 3 of 3. Control D. shibae aerob, Sample D. shibae 5min anaerob


title: Urothelial Carcinoma, Sample 24


title: Urothelial Carcinoma, Sample 23


title: Urothelial Carcinoma, Sample 22


title: Urothelial Carcinoma, Sample 25


title: Urothelial Carcinoma, Sample 26


title: Urothelial Carcinoma, Sample 14


title: AG0136_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AG0136


title: AG0403_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AG0403


title: AB0350_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AB0350


title: Urothelial Carcinoma, Sample 20

value: Ta


title: Urothelial Carcinoma, Sample 18


title: Urothelial Carcinoma, Sample 13


title: AA0284_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AA0284


title: Urothelial Carcinoma, Sample 12


title: Urothelial Carcinoma, Sample 27


title: Urothelial Carcinoma, Sample 11


title: Urothelial Carcinoma, Sample 17


title: Urothelial Carcinoma, Sample 15


title: Urothelial Carcinoma, Sample 10


title: Urothelial Carcinoma, Sample 16


title: Urothelial Carcinoma, Sample 9


title: Topotecan_dose_response_vehicle_2

description:
MoGene-1_1-st-v1
Gene Expression data for dose response to Topotecan  treatment of  mouse cultured cortical neurons


title: Topotecan_dose_response_vehicle_1


title: Urothelial Carcinoma, Sample 4


title: Urothelial Carcinoma, Sample 21


title: Urothelial Carcinoma, Sample 2


title: Urothelial Carcinoma, Sample 3


title: 150nM_Topotecan

description:
MoGene-1_1-st-v1
Gene Expression data for Topotecan treated mouse cultured cortical neurons


title: 500nM_Topotecan

description:
MoGene-1_1-st-v1
Gene Expression data for ICRF-193 treated mouse cultured cortical neurons


title: Topotecan_dose_response_vehicle_3


title: 300nM_Topotecan_1


title: Mop3fxfxCreAlb_kidney_20week_ZT12

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

institute: UW-Madison

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9..5 for background subtraction - localbackground and normalization Linear LOWESS, Goodspots were designated as those features with both channels r and g where controltype=0, issaturated=0,isfeatnonunifol=0,isfeatpopnol=0,iswellabovebg=1 in 80% of arrays

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

extract_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Sacrificed and dissected at given time and placed in RNAlater

tag: time of sacrifice

tag: genotype

tag: age

value: 20 weeks

tag: tissue

value: Kidney

source_name: Kidney reference pool, pooled kidney RNA from all 10 week Mop3fxfx and Mop3fxfxCreAlb mice.

tag: reference


title: Mop3fxfxCreAlb_kidney_20week_ZT20

value: Kidney reference pool, pooled kidney RNA from all 10 week Mop3fxfx and Mop3fxfxCreAlb  mice.


title: Mop3fxfxCreAlb_kidney_20week_ZT16


title: Urothelial Carcinoma, Sample 5


title: 300nM_Topotecan_2


title: 3nM_Topotecan


title: 30nM_Topotecan


title: Urothelial Carcinoma, Sample 7


title: Mop3fxfxCreAlb_kidney_20week_ZT8


title: Urothelial Carcinoma, Sample 1


title: Mop3fxfxCreAlb_kidney_20week_ZT4


title: Mop3fxfx_kidney_20week_ZT12


title: Mop3fxfx_kidney_20week_ZT20


title: Mop3fxfx_kidney_20week_ZT8


title: 1000nM_Topotecan


title: Mop3fxfx_kidney_20week_ZT0


title: Mop3fxfxCreAlb_kidney_20week_ZT0


title: Mop3fxfx_kidney_20week_ZT4


title: Urothelial Carcinoma, Sample 6


title: Technical replicate 3 of 3, Control D. shibae aerob, Sample D. shibae 5 min anaerob


title: Mop3fxfxCreAlb_kidney_10week_ZT16

value: 10 weeks


title: 20Large2

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing: Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: 20 large physaliferous cells

label_protocol: GeneChip® Human Gene 1.0 ST Arrays (Cat. No. 901087)   Labeling: Encore™ Biotin Module (Cat No. 4200-12)

growth_protocol: MUG-Chor1 were cultured in IMDM/RPMI 4:1 (PAA Laboratories, Pasching, Austria) supplemented with 2 mM L-Glutamin (PAA), 10% FBS (PAA) and 1% PS (PAA) at 37°C and 5% CO2.

extract_protocol: Extraction and amplification:NuGENE WT-Ovation™ One-Direct, RNA Amplification System, version 1.0 (Cat No. 3500-12)

treatment_protocol: Immediately after trypsinization (0.05% Trypsin-EDTA), MUG-Chor1 cells were and cytocentrifuged onto PEN membrane coated slides or object slides

tag: cell line

value: MUG-Chor1 cell line (chordoma derived)


title: 20Large4


title: Urothelial Carcinoma, Sample 19


title: 20Small5

source_name: 20 small non-vacuolated cells


title: 20Small7


title: 20Large3


title: Mop3fxfxCreAlb_kidney_10week_ZT12


title: 20Small6


title: Mop3fxfx_kidney_20week_ZT16


title: Mop3fxfxCreAlb_kidney_10week_ZT8


title: Mop3fxfxCreAlb_kidney_10week_ZT20


title: Mop3fxfx_kidney_10week_ZT20


title: Mop3fxfxCreAlb_kidney_10week_ZT0


title: Mop3fxfxCreAlb_kidney_10week_ZT4


title: Mop3fxfx_kidney_10week_ZT16


title: Mop3fxfx_kidney_10week_ZT8


title: Mop3fxfx_kidney_10week_ZT12


title: EPN_691_3

city: Aurora

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

description:
included_in_corresponding_manuscript:no
Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 17,664 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: Recurrent

value: brain tumor (ependymoma)


title: Mop3fxfxCreAlb_liver_20week_ZT8

value: Liver

source_name: Liver reference pool, pooled liver RNA from all 10 week Mop3fxfx and Mop3fxfxCreAlb mice.


title: Mop3fxfxCreAlb_liver_20week_ZT12

value: Liver reference pool, pooled liver RNA from all 10 week Mop3fxfx and Mop3fxfxCreAlb  mice.


title: Mop3fxfx_kidney_10week_ZT0


title: EPN_691_1_repeat

description:
included_in_corresponding_manuscript:yes
Gene expression data from surgical tumor sample of ependymoma

value: Primary


title: Mop3fxfx_kidney_10week_ZT4


title: Mop3fxfx_liver_20week_ZT20


title: Mop3fxfx_liver_20week_ZT4


title: Mop3fxfxCreAlb_liver_20week_ZT16


title: Mop3fxfxCreAlb_liver_20week_ZT4


title: Mop3fxfx_liver_20week_ZT8


title: Mop3fxfxCreAlb_liver_10week_ZT16


title: Mop3fxfxCreAlb_liver_10week_ZT12


title: Mop3fxfxCreAlb_liver_10week_ZT20


title: EPN_393_2


title: Mop3fxfx_liver_20week_ZT0


title: Mop3fxfx_liver_20week_ZT16


title: Mop3fxfx_liver_10week_ZT12


title: Mop3fxfx_liver_10week_ZT20


title: Mop3fxfxCreAlb_liver_20week_ZT0


title: Mop3fxfxCreAlb_liver_10week_ZT8


title: Urothelial Carcinoma, Sample 8


title: Mop3fxfx_liver_20week_ZT12


title: Mop3fxfx_liver_10week_ZT16


title: Mop3fxfxCreAlb_liver_10week_ZT4


title: Mta1 over expression in the P53 knockout,rep1

city: washington

first: krishna

last: ghanta

state: DC

address: 2300 eye st NW

institute: GWU

description: Mta1 over expression in the P53 knockout mice

hyb_protocol: Samples were processed using the Affymetrix hybridization, wash and stain kits. 200µl of the hybridization mixture was hybridized onto each Mouse Exon 1.0 st array. Hybridized at 45°C with 60rpm rotation for 17 hours in Affymetrix hybridization oven 640

scan_protocol: Affymetrix Genechip scanner 3000 7G

data_processing:
Data were processed using Genespring GX 10.0.2 (Affymetrix Technologies,Inc) . The raw data was summerized using RMA16 algorithm which is inbuilt in Genespring GX,followed by the log transformation, baseline transformation and finally quantile normalization.
Normalized gene level expression values from Genespring software (Affymetrix)

label_protocol: rRNA reduced samples were amplified and labelled using Genechip WT cDNA Synthesis/Amplification Kit and GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Fibroblasts isolated from day 9.0 old mouse embryos for the Mta1-/- and 12.5 days old for the P53-/- mice. The strain of the mice used was C57BL/6J.

extract_protocol: TRIzol was used for the RNA extraction, manufacturer's instructions were followed

value: mouse embryonic fibroblasts

tag: genotype/variation

tag: mta1 expression

value: Mta1 over expression


title: Mop3fxfxCreAlb_liver_10week_ZT0


title: Mta1 over expression in the P53 knockout,rep2


title: P53 knockout at E12.5, biological rep3

description: mouse embryonic fibroblasts from P53 knockout mice


title: Mta1 over expression in the P53 knockout,rep3


title: Mop3fxfx_liver_10week_ZT4


title: P53 knockout at E12.5, biological rep1


title: Mta1 reexpression in Knockout, rep3

description: Mta1 is re-expressed in the knockout MEFs

value: Mta1 reexpression


title: Mop3fxfx_liver_10week_ZT8


title: P53 knockout at E12.5, biological rep2


title: Mop3fxfx_liver_10week_ZT0


title: EPN_306_1


title: Mta1 reexpression in Knockout, rep1


title: Mta1 reexpression in Knockout, rep2


title: EPN_242_1


title: Mta1 knockout at E9.0, biological rep2

description: Mouse embryonic fibroblasts from mta1 knockout mice


title: Mta1 knockout at E9.0, biological rep3


title: EPN_218_1


title: EPN_195_4


title: Mta1 knockout at E9.0, biological rep1


title: Wildtype MEFs at E9.0,biological rep3

description: wildtype mouse embryonic fibroblasts

source_name: wildtype

value: wildtype


title: Hippocampus Age 12mo_SAMP8, Biological Replicate 2

city: St. Louis

first: Harvey

middle: J

last: Armbrecht

state: MO

address: #1 Jefferson Barracks Drive

department: Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology

institute: St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine

description: Gene Expression Data from hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age

hyb_protocol: Following fragmentation, 12.5μg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were normalized using gc-RMA algorithms, which consist of background adjustment and quantile normalization, accounting for probe GC content; executed using  the R statistical environment and the BioConductor package.  A balanced 2 x 2 ANOVA (4 conditions, N=4 independent biological replicates per condition)  was performed on GCRMA-normalized log2 transformed signal intensities to assess gene expression variability with regard to Strain (Control (50% SAMP8) vs SAMP8) and Age (4 vs 12 months) (FDR ≤ 0.1).

source_name: Mouse Hippocampus from 12 month-old, SAMP8 mice -- SAMP8 (senescence-accelerated) mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 μg total RNA per sample (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: The ”Control” mice were a 50% backcross of the SAMP8 (senescence-accelerated) mice with CD-1 mice (50% SAMP8 mice).  These mice were closely related to SAMP8 mice but exhibited no memory deficits at 4 or 12 months.  The SAMP8 mice had memory deficits at 12 months but not at 4 months.

extract_protocol: Total RNA was extracted from the hippocampus of individual mice using the Qiagen RNeasy Lipid Extraction Mini Kit.

treatment_protocol: In order to assess memory and cognitive function in each mouse, T-maze foot shock avoidance and novel object recognition were measured as described in the manuscript.  T-maze is a declarative memory task that requires an intact hippocampus.

value: Hippocampus

value: 12 months


title: Hippocampus Age 12mo_SAMP8, Biological Replicate 1

value: SAMP8 mice -- SAMP8 (senescence-accelerated) mice


title: Hippocampus Age 12mo_50% SAMP8, Biological Replicate 4

description: Gene Expression Data from hippocampus of 12-month-old 50% SAMP8 mice, which exhibit no memory deficits at 4 or 12 months of age

source_name: Mouse Hippocampus from 12 month-old, 50% SAMP8 mice -- 50% backcross of SAMP8 (senescence-accelerated) mice with CD-1 mice


title: Hippocampus Age 12mo_SAMP8, Biological Replicate 4


title: Hippocampus Age 12mo_SAMP8, Biological Replicate 3


title: Hippocampus Age 12mo_50% SAMP8, Biological Replicate 3

value: 50% SAMP8 mice -- 50% backcross of SAMP8 (senescence-accelerated) mice with CD-1 mice


title: Hippocampus Age 12mo_50% SAMP8, Biological Replicate 2


title: Wildtype MEFs at E9.0,biological rep1

description: wildtype mouse embryonic fibroblasts


title: Wildtype MEFs at E9.0,biological rep2

description: wildtype mouse embryonic fibroblasts


title: Hippocampus Age 12mo_50% SAMP8, Biological Replicate 1


title: EPN_135_4


title: EPN_135_2


title: EPN_176_5


title: Hippocampus Age 4mo_50% SAMP8, Biological Replicate 4

description: Gene Expression Data from hippocampus of 4-month-old 50% SAMP8 mice, which exhibit NO memory deficits at 4 or 12 months of age

source_name: Mouse Hippocampus from 4 month-old, 50% SAMP8 mice -- 50% backcross of SAMP8 (senescence-accelerated) mice with CD-1 mice

value: 4 months


title: Hippocampus Age 4mo_SAMP8, Biological Replicate 2

description: Gene Expression Data from hippocampus of 4-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age

source_name: Mouse Hippocampus from 4 month-old, SAMP8 mice -- SAMP8 (senescence-accelerated) mice


title: Hippocampus Age 4mo_SAMP8, Biological Replicate 1


title: Hippocampus Age 4mo_SAMP8, Biological Replicate 4


title: Hippocampus Age 4mo_SAMP8, Biological Replicate 3


title: L4440 PA14 - rep 3

city: La Jolla

first: Emily

last: Troemel

department: Cell and Developmental Biology

institute: University of California, San Diego

description: Gene expression data from wild-type animals infected with P. aeruginosa

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr on GeneChip Celegans Genome Array at Harvard Medical School Biopolymers Facility per their protocol in 2008

scan_protocol: GeneChips were scanned at Harvard Medical School Biopolymers Facility per their protocol in 2008

data_processing: Data were analyzed at Harvard Medical School Biopolymers Facility per their protocol in 2008

source_name: Control infected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at Harvard Medical School Biopolymers Facility per their protocol in 2008

growth_protocol: C. elegans N2 were added as L1 larvae to RNAi plates seeded with L4440 control bacterial or zip-2 RNAi bacteria at 20C for 48 hours

extract_protocol: RNA was extracted with TriReagent followed by Rneasy column clean-up

treatment_protocol: Animals were transferred to SK plates seeded with E. coli OP50 or P. aeruginosa PA14

value: young adult

tag: time

value: 4 hours


title: Hippocampus Age 4mo_50% SAMP8, Biological Replicate 3


title: L4440 PA14 - rep 2


title: zip-2 PA14 - rep 2

description: Gene expression data from zip-2 RNAi animals infected with P. aeruginosa

source_name: zip-2 infected


title: zip-2 PA14 - rep 3


title: zip-2 OP50 - rep 3

description: Gene expression data from zip-2 RNAi uninfected animals grown on E. coli

source_name: zip-2 uninfected


title: L4440 OP50 - rep 3

description: Gene expression data from wild-type uninfected animals grown on E. coli

source_name: Control uninfected


title: L4440 OP50 - rep 2


title: Hippocampus Age 4mo_50% SAMP8, Biological Replicate 1


title: Topotecan_300nM_vehicle_2

description:
Mouse430_2
Gene Expression data for dose response to Topotecan  treatment of  mouse cultured cortical neurons

source_name: cultured cortical neurons

tag: treatment

tag: cell type

value: cultured cortical neurons


title: zip-2 OP50 - rep 2


title: Mop3fxfxCreAlb_liver_20week_ZT20

tag: strain

value: 20 weeks


title: Hippocampus Age 4mo_50% SAMP8, Biological Replicate 2


title: Topotecan_300nM_vehicle_3


title: zip-2 PA14 - rep 1


title: HUVE_Physiological Chronic Normoxia_5

first: Yizhou

last: Jiang

state: Wi

address: 202 S. Park st PAB1

institute: University of Wisconsin-madison

hyb_protocol: Fragmented cRNA (10 µg/sample) were hybridized to Affymetrix U133 plus 2.0 microarray chips (Affymetrix, Santa Clara, CA). The chips were processed on Affymetrix GC450 Fluidics station.

scan_protocol: Data were extracted from GC3000 G7 scanned images using Affymetrix Expression Console software version 1.4.

data_processing: The data were analyzed with Microarray Suite version 5.0 and then were normalized with Robust Multi-Array Analysis. One outlier in the data set (one HUVEC preparation) was identified using hierarchical clustering and eliminated from the following data analysis.  EBarrays was applied to identify differentially expressed genes.

source_name: human umbilical vein endothelial cell, Physiological Standard Culture Normoxia

label_protocol: Complementary RNA (cRNA) were synthesized, labeled and fragmented using the MessageAmp II-biotin enhanced kit (Ambion, Austin, TX).

growth_protocol: Human umbilical cords from normal term pregnant patients were collected immediately after delivery. Paired umbilical cord vein and artery  endothelial cells from a single of umbililca cord were isolated using a standard collagenase enzyme digestion method.

extract_protocol: Total RNA from 6 pairs of primary PCN- and SCN-HUVE and -HUAE cell lines (total 24) were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) in conjunction with a QIAshredder.

treatment_protocol: Immediately after isolation, cells obtained from the same vein  or artery were split equally, cultured, and expanded steadily under SCN (37 oC, 5% CO2, 95% air) or PCN (37 oC, 5% CO2, 3% O2, 92% N2) up to 25 days in RPMI 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (HyClone, Logan, UT), 1% penicillin/streptomycin (HyClone), 100 µg/L heparin (EMD, Gibbstown, NJ), and 37.5 mg/L endothelial cell growth supplement (Millipore, Billerica, MA).

value: HUVE


title: Topotecan_300nM_1


title: Topotecan_300nM_2


title: HUVE_Physiological Chronic Normoxia_4


title: L4440 OP50 - rep 1


title: Topotecan_300nM_3


title: L4440 PA14 - rep 1


title: zip-2 OP50 - rep 1


title: HUVE_Physiological Chronic Normoxia_3


title: Topotecan_300nM_vehicle_1


title: ICRF193_3µM_vehicle_3


title: HUVE_Physiological Chronic Normoxia_2


title: HUVE_Physiological Chronic Normoxia_1


title: ICRF193_3µM_vehicle_2


title: ICRF193_3µM_3

description:
Mouse430_2
Gene Expression data for Irinotecan treated mouse cultured cortical neurons


title: HUVE_Standard Culture Normoxia_4

source_name: human umbilical vein endothelial cell, Standard Culture Normoxia


title: HUVE_Standard Culture Normoxia_3


title: HUVE_Standard Culture Normoxia_5


title: HUVE_Standard Culture Normoxia_2


title: ICRF193_3µM_1


title: HUVE_Standard Culture Normoxia_1


title: ICRF193_3µM_vehicle_1


title: HUAE_Physiological Chronic Normoxia_4

source_name: human umbilical artery endothelial cell, Physiological Standard Culture Normoxia

value: HUAE


title: HUAE_Physiological Chronic Normoxia_5


title: HUAE_Physiological Chronic Normoxia_3


title: HUVE_Standard Culture Normoxia_6


title: ICRF193_3µM_2


title: MTEC PR8 infected rep2 [C57Bl/6 MAVS -/-]

city: London

first: Stefania

last: Crotta

address: The Ridgeway

department: IR

country: United Kingdom

institute: The Crick- Mill Hill Laboratories

description: Gene expression data from MTEC cells

hyb_protocol: User guide Affymetrix GeneChip 3’ Express Kit (P/N 702646 Rev.8)

scan_protocol: User guide Affymetrix Expression Wash, Stain and Scan (P/N 702731 Rev. 3)

data_processing: Primary and QC analysis on Affymetrix Expression Console V1.1. Data were normalized to the median of mock infected sample (all genotypes).

source_name: tracheas from MAVS-/-

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Fully differentiated, 10-14 days-old post ALI cultures were routinely used for experiments.

extract_protocol: RNA was isolated from MTEC cultures by directly lysing the cells in the transwells, using the Qiagen RNeasy mini kit

treatment_protocol: MTEC were either mock infected or infected with PR8 (moi=0.3)

tag: background strain

value: trachea

value: MAVS-/-


title: MTEC PR8 infected rep3 [C57Bl/6 MAVS -/-]

description: Gene expression data from MTEC cells

label_protocol: User guide Affymetrix GeneChip 3’ Express Kit (P/N 702646 Rev.8)


title: HUAE_Physiological Chronic Normoxia_1


title: HUAE_Physiological Chronic Normoxia_6


title: MTEC mock infected rep3 [C57Bl/6 wt]

description: Gene expression data from MTEC cells

source_name: tracheas from C57Bl/6 wt

value: wild-type


title: MTEC PR8 infected rep2 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep3 [C57Bl/6 MAVS -/-]

description: Gene expression data from MTEC cells


title: HUAE_Standard Culture Normoxia_6

source_name: human umbilical artery endothelial cell, Standard Culture Normoxia


title: HUAE_Physiological Chronic Normoxia_2


title: HUAE_Standard Culture Normoxia_5


title: MTEC PR8 infected rep1 [C57Bl/6 MAVS -/-]

description: Gene expression data from MTEC cells


title: MTEC PR8 infected rep1 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: HUAE_Standard Culture Normoxia_3


title: HUAE_Standard Culture Normoxia_2


title: HUAE_Standard Culture Normoxia_1


title: MTEC mock infected rep2 [C57Bl/6 MAVS -/-]

description: Gene expression data from MTEC cells


title: MTEC PR8 infected rep3 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: HUAE_Standard Culture Normoxia_4


title: MTEC mock infected rep1 [C57Bl/6 MAVS -/-]

description: Gene expression data from MTEC cells


title: Ampullary oviduct, luteal phase_Alex-621

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: Biotinylated cRNAs were hybridized overnight to a high density Affimetrix Human Genome (HG) U133 Plus 2.0 oligonucleotide microarray genechip containing 54600 probe sets (42203 annotated genes and 12397 expressed sequence tags [EST]) at the Stanford University School of Medicine Protein and Nucleic Acid (PAN) Facility.

scan_protocol: Fluorescent labeling and laser confocal scanning with an HR 3000 scanner was conducted. Generated data were extracted for analysis using the Affymetrix Gene-Chip Operating Software (GCOS) version 1.1.

data_processing: The intensity values of different probe sets (genes) generated by Affymetrix GCOS (see supplementary file on Series record) were imported into GeneSpring version 7.2 software (Agilent Technologies, Santa Clara, CA, USA) for data analysis. Summarization Algorithm: RMA; Normalization: Quantile; Baseline Transformation: median of all samples.

source_name: Ampullary oviduct, luteal phase

label_protocol: Biotinylated-cRNA was then prepared using the Enzo BioArray High Yield T7 Transcript labeling kit (Enzo, Farmingdale, NY, USA) and chemically fragmented.

extract_protocol: Total RNA was isolated from the fallopian tube tissue using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, followed by DNase treatment. The purity and quality of the RNA were assessed spectrophotometrically by determining their absorbance ratio A260/A280 and electrophoresis of samples on 1.5 % denaturing agarose gels. First and second strand cDNAs were prepared according to the Affymetrix microarray preparation protocol (Affymetrix).

value: Fallopian tube

tag: menstral cycle phase

value: Luteal


title: MTEC mock infected rep1 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep4 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells

data_processing: Primary and QC analysis on Affymetrix Expression Console V1.1. Data were normalized to the median of mock infected sample (all genotypes)

source_name: tracheas from C57Bl/6-Mx IFNAR1-/IL-28ra-/-


title: MTEC mock infected rep2 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep3 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep2 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: Ampullary oviduct, luteal phase_Alex-617 I

description: Alex-617 I_U133_Plus_2.CEL


title: MTEC PR8  infected rep5 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: Ampullary oviduct, luteal phase_Alex-95


title: Ampullary oviduct, follicular phase_Alex-561

source_name: Ampullary oviduct, follicular phase

value: Follicular


title: MTEC PR8  infected rep1 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: Ampullary oviduct, follicular phase_Alex-94


title: Ampullary oviduct, follicular phase_Alex-91


title: MTEC mock infected rep5 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep4 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep3 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15979

city: Durham

first: Cynthia

last: Moylan

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

description: Gene expression data from advanced NAFLD patient

hyb_protocol: Affymetrix GeneChip  hybridization Oven 645

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: GC-RMA

source_name: NAFLD liver biopsy tissue

label_protocol: Ambion MessageAmp Premier as described by the manufacturer

extract_protocol: Qiagen Micro Kit according to manufacturer's instructions

tag: Stage

value: advanced (fibrosis stage 3-4)

value: liver


title: NAFLD liver biopsy tissue 15946


title: NAFLD liver biopsy tissue 15985

description: Gene expression data from mild NAFLD patient

value: mild (fibrosis stage 0-1)


title: MTEC PR8  infected rep4 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells

source_name: tracheas from C57Bl/6-Mx IL-28ra-/-


title: NAFLD liver biopsy tissue 15966


title: NAFLD liver biopsy tissue 15972


title: NAFLD liver biopsy tissue 15996


title: NAFLD liver biopsy tissue 15986


title: NAFLD liver biopsy tissue 15928


title: MTEC PR8  infected rep5 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15919


title: NAFLD liver biopsy tissue 15998


title: MTEC PR8  infected rep3 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep1 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15903


title: NAFLD liver biopsy tissue 15912


title: MTEC mock infected rep2 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep2 [C57Bl/6-Mx IFNAR1-/IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep5 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15914


title: MTEC PR8  infected rep1 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15893


title: MTEC PR8  infected rep2 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep4 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep1 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep3 [C57Bl/6-Mx IL-28ra-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15878


title: NAFLD liver biopsy tissue 15902


title: MTEC PR8  infected rep4 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells

source_name: tracheas from C57Bl/6-Mx IFNAR1-/-


title: NAFLD liver biopsy tissue 15757


title: NAFLD liver biopsy tissue 15864


title: NAFLD liver biopsy tissue 15771


title: MTEC mock infected rep1 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep2 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15794


title: MTEC PR8  infected rep5 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep2 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15568


title: NAFLD liver biopsy tissue 15684


title: MTEC mock infected rep3 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep1 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep2 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells

source_name: tracheas from C57Bl/6-Mx


title: NAFLD liver biopsy tissue 15777


title: MTEC mock infected rep4 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15800


title: NAFLD liver biopsy tissue 15873


title: MTEC PR8  infected rep3 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15776


title: NAFLD liver biopsy tissue 15626


title: MTEC PR8  infected rep4 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep1 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep5 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15742


title: NAFLD liver biopsy tissue 15707


title: NAFLD liver biopsy tissue 15812


title: MTEC mock infected rep5 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: MTEC PR8  infected rep3 [C57Bl/6-Mx IFNAR1-/-]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15681


title: MTEC mock infected rep5 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15557


title: NAFLD liver biopsy tissue 15445


title: MTEC mock infected rep2 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15495


title: NAFLD liver biopsy tissue 15503


title: MTEC mock infected rep3 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15442


title: MTEC PR8 rep5 [C57Bl/6 wt]

description: Gene expression data from MTEC cells

data_processing: Primary and QC analysis on Affymetrix Expression Console V1.1  . Data were normalized to the median of mock infected sample (all genotypes)


title: MTEC PR8 rep2 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15399


title: NAFLD liver biopsy tissue 15479


title: MTEC mock infected rep1 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep5 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC PR8 rep1 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15554


title: NAFLD liver biopsy tissue 15400


title: MTEC mock infected rep4 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep1 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15433


title: MTEC mock infected rep2 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC PR8 rep3 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC PR8 rep4 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: MTEC mock infected rep4 [C57Bl/6-Mx]

description: Gene expression data from MTEC cells


title: NAFLD liver biopsy tissue 15386


title: NAFLD liver biopsy tissue 15361


title: NAFLD liver biopsy tissue 15441


title: NAFLD liver biopsy tissue 15342


title: NAFLD liver biopsy tissue 15367


title: NAFLD liver biopsy tissue 15381


title: NAFLD liver biopsy tissue 15341


title: MTEC mock infected rep3 [C57Bl/6 wt]

description: Gene expression data from MTEC cells


title: colorectal adenocarcinoma, sample 15

city: Brest

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

country: France

institute: INSERM U1078-ECLA

description: colorectal adenocarcinoma biopsy

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos.

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: 1.5 - 2 µg of respective total RNA as well as 2 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

extract_protocol: Total RNA was extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.

tag: sample type

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

source_name: colorectal adenocarcinoma biopsy sample 15

value: adenocarcinoma


title: colorectal adenocarcinoma, sample 14

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 14


title: colorectal adenocarcinoma, sample 13

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 13


title: colorectal adenocarcinoma, sample 11

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 11


title: colorectal adenocarcinoma, sample 10

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 10


title: colorectal adenocarcinoma, sample 8

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 8


title: colorectal adenocarcinoma, sample 12

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 12


title: NAFLD liver biopsy tissue 15311


title: NAFLD liver biopsy tissue 15298


title: NAFLD liver biopsy tissue 15271


title: NAFLD liver biopsy tissue 15290


title: PDAC-4 human-Cy5 vs reference-Cy3

city: Amsterdam

first: Amir

last: Avan

address: DE BOELELAAN 1118

country: Netherlands

institute: VU University Medical Center

hyb_protocol: DNAs were hybridized using Agilent SurePrint G3 Human CGH Microarray Kit for the 4x180K Agilent platform (Agilent Technologies, Santa Clara, CA).

scan_protocol: The slides were scanned on Agilent Microarray Scanner, followed by data extraction and normalization by Feature Extraction v10.5 software (Agilent Technologies).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and normalization. Nexus Copy Number™ software was used to analyze the DNA copy number variations (BioDiscovery, Hawthorne, CA, USA), while computational analysis to compare the samples was performed in R v.2.10.1. Furthermore, breakpoints, gains, losses and amplifications were detected also using the algorithm CGH call. This algorithm converts raw log2ratios to absolute measures of ‘‘loss’’, ‘‘normal’’, ‘‘gain’’ or ‘‘amplification’’ by applying a segmentation algorithm.
Normalized log2 ratio (sample/references) data is available on Series records ('normalized_data.txt')

source_name: PDAC-4 human

label_protocol: DNA labeling was carried out using Enzo’s CGH Labeling Kit for Oligo Arrays (Enzo Life Sciences, FarmiDNAs were hybridized using Agilent SurePrint G3 Human CGH Microarray Kit for the 4x180K Agilent platform (Agilent Technologies, Santa Clara, CA)ngdale, NY, USA).

growth_protocol:
Primary human PDAC tissues  were injected into six-eight weeks old female athymic nude mice (Harlan, Horst, The Netherlands).
The cells were cultured in RPMI medium, supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% Pen/strep (50 IU/ml penicillin, 50 µg/ml streptomycin; Gibco, Gaithersburg, MD). The cells were kept in a humidified atmosphere of 5% CO2 and 95% air at 37 °C,

extract_protocol: Genomic DNAs were extracted using Ambion®-RecoverAll kit (Life Technologies, Breda, The Netherlands).

value: primary human PDAC

tag: primary humnam tumor id

tag: age (yrs)

tag: gender

value: female

tag: tnm stage

tag: who grading

tag: surgery

tag: survival (months)

source_name: healthy control (mix/pool of healthy volunteers DNA)

value: reference


title: PDAC-3_cells-Cy3 vs PDAC-3 mouse-Cy5

source_name: PDAC-3 cells

value: Primary PDAC culture

source_name: PDAC-3 mouse

value: PDAC tumor (mouse model)

tag: host strain

value: 6-8 wk-old female athymic nude mice


title: PDAC-3_human-Cy3 vs reference-Cy5

source_name: PDAC-3 human

value: male


title: PDAC-2_cells-Cy3 vs PDAC-2 mouse-Cy5

source_name: PDAC-2 cells

source_name: PDAC-2 mouse


title: NAFLD liver biopsy tissue 15238

source_name: NAFLD liver biopsy tissue

tag: tissue


title: colorectal adenocarcinoma, sample 6

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 6


title: colorectal adenocarcinoma, sample 7

description: colorectal adenocarcinoma biopsy

source_name: Universal Reference provided by Miltenyi Biotec GmbH

source_name: colorectal adenocarcinoma biopsy sample 7


title: NAFLD liver biopsy tissue 15202


title: NAFLD liver biopsy tissue 15277


title: NAFLD liver biopsy tissue 15262


title: NAFLD liver biopsy tissue 15251


title: NAFLD liver biopsy tissue 15214


title: PDAC-2 human-Cy3 vs reference-Cy5

source_name: PDAC-2 human


title: colorectal adenocarcinoma, sample 9

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 9


title: PDAC-1 mouse-Cy3 vs reference-Cy5

source_name: PDAC-1 mouse


title: PDAC-1 cells-Cy3 vs PDAC-4 mouse-Cy5

source_name: PDAC-1 cells

source_name: PDAC-4 mouse


title: colorectal adenocarcinoma, sample 5

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 5


title: PDAC-1 human-Cy3 vs PDAC-4 cells -Cy5

source_name: PDAC-1 human

source_name: PDAC-4 cells


title: colorectal adenocarcinoma, sample 4

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 4


title: colorectal adenocarcinoma, sample 1

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 1


title: colorectal adenocarcinoma, sample 2

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 2


title: colorectal adenocarcinoma, sample 3

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample 3


title: NAFLD liver biopsy tissue 15170


title: NAFLD liver biopsy tissue 15195


title: NAFLD liver biopsy tissue 15177


title: colorectal adenoma, sample 28

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 28

value: adenoma

tag: localisation

value: rectosigmoid junction


title: colorectal adenoma, sample 27

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 27

value: sigmoid colon


title: NAFLD liver biopsy tissue 15102

source_name: NAFLD liver biopsy tissue


title: NAFLD liver biopsy tissue 15079


title: NAFLD liver biopsy tissue 15103


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drpoS_rep2

city: Cambridge

first: Steven

middle: Douglas

last: Bowden

address: Building O, Downing Site

department: Biochemistry

institute: University of Cambridge

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 14h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.

hyb_protocol: Hybridization was achieved using a NimbleGen Hybridisation Station (FlyChip, Cambridge Systems Biology Centre, University of Cambridge) as described in NimbleGen's standard operating procedures (www.nimblegen.com).

scan_protocol: Scanning was achieved using a Genepix 4000B dual laser scanner (Axon, FlyChip, Cambridge Systems Biology Centre, University of Cambridge) using standard operating procedures (www.moleculardevices.com).

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

organism: Pectobacterium atrosepticum SCRI1043

label_protocol: Cy3-labelled cDNA was generated with reverse transcriptase (AffinityScript Multiple Temperature Reverse Transcriptase, Agilent) and Cy3-labelled dCTP (GE Healthcare Life Sciences).

growth_protocol: SB1046 was grown to early stationary phase (14h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Ltd., Manchester, UK) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality was estimated on 1% agarose TAE gels by electrophoresis and the concentration was determined by analysis with an NanoDrop 2000 spectrophotometer at the Department of Biochemistry (University of Cambridge, Cambridge, UK).

tag: genotype

value: delta rpoS::Strep

tag: phenotype

value: Stationary phase sigma factor mutant

tag: accession

tag: growth phase

value: Early stationary (14h)


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drpoS_rep1

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 14h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drpoS_rep3

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 14h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.


title: colorectal adenoma, sample 26

description: colorectal adenoma biopsy

source_name: Universal Reference provided by Miltenyi Biotec GmbH

source_name: colorectal adenoma biopsy sample 26

value: right colon


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_dexpI_rep3

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 14h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.

growth_protocol: SB1031 was grown to early stationary phase (14h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: delta expI::kan

value: Quorum sensing deficient


title: colorectal adenoma, sample 25

description: colorectal adenoma biopsy

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

source_name: colorectal adenoma biopsy sample 25


title: NAFLD liver biopsy tissue 15029

value: mild (fibrosis stage 0-1)

value: liver


title: Osteoclast_individual3

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: Osteoclast

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Regular BeadStudio processing

label: Cy5 and Cy3

source_name: Monocyte derived osteoclasts

label_protocol: Standard Illumina Protocol

growth_protocol: Osteoclast were differentiated from PBMCs during 21 days in alpha-MEM supplemented with fetal bovine serum 10%and 25ng/ml M-CSF and 50ng/ml RANKL.

extract_protocol: Proteinase K extraction

treatment_protocol: no treatment

value: Female

tag: age

tag: cell type

value: Monocyte-derived osteoclasts


title: CD14_Monocyte_individual2

description: CD14+ Monocyte

source_name: peripheral blood isolated CD14+ cells (monocytes)

value: CD14+ monocytes


title: colorectal adenoma, sample 24

description: colorectal adenoma biopsy

tag: sample type

source_name: colorectal adenoma biopsy sample 24

value: cecum


title: colorectal adenoma, sample 23

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 23

value: left colon


title: CD14_Monocyte_individual1

description: CD14+ Monocyte


title: Osteoclast_individual2

description: Osteoclast


title: CD14_Monocyte_individual3

description: CD14+ Monocyte


title: NAFLD liver biopsy tissue 15023

tag: Stage

value: advanced (fibrosis stage 3-4)


title: NAFLD liver biopsy tissue 15022


title: Osteoclast_individual1

description: Osteoclast


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drelA_rep3

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 14h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.

growth_protocol: SB1026 was grown to early stationary phase (14h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: delta relA::cat

value: Reduced for (p)ppGpp production


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_dexpI_rep1

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 14h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: NAFLD liver biopsy tissue 15066


title: colorectal adenoma, sample 22

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 22

value: adenoma

value: rectum


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drelA_rep2

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 14h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.

value: Early stationary (14h)


title: colorectal adenoma, sample 20

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 20

value: rectosigmoid junction


title: colorectal adenoma, sample 19

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 19


title: colorectal adenoma, sample 18

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 18

value: right colon


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_drelA_rep1

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 14h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_dexpI_rep2

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 14h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.

value: delta expI::kan

value: Quorum sensing deficient


title: SW480-2

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

institute: Johns Hopkins University

hyb_protocol: 0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol.

scan_protocol: Scanning was performed with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies.

data_processing: All arrays were subject to quality checks recommended by the manufacturer. Images were visually inspected for artifacts and distributions of signal and background intensity of both red and green channels were examined to identify anomalous arrays. No irregularities were observed, and all arrays were retained and used. All calculations were performed using the R statistical computing platform (version 2.6.2) and packages (Limma version 2.12.0) from Bioconductor bioinformatics software project. To determine expression levels of genes in SW480, HCT116 and RKO, the probe intensities of the Cy3 channels (mock) from the raw microarray data for these cell lines were extracted and quantile normalized. The normalized data is presented in the file named 'Processed Probe Intensity Values for GEO.txt'. Mean of duplicate samples were calculated. Expression levels of individual genes were determined by estimating the median of the intensities of all probes belonging to that gene. Gene expression levels are shown as Log2 transformed values of the median intensities in the file named 'Processed Gene Expression Values for GEO.txt". Hypermethylated genes were identified using the Infinium methylation array. Methylated and silenced genes were identified as genes that have mean probe beta-value > 0.5 and the Agilent gene expression intensity < 7 (log2 value).

source_name: SW480 mock

label_protocol: Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification.

growth_protocol: Log phase SW480, HCT116 and RKO were cultured in McCoys 5A media (Invitrogen) containing 10% BCS and 1x penicillin/streptomycin.

extract_protocol: Total RNA was harvested from log phase cells using the Qiagen kit according to the manufacturers instructions, including a DNAase step. RNA was quantified using the NanoDrop ND-100 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies). RNA concentrations for individual samples were greater than 200ng/ul, with 28s/18s ratios greater than 2.2 and RNA integrity numbers of 10 (highest).

treatment_protocol: Cells were treated with 1 uM 5-Aza-CdR (DAC) (Sigma; stock solution: 1mM in PBS) for 96 hours, replacing media and DAC every 24 hours. Control cells underwent mock treatment in parallel with addition of equal volume of PBS.

tag: cell line

value: colon cancer

source_name: SW480 AZA


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_wildtype_rep1

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 14h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.

source_name: Pectobacterium atrosepticum SCRI1043 wildtype

growth_protocol: Pectobacterium atrosepticum SCRI1043 was grown to early stationary phase (14h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: Wild type

value: Normal


title: RKO-1

source_name: RKO mock

value: RKO

source_name: RKO AZA


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_wildtype_rep2

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 14h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.


title: SDB_Welch_P_atrosepticum_ppGpp_study_14h_wildtype_rep3

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 14h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.


title: RKO-2


title: colorectal adenoma, sample 17

description: colorectal adenoma biopsy

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

source_name: colorectal adenoma biopsy sample 17


title: colorectal adenoma, sample 16

description: colorectal adenoma biopsy

source_name: Universal Reference provided by Miltenyi Biotec GmbH

source_name: colorectal adenoma biopsy sample 16


title: SW480-1


title: HCT116-3

source_name: HCT116 mock

source_name: HCT116 AZA


title: NAFLD liver biopsy tissue 15010

source_name: NAFLD liver biopsy tissue

value: mild (fibrosis stage 0-1)

value: liver


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drpoS_rep3

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 6h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.

growth_protocol: SB1046 was grown to mid-log phase (6h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: delta rpoS::Strep

value: Stationary phase sigma factor mutant

value: Exponential (6h)


title: colorectal adenoma, sample 15

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 15

value: adenoma

value: sigmoid colon


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_dexpI_rep3

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 6h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.

growth_protocol: SB1031 was grown to mid-log phase (6h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drpoS_rep2

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 6h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drpoS_rep1

description: This sample is of delta rpoS::strep Pectobacterium atrosepticum SCRI1043 (strain SB1046) grown for 6h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: NAFLD liver biopsy tissue 15004

description: Gene expression data from advanced NAFLD patient

value: advanced (fibrosis stage 3-4)


title: colorectal adenoma, sample 14

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 14

value: transversal colon


title: SRSF2 over-expression condition, rep6

description: Induction of SRSF2 over-expression upon 24 hours

hyb_protocol: Labeling with cyanine3-CTP, fragmentation of cRNA, hybridization, and washing were performed according to the manufacturer’s instructions (Agilent).

scan_protocol: update

data_processing: Software: GeneSpring GX 11.0.2, Normalization algorithm: Shift to percentile = 75, Filtered on flags: present at least 75.0% of the values in any 1 out of 2 condition.

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 6

label_protocol: Double-stranded cDNA was synthesized from 500 ng of total RNA using the Quick Amp Labeling kit, One-color, as instructed by the manufacturer (Agilent).

growth_protocol: The H358 human lung carcinoma cell line was cultured in RPMI-1640 medium (GibcoBRL), supplemented with 10% (v/v) heatinactivated fetal calf serum (GibcoBRL), 2mM L-glutamine and 100 U/ml penicillin/streptomycin, in 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent) and the 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.

treatment_protocol: The H358/Tet-On/SRSF2 inducible clone conditionally over-expressed the SRSF2 splicing factor under the control of a Tet-responsive promoter. SRSF2 over-expression was induced upon 24 hours treatment with 1 μg/mL doxycycline.

value: H358 lung carcinoma

tag: treatment

value: SRSF2 over-expression


title: SRSF2 over-expression condition, rep5

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 5


title: NAFLD liver biopsy tissue 15006


title: SRSF2 over-expression condition, rep4

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 4


title: HCT116-2


title: SRSF2 over-expression condition, rep3

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 3


title: SRSF2 over-expression condition, rep2

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 2


title: HCT116-1


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_dexpI_rep2

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 6h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.

value: delta expI::kan

value: Quorum sensing deficient


title: colorectal adenoma, sample 13

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 13

value: rectosigmoid junction


title: colorectal adenoma, sample 11

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 11

value: rectum


title: colorectal adenoma, sample 12

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 12

value: right colon


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drelA_rep2

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 6h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.

growth_protocol: SB1026 was grown to mid-log phase (6h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: delta relA::cat

value: Reduced for (p)ppGpp production


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drelA_rep3

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 6h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_dexpI_rep1

description: This sample is of delta expI::kan Pectobacterium atrosepticum SCRI1043 (strain SB1031) grown for 6h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: colorectal adenoma, sample 10

description: colorectal adenoma biopsy

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

source_name: colorectal adenoma biopsy sample 10


title: colorectal adenoma, sample 9

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 9

value: bauhin's valve


title: colorectal adenoma, sample 8

description: colorectal adenoma biopsy

source_name: Universal Reference provided by Miltenyi Biotec GmbH

source_name: colorectal adenoma biopsy sample 8


title: Expose Bacillus VOC-24h rep4

city: Daejeon

first: Choong-Min

last: Ryu

address: 125 Gwahak-ro Yuseong

country: South Korea

institute: KRIBB

description: replication 4 of 4

hyb_protocol: 7.5 µg of labeled sample RNA and 7.5 µg of labeled reference RNA were fragmented in total 250 µl mixture (50 µl of 10X blocking agent, 10 µl of 25X fragmentation buffer, H2O) at 60°C for 30 min, then put it on ice for 1 min. 250 µl of fragmentation mix and 250 µl of GE hybridization buffer HI-RPM were mixed and spinned for 1 min at RT at 13,000 rpm, and put on ice. 490 µl of the hybridization mix was applied to the slide in chamber, and put in a hybridization oven at 65°C for 17 hrs. After hybridization, the slide was washed sequentially in GE wash buffer 1 (twice) and 2.

scan_protocol: The arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Signal intensities and local backgrounds were determined by Feature Extraction software (Agilent Technologies).

data_processing: Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: control 24h

label_protocol: 1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech  dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.

extract_protocol: Total RNAs were extracted using RNeasy mini kit (Qiagen, #74104) following manufacture's instruction

value: control

tag: time

tag: strain

source_name: expose Bacillus VOC24h

value: Bacillus volatile organic compounds (VOCs)


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_drelA_rep1

description: This sample is of delta relA::cat Pectobacterium atrosepticum SCRI1043 (strain SB1026) grown for 6h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.

value: Exponential (6h)


title: SRSF2 over-expression condition, rep1

source_name: H358, 24hr induction, SRSF2 over-expression, replicate 1


title: Expose Bacillus VOC-24h rep3

description: replication 3 of 4


title: control condition, rep6

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 6


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_wildtype_rep3

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 6h in Pel Minimal Broth (PMB). It is the third of 3 biological replicates grown in separate cultures.

source_name: Pectobacterium atrosepticum SCRI1043 wildtype

growth_protocol: Pectobacterium atrosepticum SCRI1043 was grown to mid-log phase (6h) aerobically at 25°C in Pel Minimal Broth (Shih et al. 1999, Environmental Microbiology 1: p535-547).

value: Wild type

value: Normal


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_wildtype_rep2

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 6h in Pel Minimal Broth (PMB). It is the second of 3 biological replicates grown in separate cultures.


title: Expose Bacillus VOC-24h rep1

description: replication 1 of 4


title: control condition, rep5

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 5


title: Expose Bacillus VOC-24h rep2

description: replication 2 of 4


title: SDB_Welch_P_atrosepticum_ppGpp_study_6h_wildtype_rep1

description: This sample is of wild-type Pectobacterium atrosepticum SCRI1043 grown for 6h in Pel Minimal Broth (PMB). It is the first of 3 biological replicates grown in separate cultures.


title: colorectal adenoma, sample 7

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 7

value: adenoma


title: control condition, rep3

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 3

value: H358 lung carcinoma


title: control condition, rep2

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 2


title: Expose Bacillus VOC-12h rep3

description: replication 3 of 4

source_name: control 12h

source_name: expose Bacillus VOC 12h


title: colorectal adenoma, sample 6

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 6

value: sigmoid colon


title: colorectal adenoma, sample 5

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 5


title: Expose Bacillus VOC-12h rep2

description: replication 2 of 4


title: control condition, rep1

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 1


title: control condition, rep4

description: Control condition upon 24 hours

source_name: H358, 24hr induction, control, replicate 4


title: colorectal adenoma, sample 4

description: colorectal adenoma biopsy

source_name: Universal Reference provided by Miltenyi Biotec GmbH

source_name: colorectal adenoma biopsy sample 4

value: transversal colon


title: Expose Bacillus VOC-12h rep4

description: replication 4 of 4


title: Expose Bacillus VOC-12h rep1

description: replication 1 of 4


title: colorectal adenoma, sample 2

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 2


title: colorectal adenoma, sample 3

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 3


title: colorectal adenoma, sample 1

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 1


title: colorectal adenoma, sample 21

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample 21

value: cecum


title: Expose Bacillus VOC-6h rep4

description: replication 4 of 4

source_name: control 6h

value: 6 h

source_name: expose Bacillus VOC 6h


title: colorectal normal mucosa, sample 5

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample 5

value: normal mucosa


title: RKO

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using Illumina’s Infinium Human Methylation27 Beadchip Kit (WG-311-1202). Beadchip contains 27,578 CpG loci covering more than 14,000 human RefSeq genes at single-nucleotide resolution. Chip process and data analysis were performed by using reagents provided in the kit and following manufacturer’s manual. Briefly, 4 ml of bisulfite-converted genomic DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer for 20-24 hours at 37oC. Samples were fragmented using a kit-provided reagents and buffer at 37oC for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 12 ml of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48oC for 16-20 hours, chips were washed with wash buffers provided in the kit and assembled and placed into a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided in the kit.

scan_protocol: Polymer-coated chips were image- processed in Illumina’s iScan scanner.  Data were extracted and analyzed using BeadStudio v3.0 software.

data_processing: Data were extracted and analyzed using BeadStudio v3.0 software.  The methylation status of each CpG site is presented as b (beta) value based on following definition and calculation:  b value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy3 and Cy5

source_name: RKO cell line

label_protocol: Primer extension

growth_protocol: Cells were grown on serum supplemented medium (SW480 and HCT116 grown on MCCoy's 5a and RKO was frown on MEM). Cells were grown to 70% confluency, harvested and DNA was extracted.

extract_protocol: DNA was extracted usign Phenol-Chloroform extraction method. Genomic DNA quality was assessed by low agarose gel (0.5%) electrophoresis under low power voltage. Only samples with good genomic DNA integrity were used in chip assay. Bisulfite conversion of genomic DNA was done with EZ DNA methylation Kit (Zymo Research, D5002) by following manufacturer’s protocol with modifications for Illumina Infinium Methylation Assay. Briefly, one microgram of genomic DNA was first mixed with 5 ml of M-Dilution Buffer and incubate at 37oC for 15 minutes and then mixed with 100 ml of CT Conversion Reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification as instructed in the protocol. Concentration of eluted DNA was measured using Nanodrop-1000. Bisulfite-converted samples were used for chip analysis without any delay.

value: Colon cancer

value: RKO


title: Expose Bacillus VOC-6h rep1

description: replication 1 of 4


title: IVD

source_name: In vitro Sss1 Methylated DNA

value: Normal Lymphocytes


title: Expose Bacillus VOC-6h rep2

description: replication 2 of 4