title: Rubrum-17α-ethinylestradiol (EE2)-rep3

description:
Induction with 17α-ethinylestradiol (EE2)
13943587-Rubrum-ethinylest-4.gpr


title: S. cerevisiae CBS7960 xylulose Cy5

status: Public on Aug 23 2013

type: RNA

city: Rehovot

first: Zvi

last: Tamari

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Samples were hybridized using standard Agilent protocol

scan_protocol: Images were analyzed using Agilent's Feature Extraction software

data_processing: Agilent Feature Extraction Software was used for background detrending and linear LOWESS normalization.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae CBS7960 xylulose

label_protocol: The samples were amplified and labeled using agilent two-color Low Input QuickAmp Labeling Kit

growth_protocol: Strains were grown to mid-log phase in YP-glucose or YP-xylulose medium.

extract_protocol: Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (Epicentre)

tag: strain

tag: condition

value: xyulose


title: Biopsy_No_DSA_2

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

country: USA

institute: Albert Einstein College of Medicine

description: Gene expression data from DSA biopsy sample

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term. Biopsy and blood sample were processed separately.

label: biotin

organism: Homo sapiens

source_name: No DSA, PRA 0% and normal Biopsy/Mild IF/TA

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Biopsy cores were immediately placed into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified using a dissecting microscope and non-renal tissue was removed. For whole blood gene expression analysis, 2.5 ml of patient’s peripheral blood was collected into one PAXgene RNA Tube (Qiagen, Valencia, CA) containing lysis buffer and RNA-stabilizing solution. Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, Valencia, CA) for biopsy and blood samples respectively.

treatment_protocol: Biopsies were examined by light microscopy using hematoxylin and eosin, periodic acid-Schiff, trichrome and C4d immunoperoxidase stains and scored using the Banff criteria. Immunoperoxidase staining for C4d was performed on paraffin embedded sections using a polyclonal rabbit anti-human antibody (Cell Marque) at a dilution of 1:100 with the Dako Envision system. Positive peritubular capillary C4d staining was scored minimal (c4d1), focal (c4d2) or diffuse (c4d3) when there was uniform finely granular decoration involving more than 1-10%, 11-50% and greater than 50% for minimal, focal and diffuse respectively. Anti-HLA antibodies were studied by Luminex HLA Single Antigen Bead assays (LABScreen, One Lambda Inc., Canoga Park, CA) that utilize a panel of color-coded beads coated with purified single HLA antigens. The beads include HLA A, B, Cw, DR, and DQ antigens. The antibody specificity and strength were analyzed with HLA Fusion software V2.0 (One Lambda Inc.). The cutoff value for a positive DSA was a mean fluorescence intensity (MFI)  ≥1000.

tag: tissue

value: biopsy


title: S. cerevisiae YP1009 xylulose Cy5

source_name: S. cerevisiae YP1009 xylulose


title: Biopsy_No_DSA_1


title: K562_pEF1a_Pu2_rep3

city: Sydney

first: Ka Sin

last: Mak

address: High Street

country: Australia

institute: UNSW

hyb_protocol: RNA was hybridized to Affymetrix Human Gene 1.0 ST arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Microarray data was analysed using Affymetrix® Expression ConsoleTM software (Affymetrix, CA)

source_name: K562 pEF1a-Pu.2

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: Cells were cultured in Schneider's drosophila medium supplemented with 10% heat-inactivated FCS and 1% PSG at 24oC

extract_protocol: RNA extraction was performed using TRI-Reagent according to manufacturer’s protocol (Sigma-Aldrich). RNA samples were purified using RNeasy columns (Qiagen) followed by DNaseI treatment with DNA-freeTM (Ambion)

treatment_protocol: Cells were transfected with pEF1a or pEF1a-Pu.2 plasmid by electroporation using Gene Pulser Xcell electroporation system (Bio-Rad, Hercules, CA). Stable clones were kept under selection with 2ug/mL puromycin dihydrochloride and monoclonal lines were isolated.

tag: cell line


title: S. cerevisiae BY4743 xylulose Cy5

source_name: S. cerevisiae BY4743 xylulose


title: S. cerevisiae PW5 xylulose Cy3

source_name: S. cerevisiae PW5 xylulose


title: NPC_BR2

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

country: United Kingdom

institute: IGMM

hyb_protocol: 1.34μg cRNA was hybridized to Agilent SurePrint mouse oligomicroarrays (Agilent cat# G4852A) according to manufacturer instructions (hybridisation proceeded for  63C 17 hours).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner at 2μm resolution and spot intensities were extracted using Agilent Feature Extraction version 11.5.1.1.

data_processing: quantile normalisation (limma)

organism: Mus musculus

source_name: gfp FACS sorted cells after 5 days of differentiation to neural progenitor cells with NB27 and Neuro2 medium supplements

label_protocol: 1ug of total RNA from 3 biological replicates of undifferentiated and differentiated (5 day differentiation to NPC) was amplified using one round of amplification with an Amino Allyl MessageAmp II aRNA Amplification kit (Ambion, cat#AM1753) according to manufacturer instructions, and checked for quality on the Agilent 2100 Bioanalyser. The RNA was dye coupled to Cy3 using the same kit

extract_protocol: RNA was extracted using a Roche High Pure RNA isolation kit, and RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: differentiation

value: 5 day differentiation with NB27 and Neuro2 medium supplements

tag: cell type

value: NPC


title: NPC_BR3


title: K562_pEF1a_Pu2_rep1


title: Rubrum-Diclofenac (DCF)-rep1

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description:
Induction with diclofenac (DCF)
13943609-Rubrum-Diclofenac-2.gpr

hyb_protocol: The two differentially labeled cDNAs were resuspended in the universal hybridization buffer (Pronto kit; Corning-Promega, United States), mixed, and added jointly to the surface of the spotted microarray glass slide for overnight hybridization at 42°C using a HS 4800 Pro automated hybridization station (TECAN, Switzerland). The slide was washed according to the Pronto kit’s protocol and then dried in the hybridization station.

scan_protocol: Microarray spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to built-in quality criteria.

data_processing: Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15  as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide technical triplicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method . P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Rhodospirillum rubrum

source_name: non-induced culture (reference)

label_protocol: Ten micrograms of RNA was reverse transcribed by random priming according to the Pronto kit’s instructions (Corning-Promega, United States) and directly labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Bioscience, United Kingdom) for respectively control and experimental samples.

growth_protocol: Rhodospirillum rubrum S1H was obtained from the American Type Culture Collection (ATCC 25903) and grown in Sistrom Medium A (SIS) with 0.2% (w/v) succinate as sole carbon source in dark aerobic conditions at 30°C and 50 rpm [3]. Early stationary phase cells were inoculated at 2% (v/v) inoculum in 50 mL SIS.

extract_protocol: Ten mL of R. rubrum S1H culture was harvested at OD680 of 0.4 from all test cultures with and without pharmaceuticals, and 20 mL RNAProtect Bacteria Reagent (QIAGEN) was added to preserve the RNA. The fixed cell suspensions were centrifuged at 3500 rpm for 10 min, the supernatant was removed, and cell pellets were stored at -80°C. The RNA extraction was performed using the RNeasy Midi Kit (QIAGEN), following the manufacturer’s guidelines. RNA quantity and quality was assessed using the Nanodrop ND-1000 and the 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Chip Kit following the manufacturer’s instructions. Only RNA with a RNA Integrity Number (RIN-) value of 9.5 and higher was used for microarray analysis.

treatment_protocol: In accordance with a previous exposure experiment with the biocide triclosan [3], the R. rubrum S1H cultures were exposed to 86 nM of diclofenac (DCF), acetylsalicylic acid (ASA), and 17α-ethinylestradiol (EE2), which corresponded to 27.4 µg/L DCF, 15.5 µg/L ASA, and 25.5 µg/L EE2. Prior to inoculation, SIS was spiked from a stock solution of DCF or EE2 in methanol and the different samples were supplemented with equal final volumes of methanol to nullify the potential effect of differential solvent concentrations. In addition, a solvent control (with methanol) and growth control (without methanol) was prepared. ASA was spiked in the growth medium from a stock solution in water. Subsequently, SIS with and without DCF, EE2, or ASA was inoculated with early stationary phase cells.

tag: ATCC

tag: pharmaceutical agent

source_name: culture induced with diclofenac (DCF)

value: diclofenac (DCF)


title: Rubrum-Diclofenac (DCF)-rep2

description:
Induction with diclofenac (DCF)
13943588-Rubrum-Diclofenac-3.gpr


title: Rubrum-acetylsalicylic acid (ASA)-rep2

description:
Induction with acetylsalicylic acid (ASA)
13943608-Rubrum-aspirine-3.gpr

source_name: culture induced with acetylsalicylic acid (ASA)

value: acetylsalicylic acid (ASA)


title: UD446cEScell_BR3

source_name: undifferentiated 46c (sox1-gfp) ES cells

value: undifferentiated

value: ESC


title: S. cerevisiae EC1118 xylulose Cy3

source_name: S. cerevisiae EC1118 xylulose


title: NPC_BR1


title: S. cerevisiae CLIB324 xylulose Cy3

source_name: S. cerevisiae CLIB324 xylulose


title: S. cerevisiae Y12 xylulose Cy3

source_name: S. cerevisiae Y12 xylulose


title: S. cerevisiae T73 xylulose Cy3

source_name: S. cerevisiae T73 xylulose


title: K562_pEF1a_Pu2_rep2


title: UD46cEScell_BR2


title: Rubrum-acetylsalicylic acid (ASA)-rep3

description:
Induction with acetylsalicylic acid (ASA)
13943604-Rubrum-aspirine.4.gpr


title: K562_pEF1a_rep3

source_name: K562 pEF1a


title: UD46cEScell_BR1


title: Rubrum-acetylsalicylic acid (ASA)-rep1

description:
Induction with acetylsalicylic acid (ASA)
13943591-Rubrum-aspirine-2.gpr


title: CD14 positive bone marrow cells from gastric cancer patient  (GC1)

city: Tokyo

first: Ken

last: Okano

address: Toyo Ekimae bldg. 2-20, Toyo 2-Chome, Koto-Ku

country: Japan

institute: Cosmo Bio Co., LTD.

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

scan_protocol: Hybridization signals were detected by DNA microarray scanner G2505C (Agilent Technologies) with resolution of 10 micrometres . The scanned images were analyzed using Agilent Feature Extraction ver. 10.7.3.1.

data_processing: Each signal value of unique probe ID was calculated from average of Hy3 signal intensities of replicated probes.

source_name: CD14 positive bone marrow cells

label_protocol: Total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

extract_protocol: Total RNA extracted using miRNeasy Mini Kirt (QIAGEN) following manufacturer's instructions

tag: gastric cancer patient

tag: bone marrow fraction

value: CD14 positive

tag: age

tag: gender

value: Male

tag: tnm stage

value: IV

tag: distant metastasis

value: peritonitis carcinomatosa


title: CD45 negative/EpCAM positive bone marrow cells from gastric cancer patient  (GC1)

value: CD45 negative/EpCAM positive


title: CD45 positive bone marrow cells from gastric cancer patient (GC1)

source_name: CD45 positive bone marrow cells

value: CD45 positive


title: CD14 positive bone marrow cells from gastric cancer patient (GC4)


title: S. cerevisiae SK1 xylulose Cy3

source_name: S. cerevisiae SK1 xylulose


title: CD45 negative/EpCAM positive bone marrow cells from gastric cancer patient (GC4)


title: K562_pEF1a_rep2


title: K562_pEF1a_rep1


title: S. cerevisiae PW5 xylulose Cy5


title: S. cerevisiae T73 xylulose Cy5


title: S. cerevisiae CLIB324 xylulose Cy5


title: CD45 positive bone marrow cells from gastric cancer patient (GC4)


title: whole bone marrow cells from gastric cancer patient (GC1)

source_name: whole bone marrow cells

value: whole


title: Wheat leaves biological replicate 2 of Cold-Acclimated (CA) at Ambient CO2 (AC)

city: Montreal

first: Khalil

last: kane

state: Quebec

address: 2080 saint-urbain

department: Sciences biologiques

country: Canada

institute: University of Quebec in Montreal

hyb_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin

scan_protocol: Arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: Cel files obtained from chip images were imported in Flexarray (http://gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=ehttp://genomequebec.mcgill.ca/Flexarray); the data were normalized and corrected for background in R2.5.1 environment with the robust multi-array (RMA) method. To identify the probe-sets differentially regulated between two conditions, analysis of variance (ANOVA) was performed on the expression of three biological replicates for each condition.

organism: Triticum aestivum

source_name: Wheat leaves of Cold-Acclimated (CA) at Ambient CO2 (AC)

label_protocol: Synthesized cDNAs were transcribed to cRNAs with the 3’IVT labelling kit (Santa Clara, CA, USA)

growth_protocol: Seeds of winter (cv Norstar) wheat (Triticum aestivum L.) were grown in controlled environmental growth chambers (Model: GCW15 chamber, Environmental Growth Chambers, Chagrin Falls, OH, USA) at either ambient CO2 (380 ± 10 µmol C mol-1) or at EC (700 ± 25 µmol C mol-1). NA plants were grown from seed at the day/night temperature regimes of 20/16°C and those of CA at 5/5°C from seed sowing. The plants were grown at a PPFD of 250 ± 20-µmol photons m-2 s -1, 50% to 60% relative humidity and a 16/8 hr photoperiod. The CO2 concentrations in the growth chamber were monitored continuously with a computer-controlled CO2 infra-red gas analyzer (Model: WMA-4 CO2 Analyzer, PP Systems International, Inc. Amesbury, MA, USA) installed in each CO2 growth chamber. In addition, the temperature, relative humidity, irradiance level and photoperiod in each chamber were computer-controlled and monitored continuously. The seedlings were grown in coarse vermiculite in plastic pots at a density of three plants per pot and fertilized with Hoagland solution. In order to minimize rooting volume constraints and sink limitations, the plants were grown in 4L-sized plastic pots regardless of CO2 conditions and growth temperatures.

extract_protocol: The different biological samples of Norstar winter wheat leaves were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100).

treatment_protocol: Plants were grown under each condition until the 3rd leave was fully expanded. The experimental design consisted of three biological replicates for each of the four growth conditions, 1: Non-acclimated (NA) at ambient CO2 (AC) (NAAC); 2: Cold-acclimated (CA) at ambient CO2 (AC) (CAAC); 3: Non-acclimated (NA) at elevated CO2 (EC) (NAEC); 4: Cold-acclimated (CA) at elevated CO2 (EC) (CAEC).

tag: cultivar

value: Norstar

value: fully expanded 3rd leaves


title: Wheat leaves biological replicate 3 of Non-Acclimated (NA) at Ambient CO2 (AC)

source_name: Wheat leaves of Non-Acclimated (NA) at Ambient CO2 (AC)


title: S. cerevisiae EC1118 xylulose Cy5

value: xyulose


title: Wheat leaves biological replicate 3 of Cold-Acclimated (CA) at Ambient CO2 (AC)


title: Wheat leaves biological replicate 2 of Non-Acclimated (NA) at Ambient CO2 (AC)


title: S. cerevisiae SK1 xylulose Cy5


title: Wheat leaves biological replicate 1 of Cold-Acclimated (CA) at Ambient CO2 (AC)


title: whole bone marrow cells from gastric cancer patient (GC4)


title: CHP-212 100nM, biological replicate 3

city: Collegeville

first: Gopinath

last: Ganji

state: PA

address: 1250 South Collegeville Road

institute: GSK

description: Gene expression data from CHP-212 cell line treated with 100nM of iBET-726

hyb_protocol: According to manufacturer's instructions

data_processing: Data was analyzed using Cubic Spline normalisation method

label: Biotin

growth_protocol: Cells were grown as recommended by ATCC and DSMZ

extract_protocol: RNA extracted with Trizol reagent and purified per Trizol protocol; RNA further purified using RNeasy kit columns

treatment_protocol: 2x10^5 cells were seeded in 3 ml cell culture media into 6-well dishes and allowed to equilibrate overnight at 37 degrees Celsius and 5% CO2. The following day, DMSO or iBET-726 were added to final concentrations of 0.1% DMSO or 100 nM/1uM iBET-726. After 16 hours, cells were harvested by centrifugation, lysed with 750 ul Trizol reagent, and frozen at -80 degrees Celsius.

value: Neuroblastoma


title: CHP-212 1uM, biological replicate 2

description: Gene expression data from CHP-212 cell line treated with 1uM of iBET-726

scan_protocol: According to manufacturer's instructions


title: S. cerevisiae YJM269 xylulose Cy3

source_name: S. cerevisiae YJM269 xylulose


title: CHP-212 100nM, biological replicate 2

label_protocol: According to manufacturer's instructions


title: CHP-212 1uM, biological replicate 1


title: Wheat leaves biological replicate 3 of Cold-Acclimated (CA) at Elevated CO2 (EC)

source_name: Wheat leaves of Cold-Acclimated (CA) at Elevated CO2 (EC)


title: CD14 positive bone marrow cells from gastric cancer patient (GC3)


title: CHP-212 1uM, biological replicate 3


title: S. cerevisiae CLIB215 xylulose Cy3

source_name: S. cerevisiae CLIB215 xylulose


title: S. cerevisiae Y12 xylulose Cy5


title: CHP-212 100nM, biological replicate 1


title: Wheat leaves biological replicate 2 of Cold-Acclimated (CA) at Elevated CO2 (EC)


title: Wheat leaves biological replicate 1 of Non-Acclimated (NA) at Ambient CO2 (AC)


title: CD45 negative/EpCAM positive bone marrow cells from gastric cancer patient (GC3)


title: CHP-212, vehicle, biological replicate 3

description: Gene expression data from CHP-212 cell line treated with DMSO


title: S. cerevisiae YP1009 xylulose Cy3

source_name: S. cerevisiae YP1009 xylulose


title: CD45 positive bone marrow cells from gastric cancer patient (GC3)


title: S. cerevisiae CBS7960 xylulose Cy3

source_name: S. cerevisiae CBS7960 xylulose


title: Wheat leaves biological replicate 3 of Non-Acclimated (NA) at Elevated CO2 (EC)

source_name: Wheat leaves of Non-Acclimated (NA) at Elevated CO2 (EC)


title: CHP-212, vehicle, biological replicate 2


title: CHP-212, vehicle, biological replicate 1


title: S. cerevisiae T7 xylulose Cy3

source_name: S. cerevisiae T7 xylulose


title: S. cerevisiae BY4743 xylulose Cy3

source_name: S. cerevisiae BY4743 xylulose


title: Wheat leaves biological replicate 1 of Cold-Acclimated (CA) at Elevated CO2 (EC)


title: Wheat leaves biological replicate 2 of Non-Acclimated (NA) at Elevated CO2 (EC)


title: whole bone marrow cells from gastric cancer patient (GC3)


title: BE(2)M17 miR-142 rep 2

city: Omaha

first: Amrita

last: Datta Chaudhuri

state: NE

address: 985800 Nebraska Medical Center

department: Pharmacology & Experimental Neuroscience

institute: University of Nebraska Medical Center

description: BE(2)M17 neuroblastoma cell line miR-142 clone

hyb_protocol: Overnight in affymetrix hybridization oven at 42 C

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Partek genomics suite
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEX-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Commercially available assays for generating biotin labeld samples

growth_protocol: DMEM/F12 media supplemented with 10% FBS and puromycin 4 ug/mL, 37 C

extract_protocol: Cells harvested in cold PBS, spun down. RNA extracted using Trizol, chloroform, isopropanol precipitation method.

treatment_protocol: Stable transfection with miR-142 or miR-null

value: BE(2)M17 neuroblastoma

tag: transfection


title: CD14 positive bone marrow cells from gastric cancer patient (GC2)


title: BE(2)M17 miR-142 rep 1

source_name: BE(2)M17 neuroblastoma cell line miR-142 clone


title: BE(2)M17 miR-null rep 3

description: BE(2)M17 neuroblastoma cell line miR-null clone

value: miR-null


title: BE(2)M17 miR-142 rep 3


title: S. cerevisiae CLIB215 glucose Cy3

source_name: S. cerevisiae CLIB215 glucose

value: glucose


title: CD45 negative/EpCAM positive bone marrow cells from gastric cancer patient (GC2)


title: BE(2)M17 miR-null rep 1

source_name: BE(2)M17 neuroblastoma cell line miR-null clone


title: whole bone marrow cells from gastric cancer patient  (GC2)


title: CD45 positive bone marrow cells from gastric cancer patient (GC2)


title: S. cerevisiae CBS7960 glucose Cy3

source_name: S. cerevisiae CBS7960 glucose


title: BE(2)M17 miR-null rep 2


title: S. cerevisiae BY4743 glucose Cy3

source_name: S. cerevisiae BY4743 glucose


title: Wheat leaves biological replicate 1 of Non-Acclimated (NA) at Elevated CO2 (EC)


title: SK-N-SH 1uM, biological replicate 2

description: Gene expression data from SK-N-SH cell line treated with 1uM of iBET-726

value: SK-N-SH


title: SK-N-SH 1uM, biological replicate 1


title: S. cerevisiae YPS1009 glucose Cy3

source_name: S. cerevisiae YPS1009 glucose


title: Bulk population, day 17 (drug washed at day 1)

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Matlab

source_name: HL60 cell line

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: treatment

value: day 17 (drug washed at day 1)


title: SK-N-SH vehicle, biological replicate 3

description: Gene expression data from SK-N-SH cell line treated with DMSO


title: S. cerevisiae EC1118 glucose Cy5

source_name: S. cerevisiae EC1118 glucose

tag: strain


title: Bulk population, day 7 (drug washed at day 1)

description: replicate 1

value: day 7 (drug washed at day 1)


title: SK-N-SH 100nM, biological replicate 1

description: Gene expression data from SK-N-SH cell line treated with 100nM of iBET-726


title: SK-N-SH 100nM, biological replicate 3


title: SK-N-SH 1uM, biological replicate 3


title: SK-N-SH 100nM, biological replicate 2


title: S. cerevisiae T7 glucose Cy3

source_name: S. cerevisiae T7 glucose

tag: condition


title: ESC46c_UD

type: genomic

description:
Dye-swapped hybridizations:
UD46cH4K16ac_cy3BR1:
554521A03_2013-04-19_13-32_Area1_532.pair (ch1)
554521A03_2013-04-19_13-32_Area1_635.pair (ch2).
UD46cH4K16ac_cy5BR1:
556276A03_2013-04-19_14-23_Area1_635.pair (ch1)
556276A03_2013-04-19_14-23_Area1_532.pair (ch2).
UD46cH4K16ac_cy3BR2:
554409A02_2013-05-15_12-06_Area1_532.pair (ch1)
554409A02_2013-05-15_12-06_Area1_635.pair (ch2).

hyb_protocol: Samples were hybridized according to standard protocol (NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: arrays were scanned on a NimbleGen MS200 Microarray Scanner (Roche) using 100% laser power at 2μm resolution.

data_processing:
The mean signal intensity of the 3 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. Log2 values were calculated by log2 of the product of division of ChIP signal by input signal
Bedgraph files were generated in R using Tobias Straub's Basic Analysis of Nimblegen ChIP-on-chip data using Bioconductor/R (PROT43), and the format is chromosome start stop Log2ChIP/Input_signal level.

label: Cy3, Cy5

molecule: genomic DNA

source_name: H4K16ac ChIP DNA from UD ES cells

label_protocol: 300ng ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Nuclei were digested with mnase and released chromatin either ChIP-ed with H4K16ac antibody [ChIP DNA samples] or not [input DNA sample].

value: undifferentiated

value: ESC

tag: chip antibody

value: H4K16ac antibody (Millipore, catalog# 07-329, lot# 2073125)

source_name: MNase digested input DNA from UD 46c ES cells

value: MNase digested input


title: NPC

description:
Dye-swapped hybridizations:
NPC46cH4K16ac_cy3BR1:
554521A02_2013-04-19_13-32_Area1_532.pair (ch1)
554521A02_2013-04-19_13-32_Area1_635.pair (ch2).
NPC46cH4K16ac_cy5BR1:
556276A02_2013-04-19_14-23_Area1_635.pair (ch1)
556276A02_2013-04-19_14-23_Area1_532.pair (ch2).
NPC46cH4K16ac_cy3BR2:
554409A01_2013-05-15_12-06_Area1_532.pair (ch1)
554409A01_2013-05-15_12-06_Area1_635.pair (ch2).

source_name: H4K16ac ChIP DNA from NPCs (day5)

value: 5 day differentiation with NB27 and Neuro2 medium supplements

value: NPC

source_name: MNase digested input DNA from day5 NPC


title: S. cerevisiae T73 glucose Cy5

source_name: S. cerevisiae T73 glucose


title: S. cerevisiae SK1 glucose Cy5

source_name: S. cerevisiae SK1 glucose


title: SK-N-SH vehicle, biological replicate 2

tag: cell line


title: LWQ-

status: Public on Aug 22 2013

type: protein

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Dog serum samples were diluted 1:250 in Protein Array Blocking buffer (PAB buffer) (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA). This suspension was incubated for 30 min at 22°C, with gentle constant shaking. Arrays were re-hydrated with PAB buffer alone for 30 min at 22°C before incubation with the primary antibody solution for 12 h at 4°C, on a rocker platform. Pads were quickly rinsed 6 times with 10mM Tris pH 8.0, 150mM NaCl, 0.05% Tween 20 (Tween-TBS), and then washed 3 times for 5 minutes each on a rocking platform. Biotin-conjugated rabbit anti-dog IgG Heavy and Light chain (Jackson ImmunoResearch, West Grove, PA) was diluted 1:200 in PAB buffer, and incubated with the pads for 1h at 22°C on a rocking platform. Arrays were washed as above, and incubated with Cy5-conjugated streptavidin (Jackson ImmunoResearch, West Grove, PA), diluted 1:200 in PAB buffer. Incubation was carried out in the dark at room temperature for 1h, on a rocking platform. Arrays were rinsed 6 times, followed by three 5-minute washes in Tween-TBS, and this process repeated with TBS alone. Slides were dismounted from their frames, rinsed in double-distilled H2O, and centrifuged 20 min at 500 x g to dry.

scan_protocol: Slides were dismounted from their frames, rinsed in double-distilled H2O and centrifuged 20 min at 500 x g to dry. Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: Antibody binding was measured by the averaged signal intensity of all pixels within each spot of printed antigen (raw data). For analysis, the raw values of signal intensity were log-transformed; negative or zero values after spot-specific background subtraction were assigned a net value of 0.

molecule: protein

organism: Canis lupus familiaris

source_name: serum

tag: breed

value: beagle

tag: serum type

value: Unexposed

tag: b. burgdorferi infection

value: Negative


title: S. cerevisiae CLIB324 glucose Cy5

source_name: S. cerevisiae CLIB324 glucose


title: OBQ-


title: OCQ-


title: Bulk population, day 1 (24h 10nM vincristine)

description: replicate 1

value: day 1 (24h 10nM vincristine)


title: Bulk population, day 2 (drug washed at day 1)

description: replicate 1

value: day 2 (drug washed at day 1)


title: Bulk population, day 0 (no drug)

description: replicate 1

value: day 0 (no drug)


title: 60_exp1

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

description: Gene expression data from MLL-AF4 ALL cell line SEM with JMJD1C knock down

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: The raw data was first analyzed with Affymetrix Power Tools (APT version: 1.14.4.1, see www.affymetrix.com) to calculate gene level RMA probe set summation values.  The APT command was:  apt-probeset-summarize -a rma -a rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true,pm-only,med-polish.expon=true -a pm-only,dabg.chisq=true -p ${affy_lib}/HuGene-2_0-st.pgf -c ${affy_lib}/HuGene-2_0-st.clf -b ${affy_lib}/HuGene-2_0-st.bgp --qc-probesets ${affy_lib}/HuGene-2_0-st.qcc -m ${affy_lib}/HuGene-2_0-st.mps ${cel_dir}/*.CEL -o ${out_dir}/gene_level.  The Affymetrix microarray annotation (HuGene-2_0-st_rev1.zip) was downloaded from http://www.affymetrix.com/support/technical/libraryfilesmain.affx on june 17 2013.  All the post-APT processing including filtering, statistical analysis and plotting was done in R.

source_name: human MLL-AF4 ALL SEM cells

label_protocol: standard Affymetrix procedure

growth_protocol: SEM Cells were transduced with pLKO-puro-IPTG-3xLacO lentiviral vectors and selected with 2 μg/ml puromycin (Sigma).

extract_protocol: RNA was purified using RNeasy Plus RNA kit (Qiagen) and reverse transcribed using TaqMan Reverse Transcription Reagents (Applied Biosystems).

treatment_protocol: For shRNA expression, culture medium was supplemented with 1 mM IPTG (Sigma).

value: MLL-AF4 ALL SEM

tag: genotype/variation

value: JMJD1C knock down


title: S. cerevisiae PW5 glucose Cy5

source_name: S. cerevisiae PW5 glucose

value: glucose


title: S. cerevisiae Y12 glucose Cy5

source_name: S. cerevisiae Y12 glucose


title: YYQ

value: Exposed

value: Positive


title: YOQ


title: 60_exp3


title: scr_exp2

description: Gene expression data from MLL-AF4 ALL cell line SEM with NO knock down

value: no knock down


title: scr_exp3


title: 60_exp2


title: scr_exp1


title: LVQ-


title: XTR


title: SK-N-SH vehicle, biological replicate 1

value: SK-N-SH

tag: cell type

value: Neuroblastoma


title: XZQ


title: XYR


title: XHR


title: ZEQ


title: XFR


title: XKR


title: ESC_D3

scan_protocol: arrays were scanned on a NimbleGen MS200 Microarray Scanner  (Roche) using 100% laser power at 2μm resolution.

data_processing: The mean signal intensity of the 4 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used to control inter array variability. Log2 values were calculated by log2 of the product of division of ChIP signal by input signal

source_name: H4K16ac ChIP DNA from retinoic acid (3 days) differentiated ES cells

label_protocol: 400ng ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol:
Nuclei were digested with mnase and released chromatin either ChIP-ed with H4K16ac antibody [ChIP DNA samples] or not [input DNA sample]. H4K16ac antibody = Millipore, cat#07-329 , lot DAM1687546  Rabbit IgG antibody = Santa Cruz, cat#sc-2027 , lot E1512
Genomic DNA for ChIP was extracted using a Qiagen PCR purification kit.

value: ES cells

tag: differentiation status

value: differentiated

source_name: MNase digested input DNA from retinoic acid (3 days) differentiated es cells


title: WFR


title: WDQ


title: WQR


title: VIR


title: VGQ


title: VSR


title: QRQ


title: Anaerobic galactose-limited chemostat pH6.0, 35°, Monoculture S. cerevisiae (FM14R)

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. cerevisiae anaerobic galactose-limited chemostat with a dilution rate of 0.1h-1.

hyb_protocol: Hybridization of Affymetrix chips was performed following the manufacturer’s instructions.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each

label: Biotin-Streptavidin

source_name: Galactose-limited chemostat culture 0.1h-1

label_protocol: Labeling of Affymetrix chips was performed following the manufacturer’s instructions.

growth_protocol: Batch and chemostat cultures were carried out in 2-l bioreactors (Applikon, Schiedam, The Netherlands), with working volumes of 1.4 l and 1.0 l, respectively. The pH was controlled at 6.0 by automated titration with 2 M KOH. The temperature was set at 35 °C and the stirring rate was set to 800 rpm. In batch cultures, anaerobicity was maintained by sparging with pure nitrogen gas or a gas mixture (2% CO2 : 98% N2) at a flow rate of 0.5 l.min-1 (CO2 2.7 and N2 5.0, Linde Gas Benelux). In chemostat cultures, the medium reservoir was sparged with pure nitrogen gas, and the culture vessel with a 2% CO2: 98% N2 gas mixture. Cultures were equipped with Norprene tubing to prevent oxygen diffusion. In chemostats, culture volume was controlled via an electrical level sensor and the dilution rate was set to 0.10 h-1. In bioreactors, the synthetic medium was supplemented with 0.3 g l-1 of antifoam A8011 (Sigma-Aldrich, St. Louis, USA). Chemostat cultures were considered to be in steady state when, after at least six volume changes, key parameters such as culture dry weight, substrate concentration and specific CO2 production rate changed by less than 2% over 2 consecutive volume changes. For each chemostat condition (yeast only, LAB only and mixed culture) three independent culture replicates were run.

extract_protocol: Yeast total RNA from pure and mixed cultures was recovered using phenol/chloroform extraction as previously described (43). Further processing of RNA into cDNA relies on reactions initiated by the polyA tail carried by eukaryotic mRNAs only. Separation of the reaction products using the Agilent bioanalyzer confirmed that carry-over of Lb. bulgaricus RNA was negligible, thereby demonstrating that no additional purification of yeast mRNA was required. Processing of total RNA was performed according to Affymetrix’s instructions. RNA target preparation for microarray expression analysis was carried out according the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, USA) using 200 ng of total RNA for both pure and mixed cultures. The protocol was carried out with minor modifications, i.e the Affymetrix polyA RNA controls were excluded from the aRNA amplification protocol and the IVT reactions were incubated for 16 h at 40°C. The quality of total RNA, cDNA, cRNA, and fragmented aRNA was checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Sampling for transcriptome analysis from pure and mixed cultures was performed as previously described, using liquid nitrogen for rapid quenching of metabolism (43). Samples were stored at -80°C in a mixture of phenol/chloroform and TEA buffer until further processing for total RNA extraction.

tag: c-source

value: Galactose


title: QPQ

value: beagle


title: QLR


title: VTQ


title: QWQ


title: QQQ


title: PXR


title: PWR


title: S. cerevisiae YJM269 glucose Cy3

source_name: S. cerevisiae YJM269 glucose


title: Anaerobic galactose-limited chemostat pH6.0, 35°, Monoculture S. cerevisiae (FM14L)


title: Anaerobic lactose-limited chemostat pH6.0, 35°, mixed cullture S. cerevisiae AND Lb. bulgaricus (FM12)

description: S. cerevisiae and Lb. bulgaricus anaerobic lactose-limited chemostat with a dilution rate of 0.1h-1.

organism:
Lactobacillus delbrueckii subsp. bulgaricus
Saccharomyces cerevisiae

source_name: Lactose-limited chemostat culture 0.1h-1

value: Lactose


title: ESC_UD

value: undifferentiated

source_name: MNase digested input DNA from UD ES cells


title: VJR


title: PRQ


title: Anaerobic lactose-limited chemostat pH6.0, 35°, mixed cullture S. cerevisiae AND Lb. bulgaricus (FM10L)


title: PLQ


title: PKQ


title: Anaerobic lactose-limited chemostat pH6.0, 35°, mixed cullture S. cerevisiae AND Lb. bulgaricus (FM11R)


title: PTQ


title: PHQ


title: OUQ


title: LXR


title: LZR


title: HME-CC-ATM1_Untreated_Replicate2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
US23502387_251485042560_S01_H.tif
US23502387_251485042560_S01_L.tif
Gene expression of HMECC-ATM deficient cells.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: HMECC-ATM Deficent;log growing, 72 hours post plating

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Cells were grown and maintained in HuMEC Ready Media (Invitrogen) with 4 μg/mL blastocydin as described in Arlander et al, Cancer Res 2008;68(1):89–97

extract_protocol: Total RNA was isolated using the Ambion mirVana miRNA isolation kit using the standard protocol for total RNA isolation (Ambion).  The isolated total RNA was then split, half was used for small RNA sequencing and half was used for gene expression analysis.

value: isogenic hTERT-immortalized normal human mammary epithelial cell lines with lentiviral construct expressing an ATM shRNA


title: HME-CC-ATM1_Untreated_Replicate1


title: HME-CC-LacZ_Untreated_Replicate3

description:
US23502387_251485042559_S01_H.tif
US23502387_251485042559_S01_L.tif
Gene expression of HMECC-Wild Type cells.

source_name: HMECC-Wild Type;log growing, 72 hours post plating

value: isogenic hTERT-immortalized normal human mammary epithelial cell lines with lentiviral vector transducing the LacZ gene


title: Anaerobic galactose-limited chemostat pH6.0, 35°, Monoculture S. cerevisiae (FM13)


title: HME-CC-LacZ_Untreated_Replicate2


title: B. subtilis_air plasma treated_replicate2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: B. subtilis grown in LB medium

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).
The normalization algorithm is defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol name: GE2_105_Dec08).
The normalization/ dye bias correction method is: Linear and Lowess.

organism: Bacillus subtilis

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare). The individual samples were labeled with Cy5, whereas the reference pool was labeled with Cy3.

growth_protocol: The Bacillus subtilis 168 wild type strain was grown aerobically at 37 °C in LB medium.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002, PMID: 11948165).

treatment_protocol: At OD540 of 0.5, cells were treated with air plasma with a discharge power of 7.4 W for 15 min. Samples were taken 5 min after the treatment.

tag: genotype

value: wild type

source_name: air plasma treated


title: MCF-7_T8_high_TIMP1

city: Kgs. Lyngby

first: Kirstine

last: Belling

address: Kemitorvet, bldg 208

department: Department of Systems Biology

institute: Center for Biological Sequence Analysis

description: High TIMP1 expression.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were normalized using quantile normalization with IlluminaGUI in R.

source_name: MCF-7 breast cancer cell line, high TIMP1

label_protocol: aRNA was prepared with the Ambion MessageAmp II aRNA Amplification Kit.

growth_protocol: Cells were propagated in RPMI 1640 Glutamax medium (Invitrogen, Denmark) supplemented with 10% heat-inactivated fetal calf serum (FCS, Invitrogen, Denmark) and grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen protocol). Quantity of total RNA was measured using Nanodrop ND1000 (Thermo Scientific Inc, USA). Quality control was determined using the Bioanalyzer RNA 6000 Nano kit (Agilent Technologies, USA).

value: breast cancer cells

tag: timp1 (ng/mg protein)


title: B. subtilis_control_replicate2

description: B. subtilis grown in LB medium

source_name: control


title: HME-CC-ATM1_Untreated_Replicate3

description:
US23502387_251485042561_S01_H.tif
US23502387_251485042561_S01_L.tif
Gene expression of HMECC-ATM deficient cells.


title: B. subtilis_air plasma treated_replicate3

description: B. subtilis grown in LB medium


title: MCF-7_T7_high_TIMP1

description: High TIMP1 expression.


title: Liver_Wistar_Vehicle_7

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >13.3 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec).

scan_protocol: Slides were scanned immediately after washing on a GenePix™ 4000B array scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014879_D_20070207). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for 12 out of 15 microarrays or with a weight of 1 in at least 6 microarrays from at least one experimental group. At this step, 23776 spots out of 45018 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median log normalized signal of each set of replicated probes. The resulting matrix has 22244 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Rattus norvegicus

source_name: Liver, Wistar, Vehicle, replicate 7

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 1 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 2-3 month old female Wistar rat (225-250 g at the end of the experiment) were housed at room temperature on a 12h light/dark cycle (lights on at 7:00 am) and had free access to food (A04, SAFE, Augy, France) and tap water.

extract_protocol: Immediately following euthanasia, liver was removed, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies, RIN>8.7 for all samples) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific)

treatment_protocol: Rats were allocated to vehicle (n = 7) or fipronil-treated (n = 8) groups and received a daily oral dose of vehicle (aqueous methylcellulose (0.5%, w/v) and Tween 80 (0.01%, w/v) solution) or fipronil suspension (3 mg/kg/day) through feeding needles for 14 days.

tag: gender

value: female

value: Wistar Crl:WI

tag: age

value: 2-3 months

tag: tissue

value: liver

value: Vehicle per os for 14 days


title: MCF-7_T5_high_TIMP1

description: High TIMP1 expression.


title: B. subtilis_control_replicate1

description: B. subtilis grown in LB medium


title: B. subtilis_air plasma treated_replicate1

description: B. subtilis grown in LB medium


title: B. subtilis_control_replicate3

description: B. subtilis grown in LB medium


title: MCF-7_T3_intermediate_TIMP1

description: Intermediate TIMP1 expression.

source_name: MCF-7 breast cancer cell line, intermediate TIMP1


title: Liver_Wistar_Vehicle_4

source_name: Liver, Wistar, Vehicle, replicate 4

tag: treatment


title: HME-CC-LacZ_Untreated_Replicate1


title: MCF-7_T9_high_TIMP1

description: High TIMP1 expression.


title: Liver_Wistar_Vehicle_5

source_name: Liver, Wistar, Vehicle, replicate 5

tag: strain


title: Liver_Wistar_Vehicle_3

source_name: Liver, Wistar, Vehicle, replicate 3


title: Liver_Wistar_Vehicle_6

source_name: Liver, Wistar, Vehicle, replicate 6


title: MCF-7_V1_low_TIMP1

description: Low TIMP1 expression.

source_name: MCF-7 breast cancer cell line, low TIMP1


title: MCF-7_T2_low_TIMP1

description: Low TIMP1 expression.


title: Liver_Wistar_Vehicle_2

source_name: Liver, Wistar, Vehicle, replicate 2


title: Liver_Wistar_Fipronil_8

source_name: Liver, Wistar, Fipronil, replicate 8

value: Fipronil, 3mg/kg/d, per os for 14 days


title: MCF-7_T4_intermediate_TIMP1

description: Intermediate TIMP1 expression.


title: MCF-7_T6_high_TIMP1

description: High TIMP1 expression.


title: Liver_Wistar_Vehicle_1

source_name: Liver, Wistar, Vehicle, replicate 1


title: LF endometrium day 14, biological rep7, animal 7446

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

description: Gene expression data from late-luteal endometrium of low fertility heifers

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GCOS v 1.x

data_processing: All microarray analyses including preprocessing, normalization and statistical analysis were carried out using R (R, 2007) version 2.6 and Bioconductor version 2.1. Data were quality assessed before and after normalization using a number of in-built quality control methods implemented in the Bioconductor affycoretools and associated packages. Microarray data were preprocessed using the mmgMOS normalization method using the default settings and differential expression (DE) was calculated using the puma DE method both implemented in the Bioconductor package “puma”. As many of the original annotations for the Affymetrix bovine chip are erroneous, remapped annotations were determined using the “bovinedaiplusv6cdf” chip definition file (CDF) which returned ‘Entrez Gene’ gene name identifiers. This annotation is based on the CDF-Merger procedure, which generates a hybrid CDF based on the standard Affymetrix CDF (version 26) and the custom Brainarray (version 11.0.1) CDF.

organism: Bos taurus

source_name: Bovine endometrium in late-luteal phase; low fertility

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (Genechip® Expression Analysis Technical Manual, 2005-2008, Affymetrix). cRNA was subjected to two rounds of linear amplification using the GeneChip® Expression 3’-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer’s instructions. cDNA was synthesized during the first cycle and biotin-labeled nucleotides were incorporated during the second in vitro transcription reaction.

extract_protocol: Total RNA was prepared from 100-200 mg of fragmented frozen endometrial tissue using the TRIzol extraction method. Samples were subsequently purified and treated for contaminating genomic DNA using RNeasy clean-up kits in accordance with manufacturer’s guidelines supplied (QIAGEN, Crawley, West Sussex, UK).

value: uterine endometrium

tag: phase

value: late-luteal

tag: fertility

value: low


title: LF endometrium day 14, biological rep5, animal 7698

value: Charolais X


title: Liver_Wistar_Fipronil_7

source_name: Liver, Wistar, Fipronil, replicate 7


title: LF endometrium day 14, biological rep6, animal 7728

value: Limousin X


title: LF endometrium day 14, biological rep4, animal 7685

value: Simmental X


title: SPF Beagle Pool

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: Antibody binding was measured by the averaged signal intensity of all pixels within each spot of printed antigen (raw data). Background signal was calculated for each individual dog serum by averaging the signal of 6 “no DNA” spots. The net value for each ORF was determined by subtracting the background from the raw values for each serum sample; for antigens printed as purified proteins, the raw value was used for data analysis. For analysis, the net value of signal intensity were log-transformed; negative or zero values after background subtraction were assigned a net value of 0.

source_name: serum

value: beagle

value: Unexposed

value: Negative


title: Liver_Wistar_Fipronil_6

source_name: Liver, Wistar, Fipronil, replicate 6


title: Liver_Wistar_Fipronil_4

source_name: Liver, Wistar, Fipronil, replicate 4


title: LF endometrium day 14, biological rep3, animal 7667


title: LF endometrium day 14, biological rep2, animal 7726


title: LF endometrium day 14, biological rep1, animal 7662


title: Liver_Wistar_Fipronil_5

source_name: Liver, Wistar, Fipronil, replicate 5


title: HF endometrium day 14, biological rep7, animal 7451

description: Gene expression data from late-luteal endometrium of high fertility heifers

source_name: Bovine endometrium in late-luteal phase; high fertility

value: high


title: Liver_Wistar_Fipronil_3

source_name: Liver, Wistar, Fipronil, replicate 3


title: HF endometrium day 14, biological rep8, animal 7366


title: Liver_Wistar_Fipronil_1

source_name: Liver, Wistar, Fipronil, replicate 1


title: HF endometrium day 14, biological rep6, animal 7645


title: MCF-7_T10_high_TIMP1

description: High TIMP1 expression.

source_name: MCF-7 breast cancer cell line, high TIMP1

tag: cell line

value: breast cancer cells


title: OBQ-

tag: breed


title: OCQ-

tag: serum type


title: Liver_Wistar_Fipronil_2

source_name: Liver, Wistar, Fipronil, replicate 2

value: female


title: HF endometrium day 14, biological rep5, animal 7637


title: OUQ-

tag: b. burgdorferi infection


title: XZQ

value: Exposed

value: Positive


title: Early maturation-stage embryonic cotyledons [RNA-seq]

type: SRA

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Embryonic cotyledons from seeds 6.0 - 7.0 mm in length were collected.

library_source: transcriptomic

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the qseq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max genome (v1.0) using bowtie v0.12.7 with parameters -v 2 -5 6 -3 0 -m 3 --best --strata.
Read counts to Glycine max gene models (v1.1) models were computed using BedTools.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008).
Genome_build: Glyma version 1.0
Supplementary_files_format_and_content: tab-delimited text file including gene model and normalized RPKM value.

organism: Glycine max

source_name: Soybean early maturation-stage embryonic cotyledons

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo

extract_protocol: Total RNA was isolated from three seed parts (axis, cotyledon, and seed coat) using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Total RNA was treated with RNase-free DNaseI (Ambion, Austin, TX) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300. Approximately 20 nanogram of total RNA was amplified with Nugen Ovation Pico WTA system v.1 (Nugen, San Carlos, CA).  Double-stranded cDNA was generated using WT-Ovation Exon Module (Nugen, San Carlos, CA) and quantified with Picogreen on the Nanodrop ND-3300 (Nanodrop Technologies).  One microgram of double-stranded cDNA was fragmented using NEB Fragmentase for 15 minutes at 37oC for the standard protocol (NEB, Ipswich, MA).  The Illumina TruSeq DNA Sample prep kit was used to prepare the Illumina library with modifications (Illumina, San Diego, CA).  Specifically, the Covaris shearing step was omitted, the final PCR enrichment step was performed using Agilent Pfu Turbo Cx DNA polymerase (Agilent, Santa Clara, CA) instead of the TruSeq PCR mix, and 12 cycles of PCR were performed. Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument. Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing

tag: cultivar

value: Williams 82

tag: developmental stage

value: Early maturation-stage

value: embryonic cotyledons


title: Early maturation-stage seed coat [RNA-seq]

description: Seed coats from seeds 6.0 - 7.0 mm in length were collected.

source_name: Soybean early maturation-stage seed coat

value: seed coat


title: XKR


title: XTR


title: XYR


title: YOQ


title: HF endometrium day 14, biological rep4, animal 7612

value: uterine endometrium

value: late-luteal


title: HF endometrium day 14, biological rep3, animal 7429


title: YYQ


title: HF endometrium day 14, biological rep2, animal 7425

value: Charolais X


title: WQR


title: XFR


title: WFR


title: XHR


title: LF endometrium day 14, biological rep8, animal 7502

value: low


title: HF endometrium day 14, biological rep1, animal 7744

value: Simmental X


title: MDA-MB-231_GFP_sample

city: Shanghai

first: Gang

last: Xiao

address: 227 South Chongqing Road

country: China

institute: Shanghai Jiao-Tong University School of Medicine

description:
CGCA_OE
Gene expression in MDA-MB-231 cell line, control

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 12.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human breast cancer cell lines MDA-MB-231 and the immortalized epithelial cells HBL-100 were maintained in DMEM (Hyclone), supplement with 10% FBS (GIBCO) and 1% penicillin/streptomycin. Cells were cultured at 37℃ water-saturated 5% CO2 atmosphere.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: For restoring expression of HIC1 in MDA-MB-231 cells, human full-length HIC1 cDNA was inserted into lentivirus vector pHR-SIN-CSIGW. For the production of lentivirus, lenti-x cells were transfected with the PMD2.G, PSPAX2 and HIC1 expression vector using the lipofectamine 2000 (Invitrogen). After 48 hours, culture supernatants were collected and passed through 0.45µm filters, mixed with fresh media (1:1) and polybrene (8μg/ml) to infect target cells. For generation of a stable HIC1 knockdown cell line, GV248 lentiviral vectors expressing short hairpin RNAs targeting HIC1 were purchased from GeneChem Company (China, Shanghai). Lentiviruses were produced as described above and infected cells were selected by puromycin treatment at 1μg/ml.

tag: cell type

value: human breast cancer cells

tag: genotype/variation

value: control


title: WDQ

value: beagle


title: VTQ


title: MDA-MB-231_HIC1_sample

description:
CGCB_OE
Gene expression in MDA-MB-231 cell line, H1C1 over-expressed

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 12.0 (Agilent technologies, Santa Clara, CA, US).

source_name: MDA-MB-231_HIC1 gene

value: HIC1 overexpression


title: Visceral fat samples 5 and 6, biological replicate 3

city: Danville

first: George

last: Argyropoulos

state: Pa

address: 100 North Academy Ave

department: Weis Center for Research

institute: Geisinger Medical Center

hyb_protocol: GeneChips were hybridized in GeneChip Hybridization Oven 640 and washed in the GeneChip Fluids Station 480 (Affymetrix).

scan_protocol: Genechips were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Quality control analysis was completed with RMA Sketch (Affymetrix) and anaylsis was completed on Spotfire Decision Site version 9.1.2 using Decision site for functional genomics (TIBCO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: Visceral fat from 2 patients

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Samples were collected for all tissue during open gastric bypass surgery and placed in RNAlater solution.  RNA was extracted using Qiagen's Rneasy Lipid Tissue Mini Kit.

tag: mean age

tag: male/female ratio

tag: ethnicity

value: white

tag: mean bmi

tag: surgery

value: Open Gastric Bypass

value: Visceral fat


title: VSR

value: Exposed

value: Positive


title: Lam3_24_b

city: New Haven

first: Christopher

last: Bolen

state: CT

address: 300 George Street, Suite 505

department: Pathology

institute: Yale University

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 24 hours

hyb_protocol: 1.5 µg of cRNA was combined with hybridization controls and hybridized to the array for 16 hours in a hybridization oven at 58°C. The chip was then washed and stained with streptavidin-Cy3.

scan_protocol: The array was scanned using the Illumina BeadArray reader.

data_processing: Microarray data from the validation cohort underwent quantile normalization using the Beadarray package in bioconductor.

source_name: Huh7 cell, IFNL3 treated,24h

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.

growth_protocol: Human Huh7 hepatoma cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with the addition of 10% heat-inactivated fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate, 1X MEM non-essential amino acids and 10 mM HEPES buffer (Invitrogen)

extract_protocol: Total RNA was harvested and isolated at 0.5, 1, 2, 4, 6, 12 and 24 hours post-incubation using RNeasy Mini Kit (Qiagen)

treatment_protocol: Huh7 cells were seeded into 6-well plates at the density of 3✕105 cells/well and cultured overnight before stimulation with either 500 U/ml of IFN-α or IFN-β, or 10 ng/ml of IFN-λ1, IFN-λ2, or IFN-λ3.

tag: treatment

tag: time


title: VJR


title: Alpha_24_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 24 hours

source_name: Huh7 cell, IFNa treated,24h

value: Alpha


title: Lam2_24_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 24 hours

source_name: Huh7 cell, IFNL2 treated,24h


title: Visceral fat samples 1 and 2, biological replicate 1

tag: tissue


title: Lam2_24_a


title: Beta_24_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 24 hours

source_name: Huh7 cell, IFNb treated,24h

value: Beta


title: Lam3_24_a


title: Lam1_24_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 24 hours

source_name: Huh7 cell, IFNL1 treated,24h


title: Untreat_d

description: Untreated Human Huh7 cells

source_name: Huh7 cell, untreated

value: Untreat


title: Visceral fat samples 3 and 4, biological replicate 2

value: white/african american


title: Lam1_24_a


title: Beta_24_a


title: Beta_12_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 12 hours

source_name: Huh7 cell, IFNb treated,12h


title: VIR

source_name: serum


title: Alpha_12_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 12 hours

source_name: Huh7 cell, IFNa treated,12h


title: Lam1_12_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 12 hours

source_name: Huh7 cell, IFNL1 treated,12h


title: QWQ


title: Alpha_24_a


title: Subcutaneous fast samples 3 and 4, biological replicate 2

source_name: Subcutaneous fat from 2 patients

value: Subcutaneous fat


title: Lam2_12_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 12 hours

source_name: Huh7 cell, IFNL2 treated,12h


title: Subcutaneous fast samples 5 and 6, biological replicate 3


title: VGQ


title: QQQ


title: Subcutaneous fast samples 1 and 2, biological replicate 1


title: QRQ


title: Lam1_6.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 6 hours

source_name: Huh7 cell, IFNL1 treated, 6h


title: Lam3_6.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 6 hours

source_name: Huh7 cell, IFNL3 treated, 6h


title: Lam2_6.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 6 hours

source_name: Huh7 cell, IFNL2 treated, 6h


title: Epigastric fat samples 1 and 2, biological replicate 1

source_name: Epigastric fat from 2 patients

value: Epigastric fat


title: Epigastric fat samples 3 and 4, biological replicate 2


title: Epigastric fat samples 5 and 6, biological replicate 3


title: Untreat_c

description: Untreated Human Huh7 cells


title: Lam1_12_a


title: Alpha_6.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 6 hours

source_name: Huh7 cell, IFNa treated, 6h


title: Lam3_12_a

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 12 hours

source_name: Huh7 cell, IFNL3 treated,12h


title: Beta_6.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 6 hours

source_name: Huh7 cell, IFNb treated, 6h


title: Lam3_12_b


title: Beta_12_a


title: Lam2_12_a


title: QPQ


title: QLR


title: Lam3_6.0_a


title: PXR


title: KMS11_TKO-rep3

first: Shannon

last: Chuai

state: Shanghai

address: Building 8, Lane 898 Halei Road, Pudong New Aera

institute: Novartis

description: Gene expression profiling of the KMS11 cells with NSD2 knockout

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The gene expression data was normalized using the Robust Multiarray Averaging (RMA) method and log2 transformed before comparisons.

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: disease

value: Myeloma

tag: transgene

value: NSD2 knockout


title: PWR

tag: breed


title: PRQ

tag: serum type


title: Alpha_12_a

tag: cell line


title: Lam2_6.0_a


title: KMS11_TKO-rep1


title: KMS11_TKO-rep2


title: Alpha_6.0_a


title: KMS11_PAR-rep1

description: Gene expression profiling of the KMS11 cells


title: Lam1_6.0_a


title: KMS11_PAR-rep2

value: Gene expression profiling of the KMS11 cells


title: PLQ

tag: b. burgdorferi infection


title: Lam1_4.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 4 hours

source_name: Huh7 cell, IFNL1 treated,4h


title: Beta_4.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 4 hours

source_name: Huh7 cell, IFNb treated,4h


title: ZEQ


title: Lam2_4.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 4 hours

source_name: Huh7 cell, IFNL2 treated,4h


title: KMS11_PAR-rep3


title: Lam3_2.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 2 hours

source_name: Huh7 cell, IFNL3 treated, 2h


title: Lam2_2.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 2 hours

source_name: Huh7 cell, IFNL2 treated, 2h


title: Alpha_4.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 4 hours

source_name: Huh7 cell, IFNa treated,4h


title: PTQ

source_name: serum


title: Beta_6.0_a


title: PKQ


title: OUQ


title: Lam1_2.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 2 hours

source_name: Huh7 cell, IFNL1 treated, 2h


title: LXR


title: PHQ


title: Beta_2.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 2 hours

source_name: Huh7 cell, IFNb treated, 2h


title: KMS11_WT+MMSET1-rep3

description: Gene expression profiling of the KMS11 cells with WT NSD2 and MMSET I isoform

value: WT NSD2 and MMSET I isoform


title: KMS11_WT+MMSET1-rep2


title: Alpha_2.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 2 hours

source_name: Huh7 cell, IFNa treated, 2h


title: Alpha_4.0_a


title: KMS11_WT+MMSET1-rep1


title: Lam3_4.0_a

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 4 hours

source_name: Huh7 cell, IFNL3 treated,4h


title: Untreat_b

description: Untreated Human Huh7 cells

source_name: Huh7 cell, untreated


title: Beta_4.0_a


title: KMS11_WT_rep2

description: Gene expression profiling of the KMS11 cells with WT NSD2

value: WT NSD2


title: Lam3_2.0_a


title: Beta_2.0_a


title: Lam2_4.0_a


title: LZR

value: beagle


title: Lam1_2.0_a


title: Lam1_4.0_a


title: Lam2_1.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 1 hours

source_name: Huh7 cell, IFNL2 treated,1h


title: Alpha_2.0_a


title: KMS11_WT_rep3


title: KMS11_CDM_rep3

description: Gene expression profiling of the KMS11 cells with catalytic dead mutant (CDM) NSD2

value: catalytic dead mutant (CDM) NSD2


title: Lam1_1.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 1 hours

source_name: Huh7 cell, IFNL1 treated,1h


title: Beta_1.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 1 hours

source_name: Huh7 cell, IFNb treated,1h


title: KMS11_WT_rep1


title: Lam2_2.0_a


title: KMS11_CDM+MMSET1-rep3

description: Gene expression profiling of the KMS11 cells with catalytic dead mutant (CDM) NSD2 and MMSET I isoform


title: MM05 P14

city: Concord

first: Casey

middle: M

last: Wright

state: NSW

address: Gate 3, Hospital Road

institute: ADRI

hyb_protocol: After purification, the samples were hybridised to Ncode Human Long Noncoding RNA microarrays according to the Agilent protocol for one colour microarray analysis.

scan_protocol: Slides were scannned using an Agilent Scanner.

data_processing: Data was feature extracted using Agilent Feature Extraction Software FE10.5 to extract pixel intensities. The raw text files were then imported into GeneSpring v12. Probes detected in at least one out of the ten samples were included, and baseline transformation was performed to the sample median. Data was normalised to the 75th percentile. Data was log2 transformed and this value was used as the expression value.

label: Alexa Fluor 555

source_name: MPM cell line MM05

label_protocol: Briefly, 10ug of total RNA was labelled using the Superscript Plus direct cDNA labelling kit according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from MPM cell lines using the Trizol (Invitrogen) reagent according to manufacturer's instructions.

value: malignant pleural mesothelioma cells


title: Beta_0.5_b

description: Human Huh7 cells treated with 500U/ml of IFN Beta for 0.5 hours

source_name: Huh7 cell, IFNb treated, 0.5h


title: KMS11_CDM+MMSET1-rep2

value: catalytic dead mutant (CDM) NSD2 and MMSET I isoform


title: Lam3_1.0_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 1 hours

source_name: Huh7 cell, IFNL3 treated,1h


title: KMS11_CDM+MMSET1-rep1


title: Lam2_0.5_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda2 for 0.5 hours

source_name: Huh7 cell, IFNL2 treated, 0.5h


title: KMS11_CDM_rep1


title: KMS11_CDM_rep2


title: KMS11_MMSET1_rep3

description: Gene expression profiling of the KMS11 cells with NSD2 MMSET I isoform

value: NSD2 MMSET I isoform


title: Lam1_0.5_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda1 for 0.5 hours

source_name: Huh7 cell, IFNL1 treated, 0.5h


title: Alpha_1.0_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 1 hours

source_name: Huh7 cell, IFNa treated,1h


title: MET5A P23

source_name: Immortalised mesothelial cell line MeT-5A

value: immortalised pleural mesothelial cells


title: Lam2_1.0_a


title: Alpha_0.5_b

description: Human Huh7 cells treated with 500U/ml of IFN Alpha for 0.5 hours

source_name: Huh7 cell, IFNa treated, 0.5h

value: Alpha


title: Untreat_a

description: Untreated Human Huh7 cells


title: KMS11_MMSET1_rep2


title: Lam1_1.0_a


title: KMS11_H762Y_rep2

description: Gene expression profiling of the KMS11 cells with NSD2 H762Y mutation

value: NSD2 H762Y mutation


title: MM05 P15


title: MET5A P24


title: KMS11_MMSET1_rep1


title: Alpha_1.0_a


title: KMS11_H762Y_rep3


title: Beta_1.0_a

value: Beta


title: Lam3_1.0_a


title: H28 P106

source_name: MPM cell line H28


title: H226 P85

source_name: MPM cell line H226


title: KMS11_H762Y_rep1


title: H226 P86


title: KMS11_526-1365_rep2

description: Gene expression profiling of the KMS11 cells with NSD2 526-1365


title: Lam3_0.5_b

description: Human Huh7 cells treated with 10ng/ml of IFN Lambda3 for 0.5 hours

source_name: Huh7 cell, IFNL3 treated, 0.5h


title: KMS11_526-1240_rep1

description: Gene expression profiling of the KMS11 cells with NSD2 526-1240


title: H28 P101


title: Lam3_0.5_a


title: KMS11_526-1365_rep1


title: KMS11_526-1240_rep2


title: Lam1_0.5_a


title: MSTO P13

source_name: MPM cell line MSTO-211H


title: MSTO P14


title: Beta_0.5_a


title: Lam2_0.5_a


title: KMS11_526-1240_rep3


title: KMS11_526-1365_rep3


title: ComBroilA_6

status: Public on Aug 21 2013

city: Wageningen

first: richard

last: crooijmans

address: de Elst 1

department: Animal Breeding and Genomics Centre

institute: Wageningen University

scan_protocol: Agilent CHG protocols (for FFPE samples) version 1.02007 were stricktly followed for scanning . The arrays were scanned with 100% PMT laser power.

data_processing: the feature extraction software version 9.5, protocvol CGH-v4_95_feb07 from Agilent was used to generate te feature extraction data.

organism: Gallus gallus

source_name: ComBroilA

label_protocol: for each DNA sample 2.5 μg  ws used for the labeling experiments using the Agilent Genomic DNA Labeling kit PLUS. Afterwards the concentration and fluorescent dye incorporation of the labeled fragments were measured using the nanodrop. For each array equal amounts of fluorescent DNA is used for hybridization

extract_protocol: Genomic DNA was isolated with the oPuregene blood kit of the Qiagen Qiamap DNA blood kit.

tag: gender

value: female

tag: line

value: ComBroilA

source_name: UCD001 reference

value: male


title: Alpha_0.5_a


title: refractory

city: Stony Brook

first: Sumita

last: Bhaduri-Mcintosh

address: 020 Health Sciences Center

institute: Stony Brook University

description: Gene expression data from EBV-infected B cells in refractory state

hyb_protocol: Affymetrix hybridization protocol - GeneChip was pre-hybridized at 45 degree C for 10 minutes followed by hybridization to labeled probe at 45 degree C for 16h.

scan_protocol: Affymetrix scanning protocol - Microarray was scanned using GeneChip Expression Wash, Stain and Scan User Manual, P/N 702731.

data_processing: Raw microarray data were processed using Affymetrix GeneChip operating software. The CEL files were normalized using dChip software [2010 version; ExpressionStat 5.0 algorithm]. Differential gene expression comparison was performed in dChip under default settings.

source_name: HH514-16 cells

label_protocol: GeneChip Eukaryotic labeling, hybridization, and scanning were performed according to manufacturer’s (Affymetrix) standard recommendations. Briefly double stranded cDNA was synthesized from total RNA. Antisense cRNA was labeled with biotin followed by clean-up and fragmentation of cRNA.

growth_protocol: HH514-16 cells were subcultured at 3 x 10(5) cells. Cells were treated with NaB 48h later.

extract_protocol: Total RNA was extracted using the RNeasy RNA extraction kit (Qiagen). RNA collected from three independent experiments was pooled prior to array analysis.

treatment_protocol: HH514-16 cells were treated with 3mM NaB and harvested 24 h later.

value: EBV-infected B cells

tag: treated with

value: 3mM NaB

tag: cell subtype

value: FACS-separated refractory cells


title: ComBroilA_7

hyb_protocol: Agilent CHG protocols (for FFPE samples) version 1.02007


title: ComBroilA_2


title: ComBroilB_9

source_name: ComBroilB

value: ComBroilB


title: ComBroilB_8


title: lytic

description: Gene expression data from EBV-infected B cells in lytic state

value: FACS-separated lytic cells


title: ComBroilA_8


title: Silkie_002

source_name: Silkie

value: Silkie


title: ComBrownL2_3


title: ComBroilB_1


title: ComBroilB_7


title: ComBrownL2_5


title: ComBroilA_1


title: ComwhiteL_4

source_name: ComwhiteL

value: ComwhiteL


title: ComBroilB_2


title: CombroilB_6

source_name: CombroilB

value: CombroilB


title: ComwhiteL_2


title: ComBrownL2_2


title: ComBrownL2_4


title: ComBrownL1_ HN_1


title: Blood of tympanic paraganglioma case 33

city: Chieti Scalo

first: Renato

last: Mariani-Costantini

state: CH

address: Via Colle dell'Ara

department: Ageing Research Center (CeSI)

country: Italy

institute: "G. d'Annunzio" University Foundation

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genotyping data were generated using Genome Studio v2010.3 with Genotyping module v1.8.4 and GenCall v6.3.0 with score Cutoff 0.15. *replicates were used as quality controls and exluded from the main analysis after normalization and quality check. The unique lymph node metastasis was also excluded from the main analysis, being this limited to primary tumors.

source_name: Blood sample (33B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted using Qiagen Dneasy Blood e Tissue Kit, following manufacturer's instructions. DNA purity was checked by spectrophotometer, and DNA integrity by examination on agarose gel electrophoresis. DNA concentration was measured with the Quant-IT dsDNA BR assay kits with the Qubit fluorometer (Invitrogen) following manufacturer’s instructions.

tag: disease state

value: tympanic paraganglioma

tag: age

value: blood


title: BroilM_2723

source_name: BroilM

value: BroilM


title: Line7_XS764


title: Blood of tympano-jugular paraganglioma case 34

description: replicate 1

source_name: Blood sample (34B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: tympano-jugular paraganglioma


title: Lymph node metastasis of tympano-jugular paraganglioma case 34 (excluded)

description: replicate 1 (excluded*)

source_name: Lymph node metastasis (34PTJLM) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Head and Neck paraganglioma


title: Broiler2_38394581

value: unknown


title: ComBroilB_3

value: female


title: Tympanic paraganglioma case 33 - sample 1

description: replicate 1

source_name: Tumor specimen (33PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Tympanic paraganglioma


title: Tympano-jugular paraganglioma case 34

description: replicate 1

source_name: Tumor specimen (34PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Tympano-jugular paraganglioma


title: Tympanic paraganglioma case 33 - sample 2 (exluded)

description: biological replicate 2 (Second Primary Tumor of Patient 33 - excluded*)


title: Blood of tympano-jugular paraganglioma case 21

description: replicate 1

source_name: Blood sample (21B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 13 - sample 2 (excluded)

description: replicate 2 (excluded*)

source_name: Blood sample (13B, sample 2) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Line7_XS756

value: male


title: Line7_XS758


title: Line6_XS760


title: Tympano-jugular paraganglioma case 45

description: replicate 1

source_name: Tumor specimen (45PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympanic paraganglioma case 44

description: replicate 1

source_name: Blood sample (44B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 45

description: replicate 1

source_name: Blood sample (45B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympanic paraganglioma case 44

description: replicate 1

source_name: Tumor specimen (44PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Line15i_XS796

source_name: UCD001 reference


title: Line7_XS761


title: Tympano-jugular paraganglioma case 37

description: replicate 1

source_name: Tumor specimen (37PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 37

description: replicate 1

source_name: Blood sample (37B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 43

description: replicate 1

source_name: Blood sample (43B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Line15i_XS795


title: mapping_2757

source_name: mapping

value: mapping


title: Tympano-jugular paraganglioma case 43

description: replicate 1

source_name: Tumor specimen (43PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympanic paraganglioma case 32

description: replicate 1

source_name: Tumor specimen (32PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineBrL_XS773

source_name: LineBrL

value: LineBrL


title: BroilM_2718

source_name: BroilM


title: BroilM_2734


title: Tympanic paraganglioma case 36

description: replicate 1

source_name: Tumor specimen (36PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineN_S793

source_name: LineN

value: LineN


title: Tympanic paraganglioma case 20

description: replicate 1

source_name: Tumor specimen (20PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: BroilM_2665


title: ComBrownL1_ HN_3


title: BroilM_2667


title: LineN_S792


title: BroilM_2690


title: Blood of tympanic paraganglioma case 36

description: replicate 1

source_name: Blood sample (36B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineN_S056


title: Line15i_XS797


title: Tympano-jugular paraganglioma case 21

description: replicate 1

source_name: Tumor specimen (21PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Line15i_XS804


title: Line6_S789


title: Tympanic paraganglioma case 19

description: replicate 1

source_name: Tumor specimen (19PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineN_S791


title: Line15i_XS801


title: Line6_S785


title: Tympano-jugular paraganglioma case 12

description: replicate 1

source_name: Tumor specimen (12PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 13

description: replicate 1

source_name: Blood sample (13B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympanic paraganglioma case 19

description: replicate 1

source_name: Blood sample (19B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympano-jugular paraganglioma case 13

description: replicate 1

source_name: Tumor specimen (13PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Carotid body paraganglioma case 5

description: replicate 1

source_name: Tumor specimen (5PC) from multiple paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Carotid body paraganglioma


title: LineN_S054

source_name: UCD001 reference


title: Line6_S783


title: Tympanic paraganglioma case 14

description: replicate 1

source_name: Tumor specimen (14PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympano-jugular paraganglioma case 8

description: replicate 1

source_name: Tumor specimen (8PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 12

description: replicate 1

source_name: Blood sample (12B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineBrL_XS771

source_name: LineBrL


title: Tympanic  paraganglioma case 11

description: replicate 1

source_name: Tumor specimen (11PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Tympanic  paraganglioma


title: Blood of tympanic paraganglioma case 11

description: replicate 1

source_name: Blood sample (11B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Line6_S110


title: LineBrL_XS770


title: Blood of tympanic paraganglioma case 32

description: replicate 1

source_name: Blood sample (32B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: ComBrownL1_ HN_5


title: Blood of tympanic paraganglioma case 20

description: replicate 1

source_name: Blood sample (20B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: ComBrownL1_ HN_2


title: Carotid body paraganglioma case 7

description: replicate 1

source_name: Tumor specimen (7PC) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Blood of tympano-jugular paraganglioma case 8

description: replicate 1

source_name: Blood sample (8B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: LineBrL_XS767


title: LineBrL_XS769


title: Aviandiv_101_106M

source_name: Aviandiv

value: Aviandiv


title: Tympano-jugular paraganglioma case 6

description: replicate 1

source_name: Tumor specimen (6PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Aviandiv_101_74M


title: Blood of tympanic paraganglioma case 14

description: replicate 1

source_name: Blood sample (14B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Vagal paraganglioma case 5

description: replicate 1

source_name: Tumor specimen (5PV) from multiple paragangliomas patient of Gruppo Otologico clinic, Piacenza, Italy

value: Vagal paraganglioma


title: Tympano-jugular paraganglioma case 13 - sample 2 (excluded)

description: replicate 2 (excluded*)

source_name: Tumor specimen (13PTJ-2, sample 2) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: sporocyteless ovules

city: Irapuato

first: Alma

last: Armenta

address: Km 9.6 Libramiento Norte Carretera León

country: Mexico

institute: CINVESTAV

description: library strategy: MPSS

data_processing:
MPSS performed essentially as described in Meyers et al (Nature Biotechnol. 2004 Aug;22(8):1006-11. Epub 2004 Jul 11.)
Librairies were normalized on the basis of technical replicas and estimated in transcripts per million (TPM). Only signatures with more thatn 3TPM (significant) and being present in at least two technical replicas (reliable) were  considered.
Supplementary files contain abundance estimation in transcripts per million (TPM).

organism: Arabidopsis thaliana

source_name: ovules

extract_protocol:
Fully differentaited and unpollinated ovules were collected using a micro-aspiration system reported in Sanchez-Leon et al., 2012
The protocol is decribed in detail in Meyers et al (Nature Biotechnol. 2004 Aug;22(8):1006-11. Epub 2004 Jul 11.)

value: ovules

tag: developmental stage

value: fully differentiated and unpollinated ovules

tag: genotype

value: spl mutant in Columbia-0


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 80 Cy5 0

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

description: The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-3

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: Continuous anaerobically grown cultures in Evans medium, prior to CORM-3 addition

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

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

tag: strain

value: Wild type strain MG1655

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min


title: wild-type ovules

description: library strategy: MPSS

value: wild-type Columbia-0


title: Aviandiv_101_72M

source_name: UCD001 reference


title: Tympano-jugular paraganglioma case 2

description: replicate 1

source_name: Tumor specimen (2PTJ) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: Head and Neck paraganglioma


title: Broiler2_37759653

value: female


title: Broiler2_37649056


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 40 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min


title: Blood of tympano-jugular paraganglioma case 4

description: replicate 1

source_name: Blood sample (4B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: tympano-jugular paraganglioma

value: blood


description: replicate 1

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <700 in more than 1 group were excluded. Data were analyzed with Genome Studio Software (Differential Expression Analysis with Mann-Whitney error model plus False Discovery Rate, FDR). *SH-SY5Y cells replicates were used as quality controls and excluded from the main analysis after normalization and quality check.

source_name: Tumor specimen (33PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

extract_protocol: Total RNA was extracted using the Qiagen miRNeay Kit, following manufacturer's instructions. Quality control was performed with Biorad Experion.

value: Tympanic paraganglioma

value: Paraganglioma Tumor Specimen


title: Tympanic paraganglioma case 3

description: replicate 1

source_name: Tumor specimen (3PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 10 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min


title: Blood of carotid body paraganglioma case 7

description: replicate 1

source_name: Blood sample (7B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy

value: carotid body paraganglioma


title: Blood of tympano-jugular paraganglioma case 6

description: replicate 1

source_name: Blood sample (6B) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy


title: Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 20 Cy5 0

source_name: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min


title: Tympanic paraganglioma case 33 - sample 2

description: biological replicate 2 (Second Primary Tumor of Patient 33)


title: Blood of vagal (5PV) and carotid body (5PC) multiple paragangliomas case 5

description: replicate 1

source_name: Blood sample (5B) from multiple paragangliomas patient of Gruppo Otologico clinic, Piacenza, Italy


title: Tympanic paraganglioma case 32

description: replicate 1

source_name: Tumor specimen (32PT) from paraganglioma patient of Gruppo Otologico clinic, Piacenza, Italy