title: Male chicken BC2 n°4145  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

value: Total liver RNA pool obtained from the 48 Male broiler chickens	(sire BC1 n°1940)


title: I1_W

status: Public on Dec 21 2014

type: genomic

city: Singapore

first: Gourvendu

last: Saxena

state: Singapore (General)

address: #05-02, 28 Medical Drive

department: The Singapore Centre on Environmental Life Sciences Engineering

country: Singapore

institute: National University of Singapore

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files were converted to CELa files and then processed using proprietary software (PhyCA).

label: biotin

molecule: genomic DNA

organism: mixed sample

source_name: Surface water from concrete paved waterways

label_protocol: TDT enzyme (Promega; Madison, WI) and GeneChip Labeling Reagent (Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol:
Genomic DNA was extracted from the about 5gm (wet weight) of sediment and 1.2L of water samples immediately after the samples were brought to the lab. Sediments were dewatered and DNA was extracted by a combination of mechanical, chemical and thermal lysis and chloroform-isoamyl alcohol purification using protocol from Zhou et al., 1996 (1). Water samples were filtered through sterile Millipore 0.22µm membrane filter (Thermo Fisher Scientific Inc.) to collect the biomass, followed by the DNA extraction protocol similar to the DNA extraction protocol for sediment samples. Humic substances were removed using OneStep™ PCR Inhibitor Removal Kit from Zymo Research Corporation (USA). The DNA quality and quantity was measured with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany) before loading onto microarrays.
amplification protocol: 0.5 - 1 ng template was used in each of 8 PCR tubes (8 different annealing temperatures were used). 300 nM primers (27F and 1492R for 16S rRNA amplicons), 200 uM each dNTP, 1 ug/uL BSA, and 1.25 U ExTaq (Takara) enzyme were used in the amplifications (95C for 3 min., 30 cycles of 95 (30 sec) ,48 - 58 C annealing temp. (30 sec), 72 C (2 min), followed by 72 C for 10 min., hold at 4 C).

tag: phase

value: Water

tag: land-use type

value: Industrial

tag: land-use region


title: R12_W

value: Residential


title: I5_W


title: O_sativa_japonica_nipponbare_4Binoculated_rep2

status: Public on Dec 22 2014

type: RNA

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

country: France

institute: Université de Lyon

description: This sample is the second replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum lipoferum 4B

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

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

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185)
Intensity values were summarized using median polish algorithm. The median value was used for the replicate method.

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Oriza sativa japonica cultivar Nipponbare inoculated with strain 4B

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

growth_protocol: Before inoculation, Azospirillum cells were grown overnight in Nfbm medium (Vial et al. J. Bacteriol. 108:5364-75). Bacterial cells were harvested in the late-exponential phase (at OD580 around 1.2), centrifuged and resuspended in a defined volume of 0.8% NaCl to obtain 2 x109 cells mL-1. Then, 109 cells were mixed with 50 ml plant agar (8 g l-1) and introduced into 120 × 120 × 17 mm square plates. Rice seed sterilization was performed as previously described by Drogue et al. 2014 (FEMS Microbiol. Ecol.). Four plant were added in each square plate. All the plates were incubated vertically, for 7 d in a growth chamber (MLR350, SANYO, UK) with a photoperiod of 16 h at 28°C (light 150 μE m-2 s-1), and 8 h at 22°C in the dark.

extract_protocol: For each experiment, 30 plant root systems were pooled and frozen using liquid nitrogen. Root cell lysis was performed by grinding root systems with a mortar and pestle under liquid nitrogen. Total RNA was isolated using the TRIzol method (Invitrogen, Carlsbad, CA, USA). RNA samples were purified using RNeasy plant mini kit (Qiagen, Courtaboeuf, France) according to the manufacturer’s protocol. RNA integrity was assessed using Agilent RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and the Agilent 2100 Bioanalyzer (Agilent Technologies) device. In order to increase mRNA representation in RNA samples, total RNA were digested with mRNA ONLYTM Procaryotic mRNA isolation kit (Epicentre Biotechnologies, Madison, WI, USA) according to the provided protocol.  The microarray cDNA (three independent samples per condition) was synthesized with the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen), using a mix (1:1) of random primers (Promega Corporation, Madison, WI, USA) and Oligo-dT(15) primers (Promega).

tag: cultivar

value: Nipponbare

tag: tissue

value: root

tag: pathogen

value: Azospirillum lipoferum strain 4B

tag: days post inoculation


title: O_sativa_japonica_nipponbare_noninoculated_rep2

description: This sample is the second replicate of non-inoculated roots of Oriza sativa japonica cv. Nipponbare

source_name: Oriza sativa japonica cultivar Nipponbare non inoculated


title: O_sativa_japonica_nipponbare_noninoculated_rep3

description: This sample is the third replicate of non-inoculated roots of Oriza sativa japonica cv. Nipponbare


title: R9_S

source_name: Surface sediment layer from concrete paved waterways

value: Sediments


title: R10_S


title: I5_S


title: R8_S


title: R6_S


title: R1_S


title: I1_S


title: O_sativa_japonica_nipponbare_noninoculated_rep1

description: This sample is the first replicate of non-inoculated roots of Oriza sativa japonica cv. Nipponbare


title: O_sativa_japonica_nipponbare_4Binoculated_rep1

description: This sample is the first replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum lipoferum 4B


title: B6 d25 Mtb lung e1 vs. 129S2 d25 Mtb lung e1

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: 1st experiment

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

organism: Mus musculus

source_name: lung

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: TB-resistant C57BL/6 (Charles River) or -susceptible 129S2 mice (129SvPas (22), aged 8-12 weeks and housed under SPF conditions at the Max Planck Institute for Infection Biology (Berlin, Germany). M.tuberculosis H37Rv were grown to mid-log phase in Middlebrook 7H9 broth (BD Biosciences) supplemented with 10% ADC enrichment (BD Biosciences), 0.05% glycerol and Tween 80.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Mice were aerosol-infected with 100–200 colony forming units (CFU)/mouse Mtb (strain H37Rv) using a Glas-Col inhalation system. RNA from five pooled lung homogenates were prepared as previously described (Dorhoi et al., The adaptor molecule card9 is essential for tuberculosis control. The Journal of experimental medicine 2010;207:777-792)

tag: strain

tag: time point

value: day 25 post infection

tag: infection

value: M. tuberculosis strain H37Rv


title: R12_S

hyb_protocol: Please refer to the He et al., 2010. The labeled target was re-suspended in 120 µl hybridization solution containing 50% formamide, 3 x SSC, 10 µg of unlabeled herring sperm DNA (Promega, Madison, WI), and 0.1% SDS, and the mix was denatured at 95°C for 5 min and kept at 50°C until it was deposited directly onto a microarray.  Hybridizations were performed with a TECAN Hybridization Station HS4800 Pro (TECAN, US) according to the manufacturer’s recommended method. This equipment allows up to 48 hybridizations at one time, and well reproducible results were obtained.

scan_protocol: Please refer to the He et al., 2010. After washing and drying, the microarray was scanned by ScanArray Express Microarray Scanner (Perkin Elmer, Boston, MA) at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%. The ImaGene version 6.0 (Biodiscovery, El Segundo, CA) was then used to determine the intensity of each spot, and identify poor-quality spots.

data_processing: Please refer to the He et al., 2010. Raw data from ImaGene were submitted to Microarray Data Manager at http://ieg.ou.edu/microarray/ and analyzed using the data analysis pipeline with the following major steps: (i) The spots flagged as 1 or 3 by Imagene and with a signal to noise ratio (SNR) less than 2.0 (He and Zhou, 2008 (4)) were removed as poor-quality spots; (ii) After removing the bad spots, normalized intensity of each spot was calculated by dividing the signal intensity of each spot by the mean intensity of the microarray; (iii) At least 0.34 time of the final positive spots (probes), or a minimum of two spots was required for each gene.

organism: environmental samples

label_protocol: Please refer to He et al., 2010 (2), for detailed protocol. Briefly, 500 ng of genomic DNA from sediment and water samples, or about 3.0 µg of amplified DNA were labeled with the fluorescent dye Cy-5 using random priming method (Wu et al., 2006 (3)). Later, the whole amplified products were mixed with 20 μL random primers, denatured at 99.9 °C for 5 min, and then immediately chilled on ice. Following denaturation, the labeling master mix containing 2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL Cy-5 dUTP (Amersham, Piscataway, NJ), 80 U of the large Klenow fragment (Invitrogen, Carlsbad, CA), and 2.5 μL water were added and then incubated at 37°C for 3 hours, followed by heating at 95 °C for 3 min. Labeled DNA was purified using the QIA quick purification kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and then dried down in a SpeedVac (ThermoSavant, Milford, MA) at 45 °C for 45 min.

extract_protocol: Genomic DNA was extracted from the about 5gm (wet weight) of sediment and 1.2L of water samples immediately after the samples were brought to the lab. Sediments were dewatered and DNA was extracted by a combination of mechanical, chemical and thermal lysis and chloroform-isoamyl alcohol purification using protocol from Zhou et al., 1996 (1). Water samples were filtered through sterile Millipore 0.22µm membrane filter (Thermo Fisher Scientific Inc.) to collect the biomass, followed by the DNA extraction protocol similar to the DNA extraction protocol for sediment samples. Humic substances were removed using OneStep™ PCR Inhibitor Removal Kit from Zymo Research Corporation (USA). The DNA quality and quantity was measured with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany) before loading onto microarrays.


title: R6_S


title: R10_S


title: B6 d14 Mtb lung e1 vs. 129S2 d14 Mtb lung e1

description: 1st experiment

value: day 14 post infection


title: R6_W


title: I6_S


title: R11_S


title: 129S2 d14 Mtb lung e1 vs. B6 d14 Mtb lung e1

description: 1st experiment


title: 129S2 d7 Mtb lung e1 vs. B6 d7 Mtb lung e1

description: 1st experiment

value: day 7 post infection


title: B6 d7 Mtb lung e1 vs. 129S2 d7 Mtb lung e1

description: 1st experiment


title: I2_S


title: 129S2 d25 Mtb lung e1 vs. B6 d25 Mtb lung e1

description: 1st experiment


title: Untransduced 2

city: Manchester

first: Kiran

last: Batta

address: Withington

country: United Kingdom

institute: CRUK Manchester Institute

description: RNA expression value

hyb_protocol: Samples were hybridized with GeneChip mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the CRUK Manchester Core Facility.

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

data_processing: Raw data were processed with the Exon Array Computational Tool (Rma) for background correction and normalization. A gene-level_analysis is available on the series level.

label: Biotin

source_name: Fibroblasts

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the Terminal Labeling Kit (Affymetrix).

growth_protocol: Fibroblasts were transduced with hematopoietic TFs ERG, GATA2, LMO2, RUNX1c and SCL. RNA was isolated from untreated fibroblasts, CDH5 positives sorted after 8 days of transduction and c-KIT positive cells sorted after 12 days of transduction.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: genotype

value: wild-type


title: D12 C-KIT+ 1

description: RNA expression value

source_name: Reprogrammed Fibroblasts

tag: days of transduction


title: D8 CDH5+ 1

description: RNA expression value


title: R1_W


title: R0_S


title: R4_W


title: 129S2 d14 Mtb lung e3 vs. B6 d14 Mtb lung e3

description: 3rd experiment


title: R10_W


title: B6 d14 Mtb lung e3 vs. 129S2 d14 Mtb lung e3

description: 3rd experiment


title: D8 CDH5+ 2

description: RNA expression value


title: Rice seedlings roots_long Cr(VI) exposures Replicate 1

city: Tainan

first: Tsai-Lien

last: Huang

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 1 of 3. Rice seedling roots with or without 50 μM Cr(VI) during long (24 h) exposures

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA)

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 50 μM Cr(VI) during long (24 h) exposures

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after Cr(VI) treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.

growth_protocol: 6-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Control and rice seedlings were exposed to to 50 μM Cr(VI) during short (pooled from 1- and 3-h treatments) exposures or long (24 h) exposures

value: Roots of rice seedlings

value: Oryza sativa L. cv. TN-67

tag: age

value: 6 day

source_name: Rice seedlings roots were exposed to water


title: Rice seedlings roots_short Cr(VI) exposures Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 50 μM Cr(VI) short (pooled from 1- and 3-h treatments) exposures

source_name: Roots of rice seedlings were exposed to 50 μM Cr(VI) during short (pooled from 1- and 3-h treatments) exposures


title: 129S2 d25 Mtb lung e2 vs. B6 d25 Mtb lung e2

description: 2nd experiment


title: 129S2 d7 Mtb lung e3 vs. B6 d7 Mtb lung e3

description: 3rd experiment


title: HT29 PLX Day3 rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays for the respective cell type Colo-205 and the HT29 were normalized together using the quantile normalization algorithm without background subtraction.

organism: Homo sapiens

source_name: HT29 cell line

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

growth_protocol: DMEM medium containing 10% FCS was used to cultivate HT29 cells. Colo-205 cells were cultured in RPMI 1640 with 10% FCS. Matrigel 3D cultures were set-up as described for MCF-10A cells (Brummer et al., J Biol Chem. 2006), except that the aforementioned cell culture medium was used in place of the MCF-10A medium.

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

treatment_protocol: Cells were seeded into matrigel and treatment with DMSO or 3 µM PLX4720 (Santa Cruz Biotechnology, CA, USA) was started at day 5. Medium was changed every 2-3 days. Cells were extracted from matrigel after the indicated period of time using the Becton Dickinson (BD) cell recovery solution and RNA was extracted as indicated.

tag: treatment

tag: time

tag: cell line

value: Colon cancer cell line

tag: array id


title: Rice seedlings roots_long Cr(VI) exposures Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 50 μM Cr(VI) during long (24 h) exposures


title: R2_W

tag: phase


title: HT29 DMSO Day8 rep2

value: DMSO


title: HT29 DMSO Day3 rep2


title: Rice seedlings roots_long Cr(VI) exposures Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 50 μM Cr(VI) during long (24 h) exposures


title: HT29 PLX Day8 rep2


title: I1_W

value: Water

tag: land-use type


title: HT29 PLX Day1 rep2


title: R12_W

tag: land-use region


title: B6 d25 Mtb lung e2 vs. 129S2 d25 Mtb lung e2

description: 2nd experiment


title: Rice seedlings roots_short Cr(VI) exposures Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 50 μM Cr(VI) short (pooled from 1- and 3-h treatments) exposures

tag: cultivar


title: I2_W

value: Industrial


title: B6 d14 Mtb lung e2 vs. 129S2 d14 Mtb lung e2

description: 2nd experiment


title: HT29 DMSO Day8 rep1

tag: tissue


title: HT29 DMSO Day1 rep2


title: Untransduced 1

description: RNA expression value


title: HT29 PLX Day1 rep1


title: HT29 DMSO Day3 rep1


title: 129S2 d14 Mtb lung e2 vs. B6 d14 Mtb lung e2

description: 2nd experiment


title: 129S2 d7 Mtb lung e2 vs. B6 d7 Mtb lung e2

description: 2nd experiment


title: HT29 PLX Day8 rep1


title: Colo-205 PLX Day 10

source_name: Colo-205 cell line


title: I6_W


title: I4_S


title: HT29 PLX Day3 rep1


title: I2_S


title: B6 d7 Mtb lung e2 vs. 129S2 d7 Mtb lung e2

description: 2nd experiment


title: Colo-205 DMSO Day 10


title: D12 C-KIT+ 2

description: RNA expression value


title: Rice seedlings roots_short Cr(VI) exposures Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 50 μM Cr(VI) short (pooled from 1- and 3-h treatments) exposures


title: 129S2 d25 Mtb lung e3 vs. B6 d25 Mtb lung e3

description: 3rd experiment


title: HT29 DMSO Day1 rep1


title: Colo-205 PLX Day 3


title: Colo-205 PLX Day 1


title: Colo-205 DMSO Day 3


title: B6 d25 Mtb lung e3 vs. 129S2 d25 Mtb lung e3

description: 3rd experiment


title: B6 d7 Mtb lung e3 vs. 129S2 d7 Mtb lung e3

description: 3rd experiment


title: R3_W

value: Residential


title: 8 h after 5 nM BoNT/A  Rep3

status: Public on Dec 20 2014

city: Osong

first: Na-Ri

last: Shin

state: Chungbuk

address: 187 Osongsangmyung2-ro

department: High-risk Pathogen Research

country: South Korea

institute: Korea Centers for Disease Control and Prevention, Korea National Institute of Health

description:
replicate 3
B7-8

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer(Illumina BeadStudio (Gene Expression Module). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test group and control group was carried out using LPE test and fold-change. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: RAW264.7 cell line

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: The murine alveolar monocyte/macrophage cell line RAW264.7 (ATCC, Manassas, VA) was grown in complete Dulbecco’s modified Eagle minimal essential medium (DMEM) (Gibco, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine (Gibco), penicillin (100 units/ml), and streptomycin (0.1 mg/ml) to 90% confluence in 75-cm2 cell culture flasks (Nunc, Roskilde, Denmark). Cultures were maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: RAW264.7 cells (5.0 × 105 cells/ml) were plated in 21.5-cm2 dishes (Nunc) in supplemented DMEM. The next day, the medium was replaced with fresh medium containing BoNT/A (1 or 5 nM). After incubation for 0, 2, 4, 6, 8, or 10 h, cells were collected for RNA isolation.

value: 8 h after 5 nM BoNT/A


title: 10 h after 5 nM BoNT/A  Rep3

description:
replicate 3
B7-10

value: 10 h after 5 nM BoNT/A


title: 10 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-10

value: 10 h after 1 nM BoNT/A


title: 10 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-10


title: 10 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-10


title: 10 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-10


title: 8 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-8

value: 8 h after 1 nM BoNT/A


title: 6 h after 5 nM BoNT/A  Rep3

description:
replicate 3
B7-6

value: 6 h after 5 nM BoNT/A


title: 8 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-8


title: 8 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-8


title: 6 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-6

value: 6 h after 1 nM BoNT/A


title: R5_W


title: 8 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-8


title: 6 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-6


title: Colo-205 DMSO Day 1


title: 4 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-4

value: 4 h after 5 nM BoNT/A


title: 4 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-4

value: 4 h after 1 nM BoNT/A


title: 2 h after 5 nM BoNT/A  Rep3

description:
replicate 3
B7-2

value: 2 h after 5 nM BoNT/A


title: 8 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-8


title: 4 h after 5 nM BoNT/A  Rep3

description:
replicate 3
B7-4


title: 6 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-6


title: 6 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-6


title: 4 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-4


title: 4 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-4


title: 6 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-6


title: 2 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-2


title: 4 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-4


title: 10 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-10


title: 2 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-2


title: 2 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-2

value: 2 h after 1 nM BoNT/A


title: 2 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-2


title: 2 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-2


title: 0 h after 5 nM BoNT/A  Rep2

description:
replicate 2
B6-0

value: 0 h after 5 nM BoNT/A


title: 0 h after 1 nM BoNT/A  Rep3

description:
replicate 3
B4-0

value: 0 h after 1 nM BoNT/A


title: 0 h after 5 nM BoNT/A  Rep3

description:
replicate 3
B7-0


title: LP CTX, biological rep1

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

country: USA

institute: Oregon National Primate Research Center - OHSU

description: Gene expression data from cortex of agonadal late pubertal (31 month-old) rhesus monkeys (orchidectomized 16-17 month) .

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten mg of target is  hybridized with the GeneChip (insert array name) array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: The  distribution of fluorescent material on the processed array is determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade. Image inspection is performed manually immediately B42following each scan. All array scanning and data processing on the Affymetrix system is performed with GeneChip Operating System (GCOS) software.

data_processing: The probe-level Cel file is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total Signal for probe sets for BioB, BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. Using MAS 5.0, array data is globally scaled to a uniform, average target intensity for all assays prior to further analysis.

organism: Macaca mulatta

source_name: CTX tissue from late pubertal rhesus monkey

label_protocol: Messenger RNA is amplified and labeled from 2 mg of total RNA in two steps. In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix). In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix.). Following  removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: The Allprep DNA/RNA mini kit (Qiagen) was used to extract DNA, total mRNA and proteins following the manufacturer recommendations. Briefly, the monkey tissue samples were homogenized in RLT buffer (provided with the kit). Lysates were then passed through Qiagen columns to recover first DNA and then RNA. Total mRNA quantity was measured by spectrophotometric trace (Agilent Technologies, Palo Alto, CA) and RNA integrity was verified by Agilent Bioanalyzer.

treatment_protocol: Ten male Rhesus monkeys were orchidectomized at 16-17 months of age, right before the onset of puberty and were housed at the Primate Research Laboratory (Primate Core, Center for Research in Reproductive Physiology, University of Pittsburgh). One group of 4 animals was euthanized at 19 months of age (juvenile group), another 4 animals were euthanized in the early phase of puberty (24-30 months) determined by LH and FSH dosage (early pubertal group) and the remaining 2 animals were euthanized at 31 months of age (late pubertal group). Tissue samples (cortex, basal hypothalamus) from the juvenile group were dissected and snap-frozen on dry ice.

tag: gender

value: MALE

tag: Stage

value: LATE PUBERTAL (LP)

value: CORTEX (CTX)


title: R99 grown in CM9+Transferrin medium rep1

city: Burjassot

first: David

last: Pajuelo Gámez

state: Valencia

address: Doctor Moliner, 50.

department: Microbiology and Ecology

country: Spain

institute: University of Valencia

description: Gene expression wild-type strain in CM9+Transferrin medium

hyb_protocol: 1.65 μg of cRNA-labled of each sample was used for the hybridization to custom european eel array during 17h at 65ºC following the instructions of Agilent’s GE Hybridization Kit.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. Txt files generated were imported into the Gene GeneSpring software GX 12.5.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples.

organism: Vibrio vulnificus

source_name: RNA from R99 grown in CM9+Transferrin medium

label_protocol: RNA samples were labelled with a single dye, Cy3. Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling were performed according to agilent Quick Amp Labelling kit instructions.

growth_protocol: Bacteria were grown at 28ºC with shaking (180 rpm) overnight. Cultures were inoculated with an overnight starter culture in CM9 at a ratio of 1:100 (vol/vol) in a final volume of 5 ml.

extract_protocol: RNA was purified by adding 0,5 ml of TRI Reagent (Sigma-Aldrich) and processed following the manufacturer’s instructions. Possible contaminating DNA in RNA solutions were eliminated using RNeasy MinElute Cleanup kit (Qiagen) with a DNase I (Qiagen) digestion at room temperature for 15 min according to manufacturer’s protocol.

treatment_protocol: Iron (ferric chloride) was added to the medium to create an excess of iron in culture media, while transferrin (a natural iron chelator) was added to create iron restricted conditions. Samples were taken, for each strain/condition, at the mid-log phase of growth (wild-type, 6h; Fur mutant, 6h; wild-type+iron, 5h; wild-type-iron,9h).

tag: strain

tag: sample point (mid-log phase of growth)


title: R99 grown in CM9+Transferrin medium rep2


title: R99 grown in CM9+Transferrin medium rep3


title: EP CTX, biological rep 1

description: Gene expression data from cortex of agonadal early pubertal (24 month-old) rhesus monkeys (orchidectomized 16-17 month) .

source_name: CTX tissue from early pubertal rhesus monkey

value: EARLY PUBERTAL (EP)


title: LJ CTX, biological rep 4

description: Gene expression data from cortex of agonadal late juvenile (19 month-old) rhesus monkeys (orchidectomized 16-17 month) .

source_name: CTX tissue from late juvenile rhesus monkey

value: LATE JUVENILE (LJ)


title: LP CTX, biological rep2


title: LJ CTX, biological rep 3


title: Fur mutant grown in CM9 medium rep3

description: Gene expression Fur mutant strain in CM9 medium

source_name: RNA from Fur mutant grown in CM9 medium

value: Fur mutant


title: EP CTX, biological rep 2

description: Gene expression data from cortex of agonadal early pubertal (30 month-old) rhesus monkeys (orchidectomized 16-17 month) .


title: 0 h after 5 nM BoNT/A  Rep1

description:
replicate 1
B5-0


title: EP CTX, biological rep 3


title: 0 h after 1 nM BoNT/A  Rep2

description:
replicate 2
B3-0


title: LP MBH, biological rep1

description: Gene expression data from mediobasal hypothalamus of agonadal late pubertal (31 month-old) rhesus monkeys (orchidectomized 16-17 month) .

source_name: MBH tissue from late pubertal rhesus monkey

value: MEDIOBASAL HYPOTHALAMUS (MBH)


title: EP CTX, biological rep 4


title: EP MBH, biological rep 4

description: Gene expression data from mediobasal hypothalamus of agonadal early pubertal (24 month-old) rhesus monkeys (orchidectomized 16-17 month) .

source_name: MBH tissue from early pubertal rhesus monkey


title: LP MBH, biological rep2


title: R99 grown in CM9+Iron medium rep1

description: Gene expression wild-type strain in CM9+Iron medium

source_name: RNA from R99 grown in CM9+Iron medium


title: R99 grown in CM9+Iron medium rep2


title: R99 grown in CM9+Iron medium rep3


title: LJ CTX, biological rep 2


title: LJ CTX, biological rep 1


title: Fur mutant grown in CM9 medium rep1


title: Fur mutant grown in CM9 medium rep2


title: R99 grown in CM9 medium rep3

description: Gene expression wild-type strain in CM9 medium

source_name: RNA from R99 grown in CM9 medium


title: EP MBH, biological rep 3

description: Gene expression data from mediobasal hypothalamus of agonadal early pubertal (30 month-old) rhesus monkeys (orchidectomized 16-17 month) .


title: I5_S

source_name: Surface sediment layer from concrete paved waterways

value: Sediments

value: Industrial


title: EP MBH, biological rep 2


title: EP MBH, biological rep 1


title: LJ MBH, biological rep 2

description: Gene expression data from mediobasal hypothalamus of agonadal late juvenile (19 month-old) rhesus monkeys (orchidectomized 16-17 month) .

source_name: MBH tissue from late juvenile rhesus monkey


title: LJ MBH, biological rep 4


title: C6cells_AngII+Los6h_rep1

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

description: Gene expression of C6 glioma cells submitted to Ang II and Losartan treatment at 6 hours interval

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G2519F-028282) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 Feb07 and Grid: 028282_D_F_20100528) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 6 hours, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA was isolated from samples at 3 and 6 hours intervals using Trizol reagent (Life Technologies, USA) and purified using RNeasy Spin Columns (Qiagen, USA). RNA quantity was determined using a Nanovue spectrophotometer (GE Healthcare, USA). The RNA quality was performed using a 2100 Bioanalyzer with an RNA 6000 Nano kit and Ladder (Agilent Technologies, USA), according to the manufacturer’s instructions.

treatment_protocol: C6 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 Units/ml penicillin and 100 µg/ml streptomycin. Cells were seeded in cell culture dishes and incubated at 37°C/ 5% CO2 until becoming confluent. Then, these cells were pre-treated (30 minutes) with either AT1 receptor antagonist (Losartan: 10-5M) or AT2 receptor antagonist (PD123319: 10-5M) followed by Ang II treatment (10-7 M) according to the treatment scheme: Group 1 – control; Group 2 – cells only treated with Ang II; Group 3 – cells pre-treated (30 minutes) with Losartan and then treated with Ang II; Group 4 – cells pre-treated (30 minutes) with PD123319 and then treated with Ang II.

tag: ang ii treatment (10-7m)

value: Ang II

tag: ang ii receptors antagonists (10-5m)

value: Losartan (AT1 antagonist)

tag: time interval

value: 6 hours


title: PHH HCV 1a

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

description: Gene expression data from PHH cells treated with 1a virus after 8hours

hyb_protocol: Following fragmentation, 3.5mg of fragmented and labeled ss-DNA were hybridized for 16h at 45C with 60rpm rotation on GeneChip® Human Gene 2.0 ST Array per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).   GeneChips were washed and stained in the Affymetrix Fluidics Station 450 per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000

data_processing: Partek Genomics Suite v6.6 was used to import and process these data using quantile normalization and RMA background correction adjusting for GC content.

source_name: Primary human hepatocytes_HCV_1a

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix)

growth_protocol: Cells were plated at 30,000 cells per well in a 24 well plate along with murine embryonic fibroblasts as a co-culture in hepatocyte culture medium (Hepregen proprietary hepatocyte culture medium). Treatment was performed on day 7 of co-culture for 8 hours.

extract_protocol: Extraction of cellular RNA was performed using QIAgen RNeasy Kit according to manufacturer's protocol.

treatment_protocol: Cells were treated with 1 µg HCV genotype 1a or 3a viral RNA (vRNA) for 8 hours. Mirus transfection kit (Trans-it mRNA transfection kit) was used to introduce the vRNA into the cellular cytoplasm.

tag: cell type

value: Primary human hepatocytes


title: R99 grown in CM9 medium rep1


title: C6cells_AngII+PD6h_rep1

description: Gene expression of C6 glioma cells submitted to Ang II and PD123319 treatment at 6 hours interval

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 6 hours, replicate 1

value: PD123319 (AT2 antagonist)


title: C6cells_AngII6h_rep4

description: Gene expression of C6 glioma cells submitted to Ang II treatment at 6 hours interval

source_name: C6 glioma cells, Angiotensin II, 6 hours, replicate 4


title: C6cells_AngII+PD6h_rep4

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 6 hours, replicate 4


title: C6cells_AngII+Los6h_rep3

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 6 hours, replicate 3


title: R99 grown in CM9 medium rep2


title: C6cells_AngII+PD6h_rep2

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 6 hours, replicate 2


title: LJ MBH, biological rep 1


title: C6cells_AngII6h_rep1

source_name: C6 glioma cells, Angiotensin II, 6 hours, replicate 1


title: LJ MBH, biological rep 3


title: C6cells_control6h_rep4

description: Gene expression of C6 glioma cells submitted to any treatment at 6 hours interval

source_name: C6 glioma cells, Control, 6 hours, replicate 4


title: C6cells_AngII+Los6h_rep2

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 6 hours, replicate 2


title: PHH HCV 3a

description: Gene expression data from PHH cells treated with 3a virus after 8hours

source_name: Primary human hepatocytes_HCV_3a


title: C6cells_AngII+PD6h_rep3

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 6 hours, replicate 3


title: C6cells_AngII6h_rep3

source_name: C6 glioma cells, Angiotensin II, 6 hours, replicate 3


title: C6cells_AngII+Los6h_rep4

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 6 hours, replicate 4


title: PHH mock transfection

description: Gene expression data from PHH cells treated with mock virus after 8hours


title: C6cells_AngII6h_rep2

source_name: C6 glioma cells, Angiotensin II, 6 hours, replicate 2


title: C6cells_control6h_rep3

source_name: C6 glioma cells, Control, 6 hours, replicate 3


title: DA-PVG d7 344

city: Kaohsiung

first: I-Hsuan

middle: Ann

last: Chen

address: 123 Ta-Pei Rd., Niao-Sung

institute: CGMH

description: miRNA expression in DA-PVG OLT

hyb_protocol: hybridization buffer (Agilent Technologies) was added to the labeled mixture to a final volume of 45ul. The mixture were heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45ul sample was hybridized onto an Agilent Rat miRNA Microarray Sanger miRBase 15.0 at 55 °C for 20 h.

scan_protocol: Slides were scanned on an Agilent microarray scanner (Agilent Technologies, model G2505C) at 100% and 5% sensitivity settings.

data_processing:
Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis. comparison across arrays using GeneSpring 7.3.1 (Agilent Technologies) default normalization settings: data transformation was set at measurements <0.01 to 0.01 (per chip, normalized to the 75th percentile; and per gene, normalized to the median).
data transformation was set at measurements <0.01 to 0.01 (per chip, normalized to the 75th percentile; and per gene, normalized to the median)

source_name: DA-PVG OLT, day 7

label_protocol: 100 ng of total RNAs were dephosphorylated and labeled with pCp-Cy3 by Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, microRNA Spike-In Apply).

extract_protocol: Total RNA will be extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified will be quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).

tag: olt model

value: natural tolerance model with long-term (>60 days)

tag: tissue donor strain

value: DA

tag: recipient strain

value: PVG

value: liver


title: DA-PVG d7 1779

description: miRNA expression in DA-PVG OLT


title: DA-PVG d7 594

description: miRNA expression in DA-PVG OLT


title: DA-PVG d6 302

description: miRNA expression in DA-PVG OLT

source_name: DA-PVG OLT, day 6


title: DA-LEW d7(no CsA)1772

description: miRNA expression in DA-Lew OLT

source_name: DA-LEW OLT, day 7

value: AR model with short-term (<14 days)

value: LEW


title: C6cells_control6h_rep1

source_name: C6 glioma cells, Control, 6 hours, replicate 1


title: C6cells_control6h_rep2

source_name: C6 glioma cells, Control, 6 hours, replicate 2


title: 1981

description: miRNA expression in Naïve DA

source_name: Naïve DA


title: Naive DA 1973(99.8.25)

description: miRNA expression in Naïve DA


title: DA-LEW d7(no CsA)1777

description: miRNA expression in DA-Lew OLT


title: 1979

description: miRNA expression in Naïve DA


title: C6cells_AngII+PD3h_rep1

description: Gene expression of C6 glioma cells submitted to Ang II and PD123319 treatment at 3 hours interval

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 3 hours, replicate 1

value: 3 hours


title: C6cells_AngII+PD3h_rep3

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 3 hours, replicate 3


title: C6cells_AngII+PD3h_rep2

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 3 hours, replicate 2


title: C6cells_AngII+PD3h_rep4

source_name: C6 glioma cells, Angiotensin II + PD123319 (AT2 antagonist), 3 hours, replicate 4


title: Sham+aPC

city: Charlotte

first: Cathy

last: Moore

address: 1000 Blythe Blvd

institute: Carolinas Medical Center

description: Sample 2 (995)

hyb_protocol: An Enzyme Linked Oligosorbent Assay (ELOSA) QC was performed to verify labeling prior to array hybridization. Hybridization, washing, staining, and scanning was performed using Affymetrix GeneChip system instrument (Affymetrix).

scan_protocol: Affymetrix GeneChip Command Console Software (AGCC) version 3.0.1 was used to analyze microarry image data and to computer intensity values.

data_processing: Affymetrix.CEL files containing raw, probe-level signal intensities were analyzed using Partek Genomics Suite (Partek). Robust multichip averaging (RMA) was used for background correction, quantile normalization and probeset summariuzation with median polish.

source_name: sham surgery+aPC (1mg/kg)

label_protocol: RNA was Poly (A) tailed and ligated to biotinylated signal molecules using the FlasTag Biotin RNA labeling Kit (Genisphere).

extract_protocol: Twelve hours after final treatment, animals were euthanized by exsanguination and liver samples collected. Liver samples were flash frozen in liquid nitrogen and stored (-80ºC). Total RNA was purified from liver tissue using the miRNeasy Mini Kit according to manufacturer protocol (Qiagen).

treatment_protocol: Male Sprague-Dawley rats underwent sham surgery or cecal ligation and puncture (CLP). Twenty-four later, animals were randomized and treated with aPC (1mg/kg) or vehicle (0.9% (w/v) saline) via an indwelling venous catheter at 12 hour intervals for 24 hours.

value: Sprague-Dawley

value: male


title: CLP+V

description: Sample 3 (624)

source_name: cecal ligation and puncture (CLP)+vehicle (0.9% (w/v) saline)


title: DA-LEW d7(no CsA)1770

description: miRNA expression in DA-Lew OLT


title: Sham+V

description: Sample 1 (535)

source_name: sham surgery+vehicle (0.9% (w/v) saline)


title: C6cells_AngII+Los3h_rep4

description: Gene expression of C6 glioma cells submitted to Ang II and Losartan treatment at 3 hours interval

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 3 hours, replicate 4


title: C6cells_AngII+Los3h_rep1

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 3 hours, replicate 1


title: CLP+aPC

description: Sample 4 (026)

source_name: cecal ligation and puncture (CLP)+aPC (1mg/kg)


title: C6cells_AngII+Los3h_rep3

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 3 hours, replicate 3


title: C6cells_AngII3h_rep4

description: Gene expression of C6 glioma cells submitted to Ang II treatment at 3 hours interval

source_name: C6 glioma cells, Angiotensin II, 3 hours, replicate 4


title: C6cells_AngII+Los3h_rep2

source_name: C6 glioma cells, Angiotensin II + Losartan (AT1 antagonist), 3 hours, replicate 2


title: ATH_Col0_2E-pentenal_30min [Agilent]

city: Kobe

first: Yasuo

last: Yamauchi

state: Hyogo

address: Rokkodai 1-1, Nada

country: Japan

institute: Kobe University

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the sample treated with (E)-2-pentenal in this experiment.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana (ecotype Columbia-0) was sown on Jiffy-7 peat pellets (Sakata Seed Co., Yokohama, Japan) and kept at 4°C for 3 days in the dark. Then plants were transferred to the conditions of a 14-h–light (80 µmol photons m–2 s–1)/10-h–dark cycle at 23°C.

extract_protocol: Total RNA was purified by using an RNeasy Plant Mini Kit (Qiagen) from at least 6 plants.The double-strand (ds) cDNA was generated with a modified procedure of the Superscript Choice System (Life Technologies, Carlsbad, CA). Briefly, the 1st strand cDNA was synthesized from 10.0 μg total RNA by 1.0 unit SuperScript II reverse transcriptase (Life Technologies) in the presence of 100 pmoles Oligo dT(20) primer. After 2nd strand synthesis, the template RNA was digested with RNase A, then the synthesized DNA was purified with phenol:chloroform:isoamyl alcohol. The purified DNA was precipitated in ethanol, and the pellet was washed, dried, reconstituted and quantified.

treatment_protocol: Plants were placed in a transparent plastic box (340 cm3, Nippon Genetics, Tokyo, Japan). Volatiles diluted with MeCN to be 1 M  tested (volume of 3 µl) was absorbed into a piece of paper towel attached to the inside of the cover. The cover was immediately set on the box, and the plants were incubated at 25°C under illumination (80 µmol photons m–2 s–1).

tag: ecotype

value: Seedlings


title: 0 h after 1 nM BoNT/A  Rep1

description:
replicate 1
B2-0

source_name: RAW264.7 cell line

tag: cell line

tag: treatment

value: 0 h after 1 nM BoNT/A


title: C6cells_AngII3h_rep3

source_name: C6 glioma cells, Angiotensin II, 3 hours, replicate 3


title: ATH_Col0_MeCN_30min [Agilent]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is control sample used in this experiment.


title: ATH_Col0_3-hepten-2-one_30min [Agilent]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the sample treated with 3-hepten-2-one in this experiment.


title: ATH_Col0_2E-hexenal_30min_rep3 [NimbleGen]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the third of three wild-type biological replicates used in this experiment.

hyb_protocol: The arrays (ATH6_60mer_expr X4) were hybridized with labeled DNA on a NimbleGen Hybridization System at 42°C for 16 h.

scan_protocol: Arrays were washed by NimbleGen wash buffer kit according to the manufacturer's protocols and scanned using an Axon GenePix 4000B scanner at 5 μm resolution.

data_processing: Data extraction, normalization and production of heat map by UPGMA clustering were performed by Subio Platform software (Subio, Kagoshima, Japan), and Microsoft Excel was used to organize and interpret the data.

source_name: Arabidopsis thaliana (ecotype Columbia-0)

label_protocol: cDNA samples were labeled using the random priming method with Cy3-labeled random nonamer as primers and Klenow DNA polymerase at 37°C for 2 h (NimbleGen One-color Labeling Kit, NimbleGen Roche, Madison, WI). The labeled DNA was precipitated in isopropanol, and the pellet was washed, dried, reconstituted and quantified. For each hybridizations, 4 μg of labeled DNA was diluted by NimbleGen sample tracking control kit buffers respectively, and be added with NimbleGen hybridization buffers according to the manufacturer's protocols.

treatment_protocol: Plants were placed in a transparent plastic box (340 cm3, Nippon Genetics, Tokyo, Japan). (E)-2-Hexenal diluted with MeCN to be 1 M  tested (volume of 3 µl) was absorbed into a piece of paper towel attached to the inside of the cover. The cover was immediately set on the box, and the plants were incubated at 25°C under illumination (80 µmol photons m–2 s–1).

value: Wild-type ecotype Columbia-0


title: ATH_Col0_crotonaldehyde_30min [Agilent]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the sample treated with crotonaldehyde in this experiment.


title: GCM_biological rep1

city: Edinburgh

first: Christopher

middle: D

last: Gregory

address: 47 Little France Crescent

institute: University of Edinburgh

hyb_protocol: Labelled cDNA was hybridized to Affymetrix Mouse Gene 1.0 GeneChip arrays as per Affymetrix instructions.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and CEL intensity files as well as Image acquisition of the hybridized chips were generated by the Affymetrix GeneChip Operating System (GCOS) software v1.4.

data_processing: CEL files for all GeneChips were imported into BioConductor and background subtraction and normalization were performed using the Robust Multichip Average (RMA) algorithm in the OneChannelGui package. Due to very low overall fluorescence levels on TAM and GCM chips following normalization, the minimum fluorescence threshold for ‘present’ transcripts (ie basal expression) was exceptionally set at 20. Statistical analysis on ‘present’ transcripts was conducted using LIMMA software, yielding raw p-values for each comparison of interest and the Benjamini and Hochberg procedure was used for multiple testing corrections.

source_name: laser-microdissected tingible-body macrophages from germinal centres of activated lymph nodes

label_protocol: Amplified cDNA was processed for sense-transcript cDNA generation using WT Ovation Exon Module (NuGEN Technologies) and fragmentation/labeling using FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

growth_protocol: Xenograft tumors were generated by s.c. injection of 10 x 106 BL2 cells into 6-12 week-old BALB/c SCID mice. Mice were humanely sacrificed and tumors excised when tumors reached dimensions equivalent to 1.44 cm2. Alternatively, whole spleens were isolated from CSF1R EGFP transgenic BALB/c mice stimulated with two doses of 5 x 108 sheep red blood cells (SRBC). Isolated tissues (tumor or spleen) were immediately snap frozen. All animal procedures and husbandry were performed under a license from the UK Home Office according to regulations described in the Animal (Scientific Procedures) Act 1986.

extract_protocol: Captured cells (1000 cells) were lysed and RNA extracted using the RNeasy Plus Micro Kit (Qiagen). RNA yield and quality was assessed using the RNA6000 Pico Assay on an Agilent Bioanalyzer (Agilent Technologies) and total RNA was amplified and cDNA synthesized for whole gene expression analysis using WT-Ovation Pico RNA Amplification Systems (NuGEN Technologies).

treatment_protocol: Laser-capture microdissection was performed on frozen 10 μm SCID/BL2 tissue sections stained with rapid one-step immunolabeling using anti-CD68 AlexaFluor-488 antibody (Life Technologies) with Protector RNase Inhibitor (4 U/ml, Roche) or splenic germinal centers from CSF1R EGFP transgenic BALB/c mice stimulated with two doses of 5 x 108 sheep red blood cells (SRBC). A PALM MicroBeam system (Palm Microlaser Technologies) was used to cut out tumor-associated CD68+ or germinal center macrophages (1000 cells per tissue).

value: Female

value: CSF1R EGFP transgenic Balb/c

value: spleen

tag: age

value: 6-12 wk old

tag: other

value: immunised with 2 doses sheep red blood cells


title: GCM_biological rep2

tag: tissue


title: C6cells_AngII3h_rep2

source_name: C6 glioma cells, Angiotensin II, 3 hours, replicate 2

value: Ang II


title: GCM_biological rep3

tag: gender


title: C6cells_AngII3h_rep1

source_name: C6 glioma cells, Angiotensin II, 3 hours, replicate 1


title: C6cells_control3h_rep3

description: Gene expression of C6 glioma cells submitted to any treatment at 3 hours interval

source_name: C6 glioma cells, Control, 3 hours, replicate 3


title: TAM_biological rep3

source_name: laser-microdissected tumour-associated macrophage of Burkitt's Lymphoma xenograft model

value: Balb/c SCID

value: tumor

value: Tumor 1.44 cm2


title: ATH_Col0_2E-hexenal_30min_rep1 [NimbleGen]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the first of three wild-type biological replicates used in this experiment.


title: C6cells_control3h_rep4

source_name: C6 glioma cells, Control, 3 hours, replicate 4


title: C6cells_control3h_rep2

source_name: C6 glioma cells, Control, 3 hours, replicate 2


title: C6cells_control3h_rep1

source_name: C6 glioma cells, Control, 3 hours, replicate 1


title: ATH_Col0_MeCN_30min [NimbleGen]


title: TAM_biological rep1


title: ATH_Col0_2E-hexenal_30min_rep2 [NimbleGen]

description: This sample is of wild-type Arabidopsis thaliana Col-0. It is the second of three wild-type biological replicates used in this experiment.


title: TAM_biological rep2


title: leaf of type I necrosis 1

status: Public on Dec 19 2014

first: Shigeo

last: Takumi

department: Graduate School of Agricultural Science

description: Gene expression in 1-week-old seedling leaves

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: hexaploid wheat hybrid

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 23°C for 1 weeks.

extract_protocol: Total RNA was extracted from the leaf tissues of WT and necrosis lines, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

treatment_protocol: no treatment

value: first leaf


title: leaf of type IV necrosis 2

organism: Triticum monococcum subsp. aegilopoides x Triticum urartu

source_name: wild diploid wheat hybrid


title: leaf of wild type 1 (wild diploid wheat)


title: leaf of wild type 2 (wild diploid wheat)


title: leaf of type I necrosis 2


title: leaf of type IV necrosis 1


title: leaf of wild type 2 (common wheat)


title: leaf of wild type 1 (common wheat)


title: EJ CTX, biological rep 2

description: Gene expression data from cortex of agonadal early juvenile (10 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .

source_name: CTX tissue from early juvenile rhesus monkey

treatment_protocol: Ten male Rhesus monkeys were orchidectomized during the first postnatal week and were housed at the Primate Research Laboratory (Primate Core, Center for Research in Reproductive Physiology, University of Pittsburgh). One group of 4 animals was euthanized at 1-3 months of age (infantile group), another 4 animals were euthanized at 6-10 months of age (juvenile group). The pubertal stage was determined by LH and FSH dosage. Tissue samples (cortex, basal hypothalamus) from the juvenile group were dissected and snap-frozen on dry ice.

value: MALE

tag: Stage

value: EARLY JUVENILE (EJ)

value: CORTEX (CTX)


title: INF MBH, biological rep 3

description: Gene expression data from mediobasal hypothalamus of agonadal infantile (1 month-old) rhesus monkeys (orchidectomized withing the first postnatal week) .

source_name: MBH tissue from infantile rhesus monkey

value: INFANTILE (INF)

value: MEDIOBASAL HYPOTHALAMUS (MBH)


title: EJ CTX, biological rep 1

description: Gene expression data from cortex of agonadal early juvenile (7 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .


title: INF MBH, biological rep 1

description: Gene expression data from mediobasal hypothalamus of agonadal infantile (3 month-old) rhesus monkeys (orchidectomized withing the first postnatal week) .


title: EJ MBH, biological rep 1

description: Gene expression data from mediobasal hypothalamus of agonadal early juvenile (7 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .

source_name: MBH tissue from early juvenile rhesus monkey


title: EJ CTX, biological rep 4


title: EJ CTX, biological rep 3

description: Gene expression data from cortex of agonadal early juvenile (6 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .


title: EJ MBH, biological rep 3

description: Gene expression data from mediobasal hypothalamus of agonadal early juvenile (6 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .


title: INF CTX, biological rep 1

description: Gene expression data from cortex of agonadal infantile (3 month-old) rhesus monkeys (orchidectomized withing the first postnatal week) .

source_name: CTX tissue from infantile rhesus monkey


title: INF CTX, biological rep 4

description: Gene expression data from cortex of agonadal infantile (1 month-old) rhesus monkeys (orchidectomized withing the first postnatal week) .


title: INF CTX, biological rep 3


title: INF CTX, biological rep 2


title: EJ MBH, biological rep 2

description: Gene expression data from mediobasal hypothalamus of agonadal early juvenile (10 month-old) rhesus monkeys (orchidectomized within the first postnatal week) .


title: EJ MBH, biological rep 4


title: INF MBH, biological rep 4


title: INF MBH, biological rep 2


title: SIV uninfected ST Bacteria (38498 ST)

city: Davis

first: Satya

last: Dandekar

state: CA

address: One Shields Ave

institute: UC Davis

description: Gene expression data from SIV uninfected ST injected Ileum tissue

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hrs at 45C on Rhesus Macaque chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: Data was analyzed with Genespring 11.0 software using default analysis settings. No minimum fluorescence cut-off was used for data analysis.

source_name: SIV uninfected Ileum - ST Bacteria injected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug of total RNA

extract_protocol: Quiagen Rneasy kit for whole tissue was used as per manufacturer's protocol

treatment_protocol: Tissue was frozen prior to RNA extraction.

value: Ileum

tag: loop content

value: Salmonella serovar Typhimurium (ST)

tag: siv status

value: SIV uninfected


title: SIV infected ST Bacteria (36001 ST)

description: Gene expression data from SIV infected ST injected Ileum tissue

source_name: SIV infected Ileum - ST Bacteria injected

value: SIV infected


title: SIV uninfected ST Bacteria (37248 ST)


title: SIV uninfected ST Bacteria (38299 ST)


title: SIV uninfected LP Bacteria (38498 LP)

description: Gene expression data from SIV uninfected LP injected Ileum tissue

source_name: SIV uninfected Ileum - LP Bacteria injected

value: Lactobacillus plantarum (LP)


title: SIV infected LP Bacteria (37362 LP)

description: Gene expression data from SIV infected LP injected Ileum tissue

source_name: SIV infected Ileum - LP Bacteria injected


title: SIV uninfected MRS Media (38498 MRS)

description: Gene expression data from SIV uninfected MRS injected Ileum tissue

source_name: SIV uninfected Ileum - MRS injected

value: MRS Media


title: SIV uninfected LP Bacteria (37248 LP)


title: SIV uninfected ST Bacteria (36782 ST)


title: SIV infected ST Bacteria (36097 ST)


title: SIV uninfected LP Bacteria (38299 LP)


title: SIV infected LP Bacteria (36097 LP)


title: SIV infected ST Bacteria (37362 ST)


title: SIV uninfected MRS Media (37248 MRS)


title: SIV uninfected LP Bacteria (36782 LP)


title: SIV infected LP Bacteria (36001 LP)


title: SIV uninfected MRS Media (38299 MRS)


title: HPV+ HNSCC_B307_Post-treatment Failure

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Human head and neck squamous cell carcinoma (HNSCC)

hyb_protocol: Total RNA from each sample was labeled using the Ambion WT Expression Kit (Ambion Inc, Austin, TX) which uses a reverse transcription priming method that specifically primes non-ribosomal RNA and provides complete and unbiased coverage of the transcriptome while significantly reducing the priming of rRNA. End labeling was performed according to the Affymetrix GeneChip® WT terminal labeling and hybridization protocol, and Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA) were hybridized at 45°C for 16 hours in a rotating hybridization oven. Arrays were washed and stained on a GeneChip® Fluidics Station 450 using standard protocols for Exon 1.0 ST arrays.

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

data_processing: The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite (6.6beta, build 6.12.0207) and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.

source_name: HPV+ HNSCC_Post-treatment Failure

label_protocol: RNA was amplified and labeled using the WT-Ovation™ FFPE System V2, WT-Ovation™ Exon Module, and the Encore™ Biotin Module (NuGEN), which enables amplification and target preparation of the low quality RNA from FFPE, LCM samples.

extract_protocol: RNA was isolated from fresh frozen or OTC-preserved tissue using RNeasy™ mini or micro kits (Qiagen). Tissue was minced and then homogenized into RLT buffer using a polytron tissue homogenizer and subsequent passage through a Qiashredder column.

tag: disease state

value: HPV-positive HNSCC

tag: response to chemoradiation

value: Post-treatment Failure


title: HPV+ HNSCC_B242_Post-treatment Failure


title: HPV+ HNSCC_R1138_Complete Responder

source_name: HPV+ HNSCC_Complete Responder

value: Complete Response


title: HPV+ HNSCC_D325_Post-treatment Failure


title: SIV uninfected MRS Media (36782 MRS)


title: SIV infected MRS Media (37362 MRS)

description: Gene expression data from SIV infected MRS injected Ileum tissue

source_name: SIV infected Ileum - MRS injected


title: SIV uninfected LB Media (37248 LB)

description: Gene expression data from SIV uninfected LB injected Ileum tissue

source_name: SIV uninfected Ileum - LB injected

value: LB Media


title: HPV+ HNSCC_T387_Complete Responder


title: HPV+ HNSCC_J315_Complete Responder


title: HPV+ HNSCC_D1302_Post-treatment Failure


title: SIV infected MRS Media (36001 MRS)


title: HPV+ HNSCC_D665_Post-treatment Failure


title: SIV infected LB Media  (37362 LB)

description: Gene expression data from SIV infected LB injected Ileum tissue

source_name: SIV infected Ileum - LB injected


title: HPV+ HNSCC_J272_Complete Responder


title: HPV+ HNSCC_G27_Post-treatment Failure


title: HPV+ HNSCC_E25_Complete Responder


title: SIV infected MRS Media (36097 MRS)


title: HPV+ HNSCC_D408_Complete Responder


title: HPV+ HNSCC_K388_Complete Responder


title: HPV+ HNSCC_G7_Post-treatment Failure


title: SIV uninfected LB Media (36782 LB)


title: HPV+ HNSCC_J381_Complete Responder


title: SIV uninfected LB Media (38299 LB)


title: HPV+ HNSCC_G385_Complete Responder


title: SIV uninfected LB Media (38498 LB)


title: HPV+ HNSCC_I306_Complete Responder


title: SIV infected LB Media  (36097 LB)


title: 982_HS-, DMSO_4h_Day 11

city: Luxembourg

first: Anke

middle: K.

last: Wienecke-Baldacchino

address: 162a, Avenue de la Faiencerie

country: Luxembourg

institute: University of Luxembourg

description: CD14 cells were isolated from healthy human blood samples and processed according to Sample_extract_protocol_ch1.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.14.0). It was log2 transformed and quantile normalized.

source_name: Individual: 28, CD14-cells, Treatment:HS-, DMSO_4h  on Day 11

label_protocol: standard as recommended by illumina

extract_protocol: Human monocyte purification and differentiation: Buffy coats of six healthy male donors were obtained from the Blood Transfer Center. Blood samples were diluted 1:1 with phosphate buffered saline (PBS) and peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll Paques Plus and Leucosep tubes. The PBMCs were washed twice with ice-cold MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and centrifuged for 10 min at 300 g at 4 degree Celsius. The numbers of PBMCs were determined using a hematocytometer. The magnetic labeling occurred by resuspending the PBMCs in 2 microl anti-CD14+-antibody conjugated microbeads and 80 microl MACS buffer per 1 x 10^7 cells. After incubating the cells for 30 min at 4  degree Celsius, they were washed by adding 1 ml MACS buffer per 10^7 total cells and centrifuged for 10 min at 300 g at 4 degree Celsius. The cells were resuspended in 500 microl MACS buffer per 1x10^8 cells and loaded onto a MACS LS separation column in a magnetic field. The CD14+ cells were eluted with MACS buffer from the column after washing and removal of the column from the magnetic field. The purity of the CD14+ cells was evaluated by flow cytometry using anti-CD14-FITC and anti-IgG2a-FITC antibodies (ImmunoTools) in a BD FACS Canto II Flow cytometry system (Becton Dickinson). Typically, a purity higher than 95% was reached. The cell number of viable CD14+ cells was determined and the cells were cultured in 5 cm^2 dishes at a minimal density of 2x10^6 cells/ml in RPMI 1640 (PAA), supplemented with 10% human serum (A&E Scientific), 0.1 mg/ml streptomycin, 100 U/ml penicillin and 0.1 mM L-glutamine at 37  degree Celsius in a 5% CO2 atmosphere. During the differentiation process of monocytes to macrophages the medium was changed at day (D) 4, 8 and 11. At D1 and D11 ligand treatment was performed for 4 and 24 h. Total RNA extraction: Total RNA was isolated using Invisorb Spin Cell RNA Mini Kit (Invitek GmbH, Berlin, Germany) according to the manufacturers instructions. 700 microl Lysis Solution R were applied to 5 cm2 dishes and the cells were collected by scraping.

tag: individual

value: male

value: DMSO_4h (0.1%) on Day 1


title: HPV+ HNSCC_D226_Complete Responder


title: 2049_HS-, DMSO_4h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:HS-, DMSO_4h  on Day 11

tag: cell type


title: 2059_T24h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:T091317_24h  on Day 11


title: 983_HS-, R4h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 11

value: R4h (0.1microM) on Day 1


title: 99_HS-, R4h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 1


title: 129_HS-, DMSO_4h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:HS-, DMSO_4h  on Day 11


title: 937_HS-, R4h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 1


title: 2056_DMSO_24h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 2057_T24h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:T091317_24h  on Day 11


title: 973_T24h_Day 11

source_name: Individual: 26, CD14-cells, Treatment:T091317_24h  on Day 11


title: 2050_HS-, R4h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 11


title: 994_T24h_Day 11

source_name: Individual: 29, CD14-cells, Treatment:T091317_24h  on Day 11


title: 136_DMSO_24h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 991_DMSO_24h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 84_DMSO_4h_Day 11

source_name: Individual: 29, CD14-cells, Treatment:DMSO_4h  on Day 11

value: DMSO_4h (0.1%) on Day 11


title: 85_T4h_Day 11

source_name: Individual: 29, CD14-cells, Treatment:T091317_4h  on Day 11

value: T091317_4h (1microM) on Day 11


title: 1877_HS-, DMSO_4h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:HS-, DMSO_4h  on Day 1

value: HS-, DMSO_4h (0.1%) on Day 1


title: 2058_DMSO_24h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 114_RD8_Day 8

source_name: Individual: 32, CD14-cells, Treatment:Rosiglitazone_D8  on Day 8

value: Rosiglitazone_D8 (0.1microM) on Day 8


title: 992_T24h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:T091317_24h  on Day 11


title: 1878_HS-, R4h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 1


title: 936_HS-, DMSO_4h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:HS-, DMSO_4h  on Day 1


title: 130_HS-, R4h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:HS-, Rosiglitazone_4h  on Day 11


title: 98_HS-, DMSO_4h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:HS-, DMSO_4h  on Day 1


title: 993_DMSO_24h_Day 11

source_name: Individual: 29, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 137_T24h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:T091317_24h  on Day 11


title: 972_DMSO_24h_Day 11

source_name: Individual: 26, CD14-cells, Treatment:DMSO_24h  on Day 11


title: 128_R4h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:Rosiglitazone_4h  on Day 11

value: Rosiglitazone_4h (0.1microM) on Day 11


title: 127_T4h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:T091317_4h  on Day 11


title: 2048_R4h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:Rosiglitazone_4h  on Day 11


title: 981_R4h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:Rosiglitazone_4h  on Day 11


title: 980_T4h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:T091317_4h  on Day 11


title: 82062_GW9662+R24h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:GW9662+Rosiglitazone_24h  on Day 11

value: GW9662+Rosiglitazone_24h (5microM/0.1microM) on Day 11


title: 963_DMSO_4h_Day 11

source_name: Individual: 26, CD14-cells, Treatment:DMSO_4h  on Day 11


title: 2061_GW966224h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:GW966224h  on Day 11

value: GW966224h (5microM) on Day 11


title: 2051_DMSO_4h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:DMSO_4h  on Day 11


title: 1880_T4h_Day 1

source_name: Individual: 23, CD14-cells, Treatment:T091317_4h  on Day 1

value: T091317_4h (1microM) on Day 1


title: 81886_DMSO_24h_Day 1

source_name: Individual: 23, CD14-cells, Treatment:DMSO_24h  on Day 1

value: DMSO_24h (0.1%) on Day 1


title: 979_DMSO_4h_Day 11

source_name: Individual: 28, CD14-cells, Treatment:DMSO_4h  on Day 11


title: 2060_R24h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:Rosiglitazone_24h  on Day 11

value: Rosiglitazone_24h (0.1microM) on Day 11


title: 2053_R4h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:Rosiglitazone_4h  on Day 11


title: HPV+ HNSCC_D383_Complete Responder

source_name: HPV+ HNSCC_Complete Responder

value: HPV-positive HNSCC


title: 2046_DMSO_4h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:DMSO_4h  on Day 11


title: 917_DMSO_4h_Day 1

source_name: Individual: 26, CD14-cells, Treatment:DMSO_4h  on Day 1


title: SIV infected LB Media  (36001 LB)

source_name: SIV infected Ileum - LB injected

value: Ileum

value: SIV infected


title: 918_T4h_Day 1

source_name: Individual: 26, CD14-cells, Treatment:T091317_4h  on Day 1


title: 1879_DMSO_4h_Day 1

source_name: Individual: 23, CD14-cells, Treatment:DMSO_4h  on Day 1


title: 2047_T4h_Day 11

source_name: Individual: 22, CD14-cells, Treatment:T091317_4h  on Day 11


title: 126_DMSO_4h_Day 11

source_name: Individual: 30, CD14-cells, Treatment:DMSO_4h  on Day 11


title: 926_DMSO_24h_Day 1

source_name: Individual: 26, CD14-cells, Treatment:DMSO_24h  on Day 1


title: 948_T24h_Day 1

source_name: Individual: 29, CD14-cells, Treatment:T091317_24h  on Day 1

value: T091317_24h (1microM) on Day 1


title: 964_T4h_Day 11

source_name: Individual: 26, CD14-cells, Treatment:T091317_4h  on Day 11

value: male


title: 81887_T24h_Day 1

source_name: Individual: 23, CD14-cells, Treatment:T091317_24h  on Day 1


title: 2052_T4h_Day 11

source_name: Individual: 23, CD14-cells, Treatment:T091317_4h  on Day 11


title: 927_T24h_Day 1

source_name: Individual: 26, CD14-cells, Treatment:T091317_24h  on Day 1


title: 105_DMSO_24h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:DMSO_24h  on Day 1


title: 946_T24h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:T091317_24h  on Day 1


title: 106_T24h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:T091317_24h  on Day 1


title: 947_DMSO_24h_Day 1

source_name: Individual: 29, CD14-cells, Treatment:DMSO_24h  on Day 1


title: KN355

city: Palo Alto

first: Rajini

last: Haraksingh

address: 3165 Porter Drive, Room 2270

institute: Stanford University

description: aCGH of hearing loss cases and controls on NimbleGen 2.1M CNV platform

hyb_protocol: 34 μg of test and control DNA were mixed together and hybridized to an array for 60-72 hrs. The arrays were washed using the NimbleGen Wash kit.

scan_protocol: The arrays were scanned using the MS 200 scanner (Roche NimbleGen) in two channels: 532nm and 635nm.

data_processing:
Images were processed using NimbleScan 2.6 with default parameters (Roche NimbleGen).
Log2-transformed raw data are reported in the EXP_chipID_532 and REF_chipID_635 columns of segMNT.txt.
The NimbleScan 2.6 segMNT algorithm with default parameters (Roche NimbleGen) was used to derive Log R Ratios (reported in the RATIO_CORRECTED column of segMNT.txt)

source_name: Genomic DNA isolated from peripheral blood of control with normal hearing

label_protocol: Genomic DNA from each sample was labeled with cy3 dye and genomic DNA from a control pool of seven female individuals (Promega) was labeled using cy5 dye according to the NimbleGen CGH protocol.

extract_protocol: Genomic DNA was isolated from peripheral blood using standard methods.

treatment_protocol: DNA extracted directly from blood

value: Male

tag: phenotype

value: normal hearing

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega

treatment_protocol: DNA was purchased from Promega - Pool of seven female human genomes

value: Female


title: KN36


title: KN347


title: KN352


title: KN345


title: KN344


title: KN338


title: KN341


title: KN335


title: 113_DMSO_D8_Day 8

source_name: Individual: 32, CD14-cells, Treatment:DMSO_D8  on Day 8

value: DMSO_D8 (0.1%) on Day 8


title: KN333


title: KN329


title: 945_DMSO_24h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:DMSO_24h  on Day 1


title: 1885_T24h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:T091317_24h  on Day 1


title: KN316


title: 97_R4h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:Rosiglitazone_4h  on Day 1

value: Rosiglitazone_4h (0.1microM) on Day 1


title: 939_T4h_Day 1

source_name: Individual: 29, CD14-cells, Treatment:T091317_4h  on Day 1


title: 81884_DMSO_24h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:DMSO_24h  on Day 1


title: 934_T4h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:T091317_4h  on Day 1


title: KN303


title: 1876_R4h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:Rosiglitazone_4h  on Day 1


title: KN301


title: 38_DMSO_4h_Day 1

source_name: Individual: 29, CD14-cells, Treatment:DMSO_4h  on Day 1

value: DMSO_4h (0.1%) on Day 1


title: 96_T4h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:T091317_4h  on Day 1


title: 1875_T4h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:T091317_4h  on Day 1


title: 95_DMSO_4h_Day 1

source_name: Individual: 30, CD14-cells, Treatment:DMSO_4h  on Day 1


title: KN283


title: KN287


title: KN279


title: KN306


title: KN266


title: 35_R4h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:Rosiglitazone_4h  on Day 1


title: KN289


title: 1874_DMSO_4h_Day 1

source_name: Individual: 22, CD14-cells, Treatment:DMSO_4h  on Day 1


title: KN299


title: KN27


title: KN251


title: KN245


title: KN242


title: KN248


title: KN237


title: KN229


title: KN223


title: KN219


title: KN313


title: KN215


title: KN213


title: 933_DMSO_4h_Day 1

source_name: Individual: 28, CD14-cells, Treatment:DMSO_4h  on Day 1


title: KN207

source_name: Genomic DNA isolated from peripheral blood of control with normal hearing


title: KN205

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega


title: KN204


title: KN191


title: KN203


title: KN158


title: KN174


title: KN163


title: KN167


title: KN140


title: KN131


title: KN139


title: KN135


title: KN14


title: KN133


title: KN126


title: KN216


title: KN123


title: KN122


title: KN120


title: KN118


title: KN116


title: KN19


title: KN115


title: KN150


title: KN124


title: KN100


title: K8056


title: KN101


title: KN111


title: KN110


title: EA7


title: K8035


title: KN106


title: KN155


title: EA60


title: EA9


title: EA41


title: EA42


title: IA

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss

value: non-syndromic hereditary hearing loss


title: EA57


title: EA43


title: EA40


title: EA39


title: EA38


title: EA37


title: KN253


title: EA8


title: EA35


title: EA36


title: EA34


title: EA32


title: EA30


title: EA65


title: EA33


title: EA31


title: Antisense oligonucleotide (ASO) targeting the knockdown of ACAT2 - 4

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

description: hepatic total RNA

hyb_protocol: 6 ug biotinylated cRNA was hybridized to the Affymetrix GeneAtlas Mouse MG-430 PM Array Strip according to current Affymetrix protocols.

scan_protocol: Strips were subsequently scanned using the GeneAtlas Imager system according to the standard Affymetrix protocol

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method.

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix 3’-IVT labeling protocol.

extract_protocol: Total RNA was isolated from mouse liver tissue using Trizol Reagent (Life Technologies 15596-026) according to manufacturer's recommendations

value: liver

tag: strain

value: female


title: non-targeting control ASO - 2

description: hepatic total RNA

source_name: non-targeting control ASO - 2


title: EA29


title: non-targeting control ASO - 4

description: hepatic total RNA

source_name: non-targeting control ASO - 4


title: Antisense oligonucleotide (ASO) targeting the knockdown of ACAT2 - 3

description: hepatic total RNA


title: EA27


title: NPC1L1-Liver-Transgenic -1

description: hepatic total RNA

source_name: NPC1L1-Liver-Transgenic -1


title: EA26


title: Antisense oligonucleotide (ASO) targeting the knockdown of ACAT2 - 1

description: hepatic total RNA


title: non-targeting control ASO - 3

description: hepatic total RNA

source_name: non-targeting control ASO - 3


title: wild type - 4

description: hepatic total RNA

source_name: wild type - 4


title: wild type - 5

description: hepatic total RNA

source_name: wild type - 5


title: EA25


title: NPC1L1-Liver-Transgenic -5

description: hepatic total RNA

source_name: NPC1L1-Liver-Transgenic -5


title: KN254


title: non-targeting control ASO - 1

description: hepatic total RNA

source_name: non-targeting control ASO - 1


title: NPC1L1-Liver-Transgenic -3

description: hepatic total RNA

source_name: NPC1L1-Liver-Transgenic -3


title: EA28


title: EA23


title: EA21


title: Antisense oligonucleotide (ASO) targeting the knockdown of ACAT2 - 2

description: hepatic total RNA


title: EA15


title: EA16


title: EA17


title: EA14


title: EA11


title: EA12


title: EA10


title: EA1


title: EA20


title: wild type - 3

description: hepatic total RNA

source_name: wild type - 3


title: E.A.


title: EA13


title: EA24


title: C9


title: C8


title: C7


title: NPC1L1-Liver-Transgenic -4

description: hepatic total RNA

source_name: NPC1L1-Liver-Transgenic -4


title: NPC1L1-Liver-Transgenic -2

description: hepatic total RNA

source_name: NPC1L1-Liver-Transgenic -2


title: wild type - 1

description: hepatic total RNA

source_name: wild type - 1


title: D9006


title: C6


title: C5


title: C4


title: C3


title: wild type - 2

description: hepatic total RNA

source_name: wild type - 2


title: C2

source_name: Genomic DNA isolated from peripheral blood of control with normal hearing


title: C10

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega


title: C1


title: C11


title: B4074


title: Colon Tissue Sample_35

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

hyb_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.

scan_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using the Illumina BeadArray scanner.

data_processing: Illumina BeadStudio v3.3.4 normalized intensity values and BAF data were imported into PARTEK Genomics Suite for statistical analysis.

label: C-Bio and A-DNP

source_name: Colon tissue, normal

extract_protocol: QIAGEN Gentra Puregene kit standard protocol.

value: colorectal cancer (CRC)

value: normal colon mucosa


title: Colon Tissue Sample_36

label_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.


title: Colon Tissue Sample_33


title: Colon Tissue Sample_40


title: Colon Tissue Sample_42


title: B4041


title: Colon Tissue Sample_29


title: Colon Tissue Sample_24

source_name: Colon tissue, tumor

value: colon tumor


title: Colon Tissue Sample_48


title: Colon Tissue Sample_45


title: B4008


title: Colon Tissue Sample_44


title: Colon Tissue Sample_46


title: Colon Tissue Sample_30


title: Colon Tissue Sample_34


title: Colon Tissue Sample_38


title: 9MP-P

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss


title: Colon Tissue Sample_27


title: Colon Tissue Sample_31


title: Colon Tissue Sample_47


title: 9CxPro


title: Colon Tissue Sample_26


title: Colon Tissue Sample_37


title: Colon Tissue Sample_25


title: 96MP-P


title: 99MP-P


title: 98MP-P


title: Colon Tissue Sample_39


title: Colon Tissue Sample_28


title: Colon Tissue Sample_21


title: 94MP-P


title: Colon Tissue Sample_23


title: Colon Tissue Sample_20


title: 92MP-P


title: 95MP-P


title: Testis_PND15_Rhox3shRNA_25

city: La Jolla

first: Miles

last: Wilkinson

address: 9500 Gilman Dr. MC 0695

department: Reproductive Medicine

institute: UCSD

hyb_protocol: Hybridistion according to Affymetrix standard protocols

scan_protocol: Scanning according to Affymetrix standard protocols

data_processing:
Raw data was normalised using robust multiarray averaging with correction for GC content of the probes.  Gene and individual exon expression levels were calculated using the mean of all probesets per gene and exon, respectively.  Changes in gene expression between control- and Rhox3a siRNA -treated cells were statistically tested using one-way ANOVA.  All microarray data analysis was carried out using Partek genomics suite v6.3 (Partek, St. Louis, MI, USA).
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: PND15 developing mouse testis

label_protocol: Biotin labelling according to Affymetrix standard protocols

growth_protocol: Mouse colonies were maintained in agreement with protocols approved by the Institutional Animal Care and Use Committee at the University of California, San Diego. All animals were housed under a 12 h light: 12 h darkness cycle and provided with food and water ad libitum.

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

tag: genotype

value: Rhox3 shRNA

tag: Sex

value: Testis

tag: developmental stage

value: post-natal day 15


title: Testis_PND15_WT_27

value: Control


title: Testis_PND15_WT_26


title: Testis_PND15_WT_28


title: 93MP-P


title: Colon Tissue Sample_43


title: 91MP-P


title: Colon Tissue Sample_22


title: Testis_PND15_Rhox3shRNA_24


title: Testis_PND15_Rhox3shRNA_23


title: Tv _rep5

city: Haifa

first: Benjamin

middle: A

last: Horwitz

state: Israel

address: Dept Biology Technion

department: Biology

country: Israel

institute: Technion

description: Gene expression at 3 days of interaction

hyb_protocol: Microarray hybridization and washing steps were performed following the Agilent protocol for single-channel arrays.

scan_protocol: The arrays were scanned at 10% laser power.

data_processing: Agilent’s Feature Extraction software was used to extract the data.

organism: Trichoderma virens

source_name: Trichoderma virens, replicate 5

label_protocol: cDNA synthesis was primed with oligo dT, and the double-stranded template was used for amplification and labelling by in vitro transcription using the MessageAmpII kit from Ambion (Austin, TX, USA);amplified RNA (aRNA) was labelled with Cy3

growth_protocol: Surface-sterilized seeds were germinated and grown for 5 days (maize) or 7 days (tomato) in hydroponic culture. T. virens mycelia were added and the cultures incubated for an additional 3 days.

extract_protocol: Roots and adhering mycelia were ground in liquid nitrogen and total RNA extracted

treatment_protocol: T. virens interaction with plant roots was compared with T. virens grown without plant roots under the same conditions.

value: fungal mycelia


title: Colon Tissue Sample_41


title: Tv _rep4

source_name: Trichoderma virens, replicate 4


title: Colon Tissue Sample_32


title: Tv _rep2

source_name: Trichoderma virens, replicate 2


title: 8MP-P


title: 8CxPro


title: Tv roots_maize_rep1

source_name: Trichoderma virens, maize roots, replicate 1

value: fungal mycelia and plant root tissue

tag: treatment

value: maize co-culture


title: 90MP-P

value: Female


title: Tv roots_tomato_rep3

source_name: Trichoderma virens, tomato roots, replicate 3

value: tomato co-culture


title: Tv _rep1

source_name: Trichoderma virens, replicate 1


title: 88MP-P

value: Male


title: Tv roots_maize_rep3

source_name: Trichoderma virens, maize roots, replicate 3


title: Tv roots_maize_rep2

source_name: Trichoderma virens, maize roots, replicate 2


title: Colon Tissue Sample_16


title: Tv roots_tomato_rep2

source_name: Trichoderma virens, tomato roots, replicate 2


title: 87MP-P


title: 86MP-P


title: 85MP-P


title: Colon Tissue Sample_17


title: 89MP-P


title: Colon Tissue Sample_11


title: 84MP-P


title: Tv _rep3

source_name: Trichoderma virens, replicate 3


title: 96-1-

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization and washing were performed according to manufacture’s recommendations in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were then within-array normalized by Loess normalization method and between-array normalized by Quantile normalization. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed calculating the median. Missing expression values were imputed by k-nearest neighbours averaging (k=10). All the 42,164 probes of the Agilent SurePrint G3 array were re-annotated using GENCODE v.16 gene annotation database.

source_name: Nasal tissue

label_protocol: Sample labelling were performed according to the Two-Color Microarray-Based Gene Expression Analysis—Low Input Quick Amp Labeling—protocol (Agilent Technologies).

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit according to the RNeasy® Micro Handbook (Qiagen).

tag: patient group and tissue group

value: HHT1 norm

tag: age (year)

value: M

tag: family number

tag: germline mutation

value: ENG

tag: mutation, hgvs

tag: epistaxis grade

tag: pavm

value: yes

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: Universal Human Reference RNA


title: 83MP-P

tag: gender

value: non-syndromic hereditary hearing loss

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega


title: 94-1-

value: no


title: 93-1+

value: HHT1 telang


title: 93-1-


title: 92-1+


title: 92-1-


title: 94-1+


title: Colon Tissue Sample_05

tag: disease state

value: colorectal cancer (CRC)

tag: tissue

value: colon tumor


title: 82MP-P

tag: phenotype


title: Colon Tissue Sample_15


title: 96-1+


title: Colon Tissue Sample_07


title: Colon Tissue Sample_09


title: Colon Tissue Sample_06


title: Tv roots_tomato_rep1

source_name: Trichoderma virens, tomato roots, replicate 1


title: 88-11

value: Sibling HHT2

value: F


title: Colon Tissue Sample_13

source_name: Colon tissue, tumor


title: 88-1+

value: HHT2 telang

value: c.155del, p.Thr52Lysfs*2


title: 94-11

value: Sibling HHT1


title: 88-2-

value: HHT2 norm


title: Colon Tissue Sample_18


title: 88-1-


title: Colon Tissue Sample_02


title: Colon Tissue Sample_03


title: 88-2+


title: 7MP-P

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss

value: Male

value: Female


title: 7CxPro


title: 80MP-P


title: 78MP-P


title: 79MP-P


title: 77MP-P


title: 76MP-P


title: Colon Tissue Sample_04


title: Colon Tissue Sample_10


title: 87-1-

value: HHT1 norm

value: M


title: 87-1+

value: ENG

value: yes


title: 69-1-

value: Universal Human Reference RNA


title: 74MP-P

value: non-syndromic hereditary hearing loss


title: 71-1-

value: c.143G>A, p.Gly48Glu

value: no


title: Colon Tissue Sample_01

value: colorectal cancer (CRC)

value: colon tumor


title: 82-1+

value: c.139_140insCG, p.Arg47Profs*8


title: 67-11

value: Control


title: 72MP-P