title: 272


title: genomic DNA from CD34- of AML patient SU029

status: Public on Oct 01 2015

type: genomic

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

department: Medicine

country: USA

institute: Johns Hopkins University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi v1.8.9; beta values not normalized

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34- of AML patient

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from AML and normal bone marrow samples using Epicentre Kit according to standard instructions

tag: subject id

tag: subject status

value: AML

tag: gender

value: female

tag: phenotype

value: LSC (leukemia stem cells)


title: 266

city: University of Helsinki

first: Kaisa

middle: Aulikki

last: Jaakkola

address: Agnes Sjöbergin katu 2

department: The Department of Food Hygiene and Environmental Health

country: Finland

institute: University of Helsinki, Faculty of veterinary medicine

hyb_protocol: Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.

data_processing: Images were processed and checked manually using GenePix Pro 6.0/6.1 software. For data analysis R software LIMMA-package (Smyth et al 2005) was used. Background intensities were fixed using normexp-algorithm (threshold 50).

organism: Yersinia enterocolitica

source_name: swine, tonsils

label_protocol: DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany). The concentration of DNA and the incorporation of the dye were checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)

growth_protocol: Frozen strains were first grown on blood agar under aerobic conditions at 28°C 24 h. To prepare for DNA isolation the strains were grown in TSB-medium at 28°C 24 h.

extract_protocol: DNA was extracted as described by Pitcher et al. (1989). DNA quality was checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)

tag: bioserotype

tag: origin

value: Finland


title: genomic DNA from CD34+38+ of AML patient SU008

source_name: CD34+38+ of AML patient

value: male

value: BLAST (blast cells)


title: 270


title: MC8

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

label: biotin

molecule: total RNA

extract_protocol: RNA was isolated with miRNeasy FFPE kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: source

value: Mayo Clinic

tag: tissue

value: HCC tumor


title: MC10

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: 290

source_name: human

value: Åland


title: 265


title: MC14

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: 229

value: BT 4

value: Estonia


title: MC12


title: MC7


title: 260


title: MC6


title: genomic DNA from CD34+38+ of AML patient SU001


title: genomic DNA from CD34+38- of AML patient SU006

source_name: CD34+38- of AML patient


title: 249

value: England


title: 244


title: genomic DNA from GMP of normal bone marrow ID2627

source_name: GMP of normal bone marrow

value: normal

value: GMP (Granulocyte-macrophage progenitor)


title: genomic DNA from MEP of normal bone marrow ID2627

source_name: MEP of normal bone marrow


title: MC4


title: MC13


title: genomic DNA from CD34- of AML patient SU008


title: genomic DNA from L-MPP of normal bone marrow ID2627

source_name: L-MPP of normal bone marrow

value: L-MPP (Late-Multipotent progenitor cells)


title: genomic DNA from CD34+38+ of AML patient SU006


title: MC1


title: 241

value: Russia


title: MC2


title: 240


title: 239


title: NY3009

value: Mount Sinai


title: genomic DNA from CMP of normal bone marrow ID2627

source_name: CMP of normal bone marrow

value: CMP (Common myeloid progenitor)


title: genomic DNA from MPP of normal bone marrow ID2627

source_name: MPP of normal bone marrow

value: MPP (Multipotent progenitor cells)


title: 236


title: NY2011


title: 234


title: NY2125


title: 238


title: MC15


title: NY2376


title: 233


title: MC42B


title: 231


title: genomic DNA from GMP of normal bone marrow ID2753

value: female


title: NY2181


title: 232


title: NY2121


title: NY5191


title: 228


title: NY2329


title: genomic DNA from L-MPP of normal bone marrow ID2753


title: 214

source_name: swine, faeces

value: Finland


title: genomic DNA from CMP of normal bone marrow ID2753


title: NY2815


title: NY2416


title: 219


title: genomic DNA from MPP of normal bone marrow ID2753


title: NY2046


title: 213


title: genomic DNA from GMP of normal bone marrow ID2712

value: male


title: genomic DNA from HSC of normal bone marrow ID2627

source_name: HSC of normal bone marrow

value: HSC (Hematopoietic stem cells)


title: NY1935


title: 210


title: genomic DNA from L-MPP of normal bone marrow ID2712


title: 208


title: NY2331B


title: genomic DNA from HSC of normal bone marrow ID2753


title: genomic DNA from MEP of normal bone marrow ID2753


title: genomic DNA from MEP of normal bone marrow ID2712


title: Dynamic2_Hot34C_GenotypeZ_MR467

city: University Park

first: John

middle: Everett

last: Parkinson

state: PA

address: 208 Mueller Lab

department: Biology

institute: Penn State University

description: Both host and symbiont RNA are present in sample.

hyb_protocol: Samples were resuspended in the appropriate tracking control and hybridization solution master mix was added following manufacturer’s instructions (Roche NimbleGen). Following two 5-minute incubations at 95°C and 42°C, the mixer was attached to the array and hybridization solutions were added according to the manufacturer’s instructions. Hybridization was performed while mixing overnight at 42°C in a MAUI hybridization instrument (BioMicro Systems, UT). Hybridized slides were washed according to the manufacturer’s instructions (Roche NimbleGen), and spun at 1000 RPM for 3 minutes in a 50 ml conical tube filled with N2 gas. Dried slides were placed in fresh tubes with 2.5 ml of DyeSaver (Genisphere Inc.) and rotated for 45 seconds to coat the slide. A final spin at 700 RPM for 3 seconds removed excess DyeSaver.

scan_protocol: Scanning was performed with an Axon GenePix 4000B

data_processing: Raw probe intensities were read into R for analysis in the Bioconductor package LIMMA (Smyth 2005; R Development Core Team 2008). Probe intensities were normalized within arrays using lowess normalization, and between arrays using the quantile normalization method which ensures that the average intensities have the same empirical distribution across arrays (Yang and Thorne 2003).

organism: Acropora palmata

source_name: Acropora palmata adult tissue homogenate

label_protocol: To prepare samples for microarray hybridization, one cycle of amplification was per-formed on 1ug of each RNA sample using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Life Technologies, AM1753) following the manufacturer’s protocol. Dye coupling of 15 ug of aRNA was performed with Cy3 or Cy5 (GE Health Care, RPN5661), and subsequently purified according to the Ambion Kit instructions. For each pair of samples that were to be hybridized to the same array, 2µg each of the Cy3 and Cy5 labeled sample were combined and fragmented using RNA Fragmentation Reagents (Ambion, AM8740) according the manufacturer’s instructions, then dried down completely in a speed-vac

growth_protocol: In Spring 2011, colonies of Acropora palmata were sampled from a reef in Puerto Morelos, Mexico (N 20°52.461', W 86°51.073') and genotyped at five neutral microsatellite loci according to Baums et al. (2005).  The Symbiodinium ‘fitti’ strain in each colony was genotyped at ten microsatellite loci (Pinzon et al. 2011).  Six of the host genotypes harbored the same strain of S ‘fitti’.  These six colonies were targeted for temperature experiments.  Colonies hosting symbionts with a small cold stress response (hosts B and Z) and a large cold stress response (hosts D and Y) were binned as replicates.  Their host gene expression was contrasted via microarray.  Each holobiont phenotype was subsequently called Dynamic and Static, respectively.

extract_protocol: Total RNA was extracted from the ~3 polyps of each host genotype at each temperature taken 3.5 h after exposure to treatment.  Extractions were performed at the Pennsylvania State University with the RNeasy Mini Kit (Qiagen, CA).  Concentration and quality of RNA extracts were quantified on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to ensure that high molecular weight RNA was present.

treatment_protocol: Fragments (~10 cm2) from each of the target coral genotypes were transported to temperature-controlled aquaria.  One piece of each genotype was transferred to one of three separate bins containing filtered seawater maintained at temperatures of 20 (cold), 27 (ambient), or 34°C (hot).  The fragments were kept in temperature treatments for three days; temperatures stayed within ±0.4°C of the targets.

value: Dynamic

tag: phenotype replicate

tag: temperature

tag: temperature class

value: Hot

tag: genotype

value: Z

tag: sample id


title: Sézary patient 23 400k oligo array

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

scan_protocol: scanned on an Agilent DNA Microarray Scanner G2565BA, Scan resolution: 2µm, Scan region: 61 x 21.6 mm, Green PMT: 100%, Red PMT: 100%

data_processing:
TIFF image processing with Agilent Feature Extraction v10.5.1.1, CGH_105_Dec08 protocol
For visualization with CGHPRO (Chen et al. BMC Bioinformatics 2005) log2 ratios of the processed signals (from FE file) were subtracted: log2(gProcessedSignal)-log2(rProcessedSignal). DNA copy number changes were defined by circular binary segmentation (Olshen et al. Biostatistics 2004) in combination with a log2 threshold of 0.2/-0.2.

source_name: Peripheral blood mononuclear cells

extract_protocol: DNA-Isolation was done according to standard protocols by performing proteinase K digestion and subsequent phenol/chloroform extraction or by using commercial DNA-cleanup kits according to the manufacture’s recommendations (QIAamp DNA Blood Mini Kit, QIAGEN, Hilden, Germany / PureLink Genomic DNA Mini Kit, Invitrogen, Karlsruhe, Germany). Samples with a low amount of DNA were amplified with the Sigma Whole Genome Amplification kit or illustra GenomiPhi V2 DNA Amplification kit (GE Healthcare), respectively.

tag: patient

tag: disease state

value: Sézary syndrome

tag: age

source_name: lymphoblastoid cells

value: healthy control


title: genomic DNA from CMP of normal bone marrow ID2712


title: genomic DNA from CD34- of AML patient SU001

value: AML

value: BLAST (blast cells)


title: Dynamic2_Cold20C_GenotypeZ_MR465

value: Cold


title: Dynamic2_Ambient27C_GenotypeZ_MR466

value: Ambient


title: Sézary patient 21 400k oligo array


title: NY5155

value: HCC tumor


title: Sézary patient 22 400k oligo array


title: 204

source_name: swine, intestines


title: NY2023

value: Mount Sinai


title: 206

value: England


title: 201

source_name: swine, organs


title: genomic DNA from MPP of normal bone marrow ID2712

value: normal

value: MPP (Multipotent progenitor cells)


title: genomic DNA from MEP of normal bone marrow ID2710

value: female


title: Dynamic1_Hot34C_GenotypeB_MR297

value: B


title: 196

value: Finland


title: genomic DNA from GMP of normal bone marrow ID2710

value: GMP (Granulocyte-macrophage progenitor)


title: NY2174


title: MC50


title: genomic DNA from L-MPP of normal bone marrow ID2710

value: L-MPP (Late-Multipotent progenitor cells)


title: genomic DNA from CMP of normal bone marrow ID2710

value: CMP (Common myeloid progenitor)


title: genomic DNA from HSC of normal bone marrow ID2712

value: male

value: HSC (Hematopoietic stem cells)


title: Dynamic1_Cold20C_GenotypeB_MR300

value: Dynamic


title: NY2051


title: Dynamic1_Ambient27C_GenotypeB_MR294


title: NY2087


title: 188

source_name: swine, carcass


title: genomic DNA from MPP of normal bone marrow ID2710


title: Static2_Hot34C_GenotypeY_MR464

value: Static

value: Hot

value: Y


title: 191


title: 192

source_name: swine, tonsils


title: NY2150

value: HCC tumor


title: 185


title: 187


title: genomic DNA from MEP of normal bone marrow ID2748


title: NY2190

value: Mount Sinai


title: NY2133


title: NY2167


title: Static1_Hot34C_GenotypeD_MR298

value: D


title: Static2_Ambient27C_GenotypeY_MR463

value: Ambient


title: Strain HV_3

source_name: unknown

value: Biotype 1

value: Unknown


title: 183


title: Strain HV_4


title: NY2199


title: genomic DNA from HSC of normal bone marrow ID2710

value: normal

value: female


title: Static1_Cold20C_GenotypeD_MR301

value: Cold


title: Static2_Cold20C_GenotypeY_MR462


title: Static1_Ambient27C_GenotypeD_MR295


title: IP32953_3

organism: Yersinia pseudotuberculosis

source_name: human

value: France


title: Strain HV_2


title: NY2095


title: NY2160B


title: NY2129


title: Strain HV_1


title: genomic DNA from L-MPP of normal bone marrow ID2748

value: L-MPP (Late-Multipotent progenitor cells)


title: NY1921C


title: IP32953_1


title: genomic DNA from CMP of normal bone marrow ID2748

value: male

value: CMP (Common myeloid progenitor)


title: MC48


title: genomic DNA from MPP of normal bone marrow ID2748

value: MPP (Multipotent progenitor cells)


title: IP32953_4


title: genomic DNA from GMP of normal bone marrow ID2748

value: GMP (Granulocyte-macrophage progenitor)


title: NY2116


title: NY2686


title: NY2983


title: genomic DNA from HSC of normal bone marrow ID2748

value: HSC (Hematopoietic stem cells)


title: Arabidopsis leaves 22 hours after mock inoculation at night, rep 1

city: York

first: Katherine

last: Denby

address: Department of Biology

country: United Kingdom

institute: University of York

hyb_protocol: Four μg of the resulting Cy3-labelled cDNA was hybridised against NimbleGen A. thaliana Gene Expression 12×135K arrays custom designed for the TAIR10 Arabidopsis thaliana genome annotation (Design ID OID37507), two duplicate arrays per sample.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

organism: Arabidopsis thaliana

label_protocol: Equal amounts of total RNA were pooled from the four biological replicates for each of the eight experimental treatments (18 hpi at CT24, 22 hpi at CT24, 18 hpi at CT42 or 22 hpi at CT42 with B. cinerea spores or half-strength grape juice) and 100 ng of each pool used as input for RNA amplification using the MessageAmp II RNA amplification kit (Life Technologies). Double stranded cDNA was synthesised using the Superscript Double-stranded cDNA synthesis kit (Life Technologies). Five hundred ng of ds cDNA was labelled using the NimbleGen One-Color DNA labelling kit (Roche), as per the manufacturer’s instructions except that half volumes of all reagents were used for all steps.

growth_protocol: Arabidopsis seeds were sown on a 1:1 mix of peat (Jiffy Products, Norway) and vermiculite and stratified for 48 h at 4 °C in the dark. Plants were grown for four weeks under a long-day photoperiod (16 h light, 8 h dark) at 22°C and 55% relative humidity, and cool white fluorescent light of 80-100 µmol m-2s-1. Plants were transferred to constant light conditions during the 16 h light period 24 h prior to inoculation.

extract_protocol: Total RNA was extracted from single Arabidopsis leaves using Trizol (Life Technologies), and subsequently cleaned up using the RNEasy kit (Qiagen) with on-column DNAse digestion.

treatment_protocol: Leaves (leaf 5 from individual plants) were detached and placed in propagator trays on 0.8% agar. Leaves were inoculated with six droplets of 10 μL of half-strength grape juice containing 5 x 104 spores mL-1. Mock inoculations used half-strength grape juice alone. Inoculations were performed at subjective dawn and subjective night (two hours after dark). Whole leaves were harvested 18 and 22 hours after inoculation.

value: four week old leaf

tag: treatment

value: mock inoculated

tag: time of treatment

value: subjective night


title: NY2040

value: Mount Sinai

value: HCC tumor


title: IP32953_2


title: Arabidopsis leaves 22 hours after mock inoculation at night, rep 2


title: DSM 13030_2

value: Germany


title: DSM 13030_1


title: DSM 13030_3


title: Strain 8081_1

value: Ohio, USA


title: Arabidopsis leaves 18 hours after mock inoculation at night, rep 1


title: NY3036


title: NY2478


title: Arabidopsis leaves 18 hours after mock inoculation at night, rep 2


title: Strain 8081_3


title: Strain 8081_2


title: Arabidopsis leaves 22 hours after inoculation with Botrytis cinerea at night, rep 1

value: infected with fungal pathogen


title: Arabidopsis leaves 22 hours after inoculation with Botrytis cinerea at night, rep 2


title: NY1930


title: Strain 8081_4


title: NY1925


title: NY1942


title: CVS [HK12C0669]

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

country: China

institute: The Chinese University of Hong Kong

hyb_protocol: After clean up and QC check, Cy3 and Cy5 labeled DNA samples were mixed together with Cot-1 DNA, blocking agent and hybridization buffer using Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit according to manufacturer's protocol. Samples were hybridized on array for 24 hours at 65oC. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction
Dye was normalized automatically according to the dye norm list in eArray generating the normalized log10 ratio (Cy5/Cy3), representing test/reference

source_name: Prenatal diagnosis_CVS

label_protocol: Three costumized aCGH approach have different procedure for DNA fragmentation and labelling; Agilent-022023:1 µg of Genomic DNA samples were fragmented. The fragmented DNA sample were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.  Agilent-068656:300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit. Agilent-035130:300 ng of Genomic DNA samples were enzyme digested. The digested DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.

growth_protocol: Uncultured samples of chorionic villus sampling, amniotic fluid,  placental tissue and blood were used for direct DNA extraction

extract_protocol: Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions

treatment_protocol: Samples were untreated

tag: sample origin

value: Prenatal diagnosis

tag: clinical indication

value: Ultrasound abnormality:multiple anomalies, 4.7mm right neck cyst, likely pre-axial polydactyly of left hand, abnormal right thumb possibly polydactyly,small left cardiac ventricle only one flow can be seen, single umbilical artery

value: Chorionic villus sampling (CVS)

value: Healthy Chinese adult control

value: blood


title: Arabidopsis leaves 18 hours after inoculation with Botrytis cinerea at night, rep 2


title: AF [HK12C0310]

source_name: Prenatal diagnosis_AF

value: Ultrasound abnormality:foetal anomalies, bilateral cerebral ventriculomegaly

value: Amniotic fluid (AF)


title: Arabidopsis leaves 22 hours after mock inoculation at dawn, rep 2

value: subjective dawn


title: Arabidopsis leaves 18 hours after inoculation with Botrytis cinerea at night, rep 1


title: NY1905


title: CVS [HK12C0637]

value: Ultrasound abnormality:increased NT 5.93mm, reverse DV, absent nasal bone


title: NY2214


title: NY1909


title: CVS [14S1064845]

value: Miscarriage


title: Arabidopsis leaves 22 hours after inoculation with Botrytis cinerea at dawn, rep 2

value: four week old leaf


title: NY2656


title: NY2219


title: Arabidopsis leaves 18 hours after mock inoculation at dawn, rep 2

value: mock inoculated


title: Arabidopsis leaves 22 hours after mock inoculation at dawn, rep 1


title: NY1913

value: Mount Sinai


title: CVS [15S0003057]


title: CVS [14S1003400]


title: Arabidopsis leaves 22 hours after inoculation with Botrytis cinerea at dawn, rep 1


title: Arabidopsis leaves 18 hours after inoculation with Botrytis cinerea at dawn, rep 2


title: NY2104

value: HCC tumor


title: NY2461


title: NY2427B


title: NY2937


title: CVS [14S0026181]


title: NY3016


title: CVS [14S1025742]


title: Arabidopsis leaves 18 hours after inoculation with Botrytis cinerea at dawn, rep 1


title: NY2615


title: CVS [14S0018740]


title: NY2346


title: Placenta [14S0026442]

source_name: Induced abortion_Placental tissue

value: Induced abortion

value: Ultrasound abnormality:gastroschisis, cleft lip, syndactylia, ectodactyle; the first fetus was diagnosed with gastroschisis and inevitable abortion for the second fetus

value: Placental tissue


title: nHEK nickel

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

description:
Sample 4
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., Bioinformatics; 23: 2700-2707, 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

label_protocol: 750 ng total RNA from sample was labelled with Hy3™ and  Hy5™ fluorescent label using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems, Naerum, Denmark)  following the manufacturer’s instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

tag: indication

value: Healthy

tag: allergen

value: nickel

value: Keratinocytes

source_name: Reference: mixture of all samples


title: CVS [14S0010549]

value: Chorionic villus sampling (CVS)

value: Healthy Chinese adult control


title: MC46


title: nHEK media

description:
Sample 3
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Vehicle


title: AF [14S0018763]

value: Prenatal diagnosis

value: Ultrasound abnormality:congenital heart disease; ventricular septal defect; syndactylia

value: Amniotic fluid (AF)

value: blood


title: Blood [14B0002710]

value: Postnatal

value: Low sets ear;torticollisk intellectual disability; poor memory

value: Blood


title: q28 nickel

description:
Sample 6
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: CVS [14S0010496]

value: Miscarriage


title: Blood [14B0013425]

value: hypospadias; short upper lip and tongue


title: CVS [14S0010337]


title: NY2529

value: Mount Sinai

value: HCC tumor


title: NY2639


title: q28 media

description:
Sample 2
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Healthy


title: q35 media

description:
Sample 5
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: NY2237B


title: FP09_medie

description:
Sample 11
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

source_name: Healthy _PBMCs_Vehicle

label_protocol: 600 ng total RNA from sample was labelled with Hy3™ and  Hy5™ fluorescent label using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

value: peripheral blood mononuclear cells (PBMCs)


title: FP09_nicl2

description:
Sample 12
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

source_name: Healthy _PBMCs_nickel

value: nickel


title: CVS [14S1003199]

value: Chorionic villus sampling (CVS)


title: NY5178


title: q35 nickel

description:
Sample 1
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Keratinocytes


title: FP07_nicl2

description:
Sample 10
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: NY2538


title: NY2555


title: NY3029


title: NY2578


title: NY2484


title: NY2507


title: MC45


title: FP10_nicl2

value: Allergic contact dermatitis


title: LS_nicl2


title: NY2935


title: NY2759B


title: NY2846


title: NY2636


title: NY2681


title: FP07_medie

description:
Sample 9
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Vehicle


title: FP10_medie


title: patient_27_medie

description:
Sample 7
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: patient_25_nicl2


title: NY2745


title: patient_25_medie


title: FP29 nickel

description:
Sample 24
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

label_protocol: 200 ng total RNA from sample was labelled with Hy3™ and  Hy5™ fluorescent label using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

value: skin

tag: sample type

value: Whole tissue extract


title: NY2369

tag: source


title: NY2059

tag: tissue


title: FP29 vaseline

description:
Sample 23
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: vehicle


title: FP27 nickel

description:
Sample 22
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: FP27 vaseline

description:
Sample 21
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: FP28 nickel

description:
Sample 20
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: FP28 vaseline

description:
Sample 19
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: FP26 nickel

description:
Sample 18
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

source_name: allergic contact dermatitis_skin_nickel

value: allergic contact dermatitis


title: NY2252


title: NY2562


title: NY2750


title: CSC 3

city: Suzhou

first: Junjie

last: Yang

address: 708 Renmin Road

institute: Institute for cardiovascular science of Soochow University

description: miRNA expression profiling  from CSCs

hyb_protocol: Labeled miRNA was hybridized to the array for 16 hours at 48 “C and 60 rpm as described in the protocol.

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the MAS5 method.

label: Biotin

organism: Rattus norvegicus

source_name: CSCs

label_protocol: Per RNA sample, 1 ug were used as input into the procedure as recommended by protocol (Genisphere FlashTagTM Biotin RNA Labeling for Affymetrix GeneChip miRNA arrays). 1ug of total RNA was used as input into the labeling reaction.

growth_protocol: Cardiac stem cells were isolated and cultured as previously reported. MSCs were isolated and cultured until Passage 4. Then exosomes from MSCs were extracted using Exo-Quick-TCTM (System Bioscience) according to the user manual.

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

treatment_protocol: For miRNA array analysis, CSCs were grown in culture medium supplemented with MSC-exosomes for 3 consecutive days. Then cells were collected for RNA extraction and subsequent experiments.

tag: background strain

value: Sprague Dawley

value: heart

tag: cell type

value: cardiac stem cells (CSCs)

value: 4 weeks


title: Arabidopsis leaves 18 hours after mock inoculation at dawn, rep 1

value: four week old leaf

value: mock inoculated

value: subjective dawn


title: NY2979

value: Mount Sinai

value: HCC tumor


title: NY2882


title: CSC 2

description: miRNA expression profiling  from CSCs


title: FP25 nickel

description:
Sample 16
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: nickel


title: FP25 vaseline

description:
Sample 15
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: CSC+Exo 3

description: miRNA expression profiling  from CSCs treated with MSC-exosomes

source_name: CSCs treated with MSC-exosomes from bone marrow


title: NY2243


title: NY2986


title: patient_27_nicl2

description:
Sample 8
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Healthy

value: peripheral blood mononuclear cells (PBMCs)


title: FP26 vaseline

description:
Sample 17
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: CSC+Exo 2


title: FP22 vaseline

description:
Sample 13
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: NY2611


title: NY2250


title: CSC+Exo 1


title: NY5078


title: NY5068


title: NY2684


title: NY2490


title: NY5063


title: CSC 1

description: miRNA expression profiling  from CSCs


title: FP22 nickel

description:
Sample 14
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: 238B

source_name: healty skin_Nonanoic Acid_day11

value: Nonanoic Acid (day 11)


title: 244C

description:
Sample 10
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: skin


title: 251A

description:
Sample 12
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

value: Whole tissue extract


title: 250C

description:
Sample 11
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: 251B

description:
Sample 6
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.

source_name: healthy skin_day0

value: NA (day 0)


title: 235A

description:
Sample 7
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: 236C


title: OoD2

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

country: Spain

institute: University Rovira i Virgili

hyb_protocol: Cy3-labeled DNA was precipitated with 1 volume isopropanol. Hybridization mixture including 2mg labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). 090324_Ooen_exp Nimblegen arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed according to manufacturer's protocol

scan_protocol: Arrays were scanned on a Genepix 4000B scanner

data_processing: Pair reports (raw data) listing the probe  intensities of the arrays were extracted and processed using Nimblescan software v2.6

organism: Oenococcus oeni PSU-1

source_name: Oenococcus oeni total RNA from cells after 3 hours of ethanol shock

label_protocol: dsDNA was generated from 10 mg RNA following Nimblegen array user's guide protocol. 1mg dsDNA was labeled by Klenow random priming with Cy3 nonamers with Nimblegen One-color DNA labeling kit (cat.# 06370411001) following manufacturer's user's guide

growth_protocol: O. oeni PSU-1 was cultured at 30ºC in MRS broth medium supplemented with L-malic acid (4 g l-1) and fructose (5 g l-1) at pH 5.0.

extract_protocol: Total RNA extractions were performed using the Roche RNeasy kit according to the manufacturer’s instructions (Mannheim, Germany).

treatment_protocol: When cultures reached the late exponential phase (OD600nm ≈ 1) they were divided into two sterile flasks. Immediately, 12% (v/v) of ethanol was added to one flask and 12% (v/v) of water was added to the other (control).

tag: strain


title: silver_nitrate_induced_replicate_4

city: Freising

first: Erich

last: Glawischnig

address: Emil-Ramann-Str. 8

department: Plant Science

institute: TU Muenchen

description: Sample name: AgNO3 4

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEX Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G4102A; DesignID 65426) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3_GX for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 065426_D_F_20140324) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Eutrema salsugineum

source_name: silver nitrate-induced

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: After 10 days of stratification at 6°C, plants were grown in a growth chamber at a 12/12 h photoperiod at a light intensity of 80 to 100 µmol m-2 s-1 at 21°C and 40% relative humidity.

extract_protocol: For each treatment, four biological replicates were investigated, generated from pooled tissues of 4 plants. Total RNA was extracted with NucleoSpin® RNA II Kit (Machery-Nagel). After DNase treatment, concentration and quality of extracted RNA was measured photometrically and with a Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For stress treatment leaves were sprayed with 5 mM AgNO3 or placed under a UV lamp (Desaga UVVIS, λ=254 nm, 8 W) at a distance of 20 cm and radiated for 2 h.

tag: stress

value: silver nitrate

value: rosette leaves


title: 244A

description:
Sample 4
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: NY2704


title: silver_nitrate_induced_replicate_1

description: Sample name: AgNO3 1


title: NY2873B


title: NY2963


title: NY2996


title: NY5093


title: NY2018


title: NY2397


title: UV_Induced_replicate_1

description: Sample name: UV 1

source_name: UV-induced

value: UV


title: UV_Induced_replicate_2

description: Sample name: UV 2


title: UV_Induced_replicate_5

description: Sample name: UV 5


title: 238A

description:
Sample 3
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: not_induced_replicate_4

description: Sample name: Ni 4

source_name: not induced

value: control


title: NY2776B


title: OoC2

source_name: Oenococcus oeni total RNA from cells after 1 hour of water addition


title: NY2830


title: silver_nitrate_induced_replicate_3

description: Sample name: AgNO3 3


title: silver_nitrate_induced_replicate_2

description: Sample name: AgNO3 2


title: 250A

description:
Sample 5
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: OoB2

source_name: Oenococcus oeni total RNA from cells after 1 hour of ethanol shock


title: 236A

description:
Sample 2
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: UV_Induced_replicate_6

description: Sample name: UV 6


title: 235C

description:
Sample 1
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.


title: NY2875


title: OoA2

source_name: Oenococcus oeni total RNA from cells before treatment


title: not_induced_replicate_3

description: Sample name: Ni 3


title: NY2301


title: not_induced_replicate_2

description: Sample name: Ni 2


title: Breast Cancer serum sample 28 BC28

status: Public on Sep 30 2015

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2.1 microarray analysis software.  Individual serum results were linearly normalized via internal reference features into diagnostically appropriate disease or control groups  using the Group Characterization function.  Group characterized samples were then compared to identify the differential expression of autoantibodies using the Two Groups Comparison feature.   More information about this process, and the exact differentiating power being addressed with each comparison, can be found in the accompanying manuscript.  Selected biomarker potential, power, and efficacy was further evaluated using Random Forest (RF) Training and Testing Set analysis and decision-tree logic.

label: Alexa Fluor 647

molecule: other

source_name: Breast Cancer

label_protocol: standard Invitrogen protocol

extract_protocol: All serum samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: gender

value: Female

value: Breast Cancer

value: serum


title: Early-Stage Parkinson's Disease serum sample 4 MJFF-PD103

source_name: Early-Stage Parkinson's Disease

value: Male

value: Early-Stage Parkinson's Disease


title: Early-Stage Parkinson's Disease serum sample 8 MJFF-PD109


title: Breast Cancer serum sample 26 BC26


title: Breast Cancer serum sample 30 BC30


title: Breast Cancer serum sample 29 BC29


title: Early-Stage Parkinson's Disease serum sample 5 MJFF-PD105


title: Breast Cancer serum sample 25 BC25


title: NY2780

value: Mount Sinai

value: HCC tumor


title: Early-Stage Parkinson's Disease serum sample 6 MJFF-PD106


title: Breast Cancer serum sample 27 BC27


title: Early-Stage Parkinson's Disease serum sample 7 MJFF-PD108


title: Breast Cancer serum sample 16 BC16


title: Breast Cancer serum sample 20 BC20


title: Breast Cancer serum sample 21 BC21


title: Breast Cancer serum sample 19 BC19


title: Breast Cancer serum sample 17 BC17


title: Breast Cancer serum sample 18 BC18


title: Breast Cancer serum sample 22 BC22


title: NY2327


title: Early-Stage Parkinson's Disease serum sample 2 MJFF-PD100


title: Early-Stage Parkinson's Disease serum sample 3 MJFF-PD102


title: Breast Cancer serum sample 23 BC23


title: Breast Cancer serum sample 24 BC24


title: not_induced_replicate_1

description: Sample name: Ni 1


title: LS_medie

value: Allergic contact dermatitis

value: Vehicle

source_name: Reference: mixture of all samples


title: Breast Cancer serum sample 15 BC15


title: Early-Stage Parkinson's Disease serum sample 1 MJFF-PD10


title: Breast Cancer serum sample 13 BC13


title: Breast Cancer serum sample 14 BC14


title: Breast Cancer serum sample 11 BC11


title: Breast Cancer serum sample 7 BC7


title: Breast Cancer serum sample 9 BC9


title: Breast Cancer serum sample 6 BC6


title: Breast Cancer serum sample 4 BC4


title: Breast Cancer serum sample 10 BC10


title: Breast Cancer serum sample 8 BC8


title: Breast Cancer serum sample 5 BC5


title: Parkinson's Disease serum sample 29 PK29

source_name: Parkinson's Disease

value: Parkinson's Disease


title: Parkinson's Disease serum sample 26 PK26


title: Breast Cancer serum sample 2 BC2


title: Breast Cancer serum sample 12 BC12


title: Breast Cancer serum sample 1 BC1


title: Parkinson's Disease serum sample 27 PK27


title: Parkinson's Disease serum sample 20 PK20


title: Parkinson's Disease serum sample 23 PK23


title: Parkinson's Disease serum sample 18 PK18


title: Parkinson's Disease serum sample 22 PK22


title: Parkinson's Disease serum sample 21 PK21


title: Parkinson's Disease serum sample 28 PK28


title: Parkinson's Disease serum sample 17 PK17


title: Parkinson's Disease serum sample 19 PK19


title: Parkinson's Disease serum sample 13 PK13


title: Parkinson's Disease serum sample 15 PK15


title: Parkinson's Disease serum sample 12 PK12

value: UNK


title: Parkinson's Disease serum sample 16 PK16


title: Parkinson's Disease serum sample 9 PK9


title: Parkinson's Disease serum sample 10 PK10


title: Breast Cancer serum sample 3 BC3


title: Parkinson's Disease serum sample 7 PK7


title: Parkinson's Disease serum sample 3 PK3


title: Parkinson's Disease serum sample 6 PK6


title: Alzheimer's Disease serum sample 40 AD40

source_name: Alzheimer's Disease

value: Alzheimer's Disease


title: Parkinson's Disease serum sample 2 PK2


title: Parkinson's Disease serum sample 14 PK14


title: Alzheimer's Disease serum sample 45 AD45


title: Alzheimer's Disease serum sample 51 AD51


title: Parkinson's Disease serum sample 4 PK4


title: Alzheimer's Disease serum sample 48 AD48


title: Alzheimer's Disease serum sample 50 AD50


title: Parkinson's Disease serum sample 5 PK5


title: Alzheimer's Disease serum sample 49 AD49


title: Alzheimer's Disease serum sample 52 AD52


title: Alzheimer's Disease serum sample 54 AD54


title: Parkinson's Disease serum sample 1 PK1


title: Alzheimer's Disease serum sample 39 AD39


title: Alzheimer's Disease serum sample 47 AD47


title: Alzheimer's Disease serum sample 38 AD38


title: Alzheimer's Disease serum sample 36 AD36


title: Alzheimer's Disease serum sample 53 AD53


title: Parkinson's Disease serum sample 11 PK11


title: Parkinson's Disease serum sample 8 PK8


title: Alzheimer's Disease serum sample 35 AD35


title: Alzheimer's Disease serum sample 34 AD34


title: Alzheimer's Disease serum sample 46 AD46


title: Alzheimer's Disease serum sample 32 AD32


title: Alzheimer's Disease serum sample 33 AD33


title: Alzheimer's Disease serum sample 31 AD31


title: Alzheimer's Disease serum sample 23 AD23


title: Alzheimer's Disease serum sample 24 AD24


title: Alzheimer's Disease serum sample 20 AD20


title: Alzheimer's Disease serum sample 25 AD25


title: Alzheimer's Disease serum sample 17 AD17


title: Alzheimer's Disease serum sample 22 AD22


title: Alzheimer's Disease serum sample 21 AD21


title: Alzheimer's Disease serum sample 18 AD18


title: Alzheimer's Disease serum sample 26 AD26


title: Alzheimer's Disease serum sample 37 AD37


title: Alzheimer's Disease serum sample 16 AD16


title: Alzheimer's Disease serum sample 19 AD19


title: Alzheimer's Disease serum sample 28 AD28


title: Alzheimer's Disease serum sample 15 AD15


title: Alzheimer's Disease serum sample 27 AD27


title: Alzheimer's Disease serum sample 13 AD13


title: Alzheimer's Disease serum sample 30 AD30


title: Alzheimer's Disease serum sample 29 AD29


title: Alzheimer's Disease serum sample 14 AD14


title: Alzheimer's Disease serum sample 9 AD9


title: Alzheimer's Disease serum sample 12 AD12


title: Alzheimer's Disease serum sample 10 AD10


title: Parkinson's Disease serum sample 25 PK25


title: Parkinson's Disease serum sample 24 PK24


title: Alzheimer's Disease serum sample 11 AD11


title: Alzheimer's Disease serum sample 8 AD8


title: Alzheimer's Disease serum sample 7 AD7


title: Alzheimer's Disease serum sample 6 AD6


title: Alzheimer's Disease serum sample 5 AD5


title: Alzheimer's Disease serum sample 1 AD1


title: Multiple Sclerosis serum sample MS7

source_name: Multiple Sclerosis

value: Multiple Sclerosis


title: Alzheimer's Disease serum sample 4 AD4


title: Multiple Sclerosis serum sample MS4


title: Alzheimer's Disease serum sample 2 AD2


title: Alzheimer's Disease serum sample 3 AD3


title: Multiple Sclerosis serum sample MS3


title: Multiple Sclerosis serum sample BioS-MS20

value: female


title: Multiple Sclerosis serum sample BioS-MS17

value: MALE


title: Multiple Sclerosis serum sample MS2


title: Multiple Sclerosis serum sample MS9


title: Multiple Sclerosis serum sample MS5


title: Multiple Sclerosis serum sample BioS-MS16

value: FEMALE


title: Multiple Sclerosis serum sample BioS-MS19


title: Multiple Sclerosis serum sample MS1


title: Multiple Sclerosis serum sample MS10


title: Multiple Sclerosis serum sample BioS-MS9


title: Multiple Sclerosis serum sample BioS-MS10


title: Multiple Sclerosis serum sample BioS-MS8


title: Multiple Sclerosis serum sample BioS-MS11


title: Multiple Sclerosis serum sample MS8


title: Multiple Sclerosis serum sample BioS-MS7


title: Multiple Sclerosis serum sample BioS-MS6


title: Multiple Sclerosis serum sample MS6


title: Multiple Sclerosis serum sample BioS-MS12


title: Multiple Sclerosis serum sample BioS-MS18


title: Multiple Sclerosis serum sample BioS-MS15


title: Multiple Sclerosis serum sample BioS-MS14


title: Multiple Sclerosis serum sample BioS-MS1


title: Multiple Sclerosis serum sample BioS-MS5


title: Multiple Sclerosis serum sample BioS-MS3


title: Normal Control Donor serum sample 155 CY19

source_name: Normal Control Donor

value: Normal Control Donor


title: Multiple Sclerosis serum sample BioS-MS2


title: Multiple Sclerosis serum sample BioS-MS4


title: Normal Control Donor serum sample 152 CY16


title: Normal Control Donor serum sample 151 CY15


title: Normal Control Donor serum sample 145 CY9


title: Normal Control Donor serum sample 150 CY14


title: Normal Control Donor serum sample 149 CY13


title: Normal Control Donor serum sample 153 CY17


title: Normal Control Donor serum sample 147 CY11

value: Female


title: Normal Control Donor serum sample 148 CY12


title: Normal Control Donor serum sample 141 CY5


title: Normal Control Donor serum sample 140 CY4


title: Normal Control Donor serum sample 142 CY6


title: Normal Control Donor serum sample 144 CY8


title: Normal Control Donor serum sample 143 CY7


title: Normal Control Donor serum sample 146 CY10


title: Normal Control Donor serum sample 138 CY2


title: Normal Control Donor serum sample 136 CO20


title: Normal Control Donor serum sample 135 CO19


title: Normal Control Donor serum sample 156 CY20


title: Normal Control Donor serum sample 139 CY3


title: Normal Control Donor serum sample 137 CY1


title: Normal Control Donor serum sample 154 CY18


title: Normal Control Donor serum sample 133 CO17


title: Normal Control Donor serum sample 130 CO14


title: Normal Control Donor serum sample 129 CO13


title: Normal Control Donor serum sample 131 CO15


title: Normal Control Donor serum sample 128 CO12


title: Normal Control Donor serum sample 132 CO16


title: Normal Control Donor serum sample 134 CO18


title: Normal Control Donor serum sample 127 CO11


title: Multiple Sclerosis serum sample BioS-MS13


title: Normal Control Donor serum sample 120 CO4


title: Normal Control Donor serum sample 126 CO10


title: Normal Control Donor serum sample 123 CO7


title: Normal Control Donor serum sample 114 NJISA-CT64


title: Normal Control Donor serum sample 121 CO5


title: Normal Control Donor serum sample 124 CO8


title: Normal Control Donor serum sample 118 CO2


title: Normal Control Donor serum sample 113 NJISA-CT63


title: Normal Control Donor serum sample 119 CO3


title: Normal Control Donor serum sample 108 NJISA-CT45


title: Normal Control Donor serum sample 117 CO1


title: Normal Control Donor serum sample 111 NJISA-CT56


title: Normal Control Donor serum sample 112 NJISA-CT62


title: Normal Control Donor serum sample 110 NJISA-CT53


title: Normal Control Donor serum sample 115 NJISA-CT65


title: Normal Control Donor serum sample 109 NJISA-CT47


title: Normal Control Donor serum sample 106 NJISA-CT4


title: Normal Control Donor serum sample 107 NJISA-CT44


title: Normal Control Donor serum sample 125 CO9


title: Normal Control Donor serum sample 105 NJISA-CT38


title: Normal Control Donor serum sample 102 NJISA-CT30


title: Normal Control Donor serum sample 104 NJISA-CT36


title: Normal Control Donor serum sample 101 NJISA-CT3


title: Normal Control Donor serum sample 98 NJISA-CT26


title: Normal Control Donor serum sample 99 NJISA-CT27


title: Normal Control Donor serum sample 116 NJISA-CT70


title: Normal Control Donor serum sample 100 NJISA-CT29


title: Normal Control Donor serum sample 97 NJISA-CT25


title: Normal Control Donor serum sample 92 BioS-CT8


title: Normal Control Donor serum sample 94 NJISA-CT20


title: Normal Control Donor serum sample 96 NJISA-CT24


title: Normal Control Donor serum sample 91 BioS-CT7


title: Normal Control Donor serum sample 95 NJISA-CT23


title: Normal Control Donor serum sample 90 BioS-CT65


title: Normal Control Donor serum sample 88 BioS-CT63


title: Normal Control Donor serum sample 80 BioS-CT56


title: Normal Control Donor serum sample 86 BioS-CT61


title: Normal Control Donor serum sample 87 BioS-CT62


title: Normal Control Donor serum sample 103 NJISA-CT34


title: Normal Control Donor serum sample 83 BioS-CT59


title: Normal Control Donor serum sample 84 BioS-CT6


title: Normal Control Donor serum sample 81 BioS-CT57


title: Normal Control Donor serum sample 79 BioS-CT55


title: Normal Control Donor serum sample 78 BioS-CT54


title: Normal Control Donor serum sample 85 BioS-CT60


title: Normal Control Donor serum sample 82 BioS-CT58


title: Normal Control Donor serum sample 77 BioS-CT53


title: Normal Control Donor serum sample 76 BioS-CT52


title: Normal Control Donor serum sample 72 BioS-CT49


title: Normal Control Donor serum sample 73 BioS-CT5


title: Normal Control Donor serum sample 75 BioS-CT51


title: Normal Control Donor serum sample 71 BioS-CT48


title: Normal Control Donor serum sample 70 BioS-CT47


title: Normal Control Donor serum sample 69 BioS-CT46


title: Normal Control Donor serum sample 93 BioS-CT9


title: Normal Control Donor serum sample 89 BioS-CT64


title: Normal Control Donor serum sample 68 BioS-CT45


title: Normal Control Donor serum sample 67 BioS-CT44


title: Normal Control Donor serum sample 66 BioS-CT43


title: Normal Control Donor serum sample 74 BioS-CT50


title: Normal Control Donor serum sample 56 BioS-CT34


title: Normal Control Donor serum sample 63 BioS-CT40


title: Normal Control Donor serum sample 58 BioS-CT36


title: Normal Control Donor serum sample 55 BioS-CT33


title: Normal Control Donor serum sample 57 BioS-CT35


title: Normal Control Donor serum sample 54 BioS-CT32


title: Normal Control Donor serum sample 61 BioS-CT39


title: Normal Control Donor serum sample 60 BioS-CT38


title: Normal Control Donor serum sample 59 BioS-CT37


title: Normal Control Donor serum sample 49 BioS-CT28


title: Normal Control Donor serum sample 48 BioS-CT27


title: Normal Control Donor serum sample 47 BioS-CT26


title: Normal Control Donor serum sample 51 BioS-CT3


title: Normal Control Donor serum sample 45 BioS-CT24


title: Normal Control Donor serum sample 52 BioS-CT30


title: Normal Control Donor serum sample 50 BioS-CT29


title: Normal Control Donor serum sample 46 BioS-CT25


title: Normal Control Donor serum sample 43 BioS-CT22


title: Normal Control Donor serum sample 44 BioS-CT23


title: Normal Control Donor serum sample 53 BioS-CT31


title: Normal Control Donor serum sample 42 BioS-CT21


title: Normal Control Donor serum sample 64 BioS-CT41


title: Normal Control Donor serum sample 65 BioS-CT42


title: Normal Control Donor serum sample 39 BioS-CT19


title: Normal Control Donor serum sample 62 BioS-CT4


title: Normal Control Donor serum sample 38 BioS-CT18


title: Normal Control Donor serum sample 40 BioS-CT2


title: Normal Control Donor serum sample 37 BioS-CT17


title: Normal Control Donor serum sample 41 BioS-CT20


title: Normal Control Donor serum sample 34 BioS-CT14


title: Normal Control Donor serum sample 33 BioS-CT13


title: Normal Control Donor serum sample 35 BioS-CT15


title: Normal Control Donor serum sample 31 BioS-CT11


title: Normal Control Donor serum sample 32 BioS-CT12


title: Normal Control Donor serum sample 36 BioS-CT16


title: Normal Control Donor serum sample 30 BioS-CT10


title: Normal Control Donor serum sample 29 BioS-CT1


title: Normal Control Donor serum sample 27 AST-CT37


title: Normal Control Donor serum sample 25 AST-CT35


title: Normal Control Donor serum sample 26 AST-CT36


title: Normal Control Donor serum sample 24 AST-CT34


title: Normal Control Donor serum sample 23 AST-CT33


title: Normal Control Donor serum sample 22 AST-CT32


title: Normal Control Donor serum sample 21 AST-CT31


title: Normal Control Donor serum sample 18 AST-CT28


title: Normal Control Donor serum sample 28 AST-CT38


title: Normal Control Donor serum sample 15 AST-CT25


title: Normal Control Donor serum sample 14 AST-CT24


title: Normal Control Donor serum sample 19 AST-CT29


title: Normal Control Donor serum sample 16 AST-CT26


title: Normal Control Donor serum sample 13 AST-CT23


title: Normal Control Donor serum sample 8 AST-CT18


title: Normal Control Donor serum sample 10 AST-CT20


title: Normal Control Donor serum sample 6 AST-CT16


title: Normal Control Donor serum sample 7 AST-CT17


title: Normal Control Donor serum sample 4 AST-CT14


title: Normal Control Donor serum sample 11 AST-CT21


title: Normal Control Donor serum sample 20 AST-CT30


title: Normal Control Donor serum sample 12 AST-CT22


title: Normal Control Donor serum sample 9 AST-CT19


title: Normal Control Donor serum sample 3 AST-CT13


title: Normal Control Donor serum sample 1 AST-CT11


title: Early-Stage Parkinson's Disease serum sample 103 MJFF-PD99


title: Early-Stage Parkinson's Disease serum sample 100 MJFF-PD94


title: Early-Stage Parkinson's Disease serum sample 98 MJFF-PD91


title: Early-Stage Parkinson's Disease serum sample 96 MJFF-PD9


title: Early-Stage Parkinson's Disease serum sample 99 MJFF-PD92


title: Early-Stage Parkinson's Disease serum sample 97 MJFF-PD90


title: Early-Stage Parkinson's Disease serum sample 94 MJFF-PD88


title: Normal Control Donor serum sample 17 AST-CT27


title: Early-Stage Parkinson's Disease serum sample 102 MJFF-PD98


title: Early-Stage Parkinson's Disease serum sample 92 MJFF-PD85


title: Early-Stage Parkinson's Disease serum sample 93 MJFF-PD87


title: Early-Stage Parkinson's Disease serum sample 90 MJFF-PD83


title: Early-Stage Parkinson's Disease serum sample 91 MJFF-PD84


title: Normal Control Donor serum sample 5 AST-CT15


title: Normal Control Donor serum sample 2 AST-CT12


title: Early-Stage Parkinson's Disease serum sample 86 MJFF-PD8


title: Early-Stage Parkinson's Disease serum sample 101 MJFF-PD96


title: Early-Stage Parkinson's Disease serum sample 85 MJFF-PD79


title: Early-Stage Parkinson's Disease serum sample 83 MJFF-PD76


title: Early-Stage Parkinson's Disease serum sample 84 MJFF-PD78


title: Early-Stage Parkinson's Disease serum sample 88 MJFF-PD81


title: Early-Stage Parkinson's Disease serum sample 79 MJFF-PD71L


title: Early-Stage Parkinson's Disease serum sample 82 MJFF-PD75


title: Early-Stage Parkinson's Disease serum sample 80 MJFF-PD72L


title: Early-Stage Parkinson's Disease serum sample 95 MJFF-PD89


title: Early-Stage Parkinson's Disease serum sample 78 MJFF-PD70L


title: Early-Stage Parkinson's Disease serum sample 77 MJFF-PD69L


title: Early-Stage Parkinson's Disease serum sample 76 MJFF-PD68L


title: Early-Stage Parkinson's Disease serum sample 74 MJFF-PD64L


title: Early-Stage Parkinson's Disease serum sample 71 MJFF-PD61L


title: Early-Stage Parkinson's Disease serum sample 75 MJFF-PD67L


title: Early-Stage Parkinson's Disease serum sample 70 MJFF-PD60L


title: Early-Stage Parkinson's Disease serum sample 81 MJFF-PD73L


title: Early-Stage Parkinson's Disease serum sample 89 MJFF-PD82


title: Early-Stage Parkinson's Disease serum sample 69 MJFF-PD6


title: Early-Stage Parkinson's Disease serum sample 72 MJFF-PD62L


title: Normal Control Donor serum sample 122 CO6


title: Early-Stage Parkinson's Disease serum sample 73 MJFF-PD63L


title: Early-Stage Parkinson's Disease serum sample 68 MJFF-PD59L


title: Early-Stage Parkinson's Disease serum sample 67 MJFF-PD58L


title: Early-Stage Parkinson's Disease serum sample 65 MJFF-PD56L


title: Early-Stage Parkinson's Disease serum sample 66 MJFF-PD57L


title: Early-Stage Parkinson's Disease serum sample 57 MJFF-PD49


title: Early-Stage Parkinson's Disease serum sample 61 MJFF-PD52L


title: Early-Stage Parkinson's Disease serum sample 60 MJFF-PD51L


title: Early-Stage Parkinson's Disease serum sample 58 MJFF-PD5


title: Early-Stage Parkinson's Disease serum sample 59 MJFF-PD50


title: Early-Stage Parkinson's Disease serum sample 62 MJFF-PD53L


title: Early-Stage Parkinson's Disease serum sample 54 MJFF-PD46


title: Early-Stage Parkinson's Disease serum sample 63 MJFF-PD54L


title: Early-Stage Parkinson's Disease serum sample 55 MJFF-PD47


title: Early-Stage Parkinson's Disease serum sample 53 MJFF-PD45


title: Early-Stage Parkinson's Disease serum sample 52 MJFF-PD44


title: Early-Stage Parkinson's Disease serum sample 56 MJFF-PD48


title: Early-Stage Parkinson's Disease serum sample 50 MJFF-PD4


title: Early-Stage Parkinson's Disease serum sample 47 MJFF-PD37


title: Early-Stage Parkinson's Disease serum sample 64 MJFF-PD55L


title: Early-Stage Parkinson's Disease serum sample 51 MJFF-PD43


title: Early-Stage Parkinson's Disease serum sample 46 MJFF-PD36


title: Early-Stage Parkinson's Disease serum sample 45 MJFF-PD35


title: Early-Stage Parkinson's Disease serum sample 49 MJFF-PD39


title: Early-Stage Parkinson's Disease serum sample 48 MJFF-PD38


title: Early-Stage Parkinson's Disease serum sample 44 MJFF-PD34


title: Early-Stage Parkinson's Disease serum sample 42 MJFF-PD32


title: Early-Stage Parkinson's Disease serum sample 37 MJFF-PD27


title: Early-Stage Parkinson's Disease serum sample 40 MJFF-PD3


title: Early-Stage Parkinson's Disease serum sample 38 MJFF-PD28


title: Early-Stage Parkinson's Disease serum sample 41 MJFF-PD30


title: Early-Stage Parkinson's Disease serum sample 36 MJFF-PD26


title: Early-Stage Parkinson's Disease serum sample 39 MJFF-PD29


title: Early-Stage Parkinson's Disease serum sample 34 MJFF-PD24


title: Early-Stage Parkinson's Disease serum sample 43 MJFF-PD33


title: Early-Stage Parkinson's Disease serum sample 30 MJFF-PD20


title: Early-Stage Parkinson's Disease serum sample 33 MJFF-PD23


title: Early-Stage Parkinson's Disease serum sample 28 MJFF-PD18


title: Early-Stage Parkinson's Disease serum sample 35 MJFF-PD25


title: Early-Stage Parkinson's Disease serum sample 26 MJFF-PD16


title: Early-Stage Parkinson's Disease serum sample 32 MJFF-PD22


title: Early-Stage Parkinson's Disease serum sample 29 MJFF-PD19


title: Early-Stage Parkinson's Disease serum sample 25 MJFF-PD15


title: Early-Stage Parkinson's Disease serum sample 27 MJFF-PD17


title: Early-Stage Parkinson's Disease serum sample 24 MJFF-PD14


title: Early-Stage Parkinson's Disease serum sample 21 MJFF-PD123


title: Early-Stage Parkinson's Disease serum sample 20 MJFF-PD122


title: Early-Stage Parkinson's Disease serum sample 18 MJFF-PD12


title: Early-Stage Parkinson's Disease serum sample 19 MJFF-PD120


title: Early-Stage Parkinson's Disease serum sample 17 MJFF-PD119


title: Early-Stage Parkinson's Disease serum sample 23 MJFF-PD13


title: Early-Stage Parkinson's Disease serum sample 22 MJFF-PD124


title: Early-Stage Parkinson's Disease serum sample 13 MJFF-PD114


title: Early-Stage Parkinson's Disease serum sample 10 MJFF-PD111


title: Early-Stage Parkinson's Disease serum sample 11 MJFF-PD112


title: Early-Stage Parkinson's Disease serum sample 31 MJFF-PD21


title: Early-Stage Parkinson's Disease serum sample 15 MJFF-PD117


title: Early-Stage Parkinson's Disease serum sample 9 MJFF-PD11


title: Early-Stage Parkinson's Disease serum sample 16 MJFF-PD118


title: Early-Stage Parkinson's Disease serum sample 14 MJFF-PD116


title: Early-Stage Parkinson's Disease serum sample 12 MJFF-PD113


title: Nasal wash vs. Blood RNA 72 hrs [Sp3056]

status: Public on Sep 19 2015

city: Adelaide

first: Mark

middle: B

last: Van der Hoek

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

hyb_protocol: The fluorescently labeled cDNAs for each pair-wise comparison were combined and hybridized to the surface of the microarray, essentially as described (McCluskey et al., 2004; Ogunniyi et al., 2010).

scan_protocol: Slides were scanned at 10 µM resolution using a GenePix 4000B Scanner (Molecular Devices, USA). Detector PMT voltages were adjusted individually for each slide so that the total red (Alexa Fluor 647) and green (Alexa Fluor 546) fluorescence signals for each channel were approximately equal while minimising the total number of features with signal above the maximum detectable.

data_processing:
Image features extracted using Spot (CSIRO, Australia).
Data analysis using Limma (Smyth G.K. 2004).
The ID_REFs in the Sample data table (1-5776) correspond to the indexes in the raw data file (0-5775) with an offset of 1.

label: Alexa 546

organism: Streptococcus pneumoniae

source_name: WCH43 (serotype 4), nasal wash, 72 hrs

label_protocol: RNA samples from pneumococci harvested from nasal wash or blood were reverse-transcribed using SuperScript III (Invitrogen) and then labeled with either Alexa Fluor 546 or Alexa Fluor 647 dye using the 3DNA Array 900 MPX labeling kit (Genisphere).

growth_protocol: For each of WCH16 and WCH43 challenge experiments, groups of 40 mice were used. The mice were anesthetized by i.p. injection of pentobarbital sodium (Nembutal; Rhone-Merieux) at a dose of 66 mg per g of body weight and challenged i.n. with 50 µl of bacterial suspension containing approximately 1 x 107 CFU in serum broth.

extract_protocol: RNA for microarray experiments was isolated and purified from either the nasopharynx or blood with acid-phenol-chloroform-isoamyl alcohol (125:24:1; pH 4.5; Ambion). Extracted RNA samples were checked for purity and integrity as described previously (LeMessurier et al., 2006; Mahdi et al., 2008). Bacterial-RNA samples from a minimum of five mice that satisfied these criteria from a specific niche were pooled. The RNA was then purified further using a Qiagen RNeasy mini kit. RNA was further enriched for prokaryotic RNA using the MicrobEnrich kit (Ambion). The amount of RNA recovered following purification/enrichment was determined by A260/280 measurements.

treatment_protocol: At each of 48, 72 and 96 h post-challenge, at least 12 mice were sacrificed by CO2 asphyxiation, and nasal wash and blood samples were processed essentially as described previously (Ogunniyi et al., 2002; LeMessurier et al., 2006; Mahdi et al., 2008).

tag: strain/background

tag: serotype

tag: mouse tissue

value: nasopharynx

tag: time point

label: Alexa 647

source_name: WCH43 (serotype 4), blood, 72 hrs

value: blood


title: Nasal wash vs. Blood RNA 48 hrs [Sp3024]

source_name: WCH43 (serotype 4), nasal wash, 48 hrs

source_name: WCH43 (serotype 4), blood, 48 hrs


title: Nasal wash vs. Blood RNA 96 hrs [Sp3028]

source_name: WCH43 (serotype 4), nasal wash, 96 hrs

source_name: WCH43 (serotype 4), blood, 96 hrs


title: Blood vs. Nasal wash RNA 48 hrs [Sp3072]


title: Blood vs. Nasal wash RNA 96 hrs [Sp3177]


title: Blood vs. Nasal wash RNA 72 hrs [Sp3174]


title: Nasal wash vs. Blood RNA 72 hrs [Sp3022]


title: Nasal wash vs. Blood RNA 96 hrs [Sp2940]


title: Nasal wash vs. Blood RNA 48 hrs [Sp2928]


title: Blood vs. Nasal wash RNA 96 hrs [Sp2934]

source_name: WCH16 (serotype 6A), blood, 96 hrs

source_name: WCH16 (serotype 6A), nasal wash, 96 hrs


title: Nasal wash vs. Blood RNA 96 hrs [Sp2919]


title: Nasal wash vs. Blood RNA 96 hrs [Sp2912]


title: A

city: Shanghai

first: Zhaogui

last: Sun

state: Shanghai

address: Road Xietu 2140

institute: Shanghai Institute of Planned Parenthood Research

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using the iScan Microarray Scanner.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio GeneExpression Module.

organism: Mus musculus

source_name: ovaries, wild type

label_protocol: Biotinylated cRNA were prepared with TotalPrep RNA Amplification Kit (Cat: AMIL1791, Ambion) for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 1.5% agarose gel electrophoresis.

tag: genetic background

tag: genotype/variation

value: wild type

tag: Sex

value: ovaries


title: Nasal wash vs. Blood RNA 48 hrs [Sp2913]

source_name: WCH16 (serotype 6A), nasal wash, 48 hrs

source_name: WCH16 (serotype 6A), blood, 48 hrs


title: N2_4 in pretzel-stage embryos

status: Public on Sep 22 2015

city: Goettingen

first: Michal

last: Turek

address: Am Fassberg 11

department: Sleep and Waking

institute: Max Planck Institute for Biophysical Chemistry

description: Gene expression in N2 wild type pretzel-stage embryos

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65uC in the Hybridization Oven (Agilent).

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B).

data_processing: Intensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor.

organism: Caenorhabditis elegans

source_name: N2, replicate 4

label_protocol: 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer’s recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 21.5°C. For each sample approximately 3000 pretzel-stage embryos were picked individually with a platinum wire pick and were immediately placed into a tube containing one ml of Trizol (Invitrogene).

extract_protocol: RNA was extracted from the Trizol using standard procedure.

treatment_protocol: For performing the experiment ‘‘Low RNA Input linear Amplification Kit Plus, One Color’’ protocol (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5282)were used following the manufacturer’s standard protocol.

value: whole animal

value: hermaphrodite

tag: age

value: pretzel-stage embryo

value: N2 wild type pretzel-stage embryos


title: Nasal wash vs. Blood RNA 72 hrs [Sp2516]

source_name: WCH16 (serotype 6A), nasal wash, 72 hrs

source_name: WCH16 (serotype 6A), blood, 72 hrs


title: Blood vs. Nasal wash RNA 48 hrs [Sp2936]


title: C

description:
Homozygotic type
9481416012_B_Grn

source_name: ovaries, LepR mutant

value: LepR mutations


title: Blood vs. Nasal wash RNA 72 hrs [Sp2938]


title: aptf-1_4 in pretzel-stage embryos

description: Gene expression in aptf-1(gk794) mutant pretzel-stage embryos

source_name: aptf-1(gk794) mutant, replicate 4


title: N2_3 in pretzel-stage embryos

source_name: N2, replicate 3


title: aptf-1_1 in pretzel-stage embryos

source_name: aptf-1(gk794) mutant, replicate 1

value: aptf-1(gk794) mutant pretzel-stage embryos


title: aptf-1_3 in pretzel-stage embryos

source_name: aptf-1(gk794) mutant, replicate 3


title: Nasal wash vs. Blood RNA 48 hrs [Sp2513]


title: N2_2 in pretzel-stage embryos

source_name: N2, replicate 2


title: Nasal wash vs. Blood RNA 72 hrs [Sp2915]


title: Early-Stage Parkinson's Disease serum sample 87 MJFF-PD80

source_name: Early-Stage Parkinson's Disease

value: Male

tag: disease state

value: Early-Stage Parkinson's Disease

value: serum


title: EGFP-positive 2

status: Public on Jul 14 2015

city: Boston

first: Gabriel

last: Musso

state: MA

address: 75 Francis St, Thorn 1123

institute: Harvard Medical School

description: Gene expression data from embryonic zebrafish (2ss)

hyb_protocol: Samples were processed by the Boston Children’s Hospital Molecular Genetics Core Facility for hybridization and analysis using Affymetrix Zv9 microarray chips.

data_processing: Normalized (MAS background correction and RMA normalization) gene-level expression data were computed from Affymetrix ZebGene-1_1-st CEL files using Affymetrix ExpressionConsole software. Regulated gene lists were computed from the normalized data using the R/Bioconductor package siggenes and an FDR threshold of 0.09.

organism: Danio rerio

source_name: Zebrafish embryos, 2 somite stage

label_protocol: Not provided

growth_protocol: Three independent times the same family of homozygous drl:EGFP transgenic zebrafish were mass-mated and their embryos collected at 2 ss.

extract_protocol: Embryos were de-chorionated, homogenized in PBS with 5% FCS with a hand-held motor pistil, and filtered twice through 40 µm cell strainers (BD Biosciences). Propidium iodide (PI) was added and the cell suspension sorted through a BD LSR II Flow Cytometer (BD Biosciences) for EGFP positive, PI negative, and EGFP negative, PI negative into Trizol LS with subsequent mRNA isolation as per manufacturer's protocol and added phenol/chloroform precipitation.

treatment_protocol: Control cells are sorted as being GFP-negative, and are compared in expression to EGFP-positive cells (from drl:EGFP transgenic fish)

value: embryonic tissue, post cell sorting

value: 2 somite stage

tag: cell population

value: EGFP-positive


title: ApoE knockout aorta, biological replicate 5

status: Public on Aug 21 2015

city: Philadelphia

first: Xiao-Feng

address: 3500 N. Broad St

department: Cardiovascular Research Center

institute: Temple University School of Medicine

description: Gene expression data from the aorta of ApoE knockout mice fed with 3 weeks of high fat diet starting from 8-week of age

hyb_protocol: Samples were hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Expression Microarray Core Facility in the Fox Chase Cancer Center, Temple University.

scan_protocol: Scanned microarray images were analyzed using the Affymetrix Gene Expression Console with Robust Multi-array Average normalization algorithm.

data_processing: Our affymetrix data analysis was done in the R statistical environment using “oligo” and “limma” packages. Venn diagram analysis was performed in the R statistical environment using the package “VennDiagram”. Heat map and scatter plot were performed using the statistical tools provided by the R and Bioconductor projects.

source_name: ApoE Knockout

label_protocol: Samples were labeled and hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Expression Microarray Core Facility in the Fox Chase Cancer Center, Temple University.

growth_protocol: All animal experiments were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) Guidelines and Authorization for the use of Laboratory Animals and were approved by the IACUC of Temple University School of Medicine.  All animals were housed in the Temple University Central Animal Facility under controlled temperature (23±1°C) with a 12-hour light-dark cycle. Animals had Ad libitum access to standard chow diet and water. Wild-type (WT) and ApoE-/- mice were purchased from the Jackson Laboratories (Bar Harbor, Maine). Caspase 1-/- mice were generously provided by Dr. Flavell’s laboratory (Department of Immunobiology, Yale University School of Medicine). ApoE/caspase-1 double gene deficient (ApoE-/-/caspase-1-/-) mice were generated by crossing caspase-1-/- mice into ApoE-/- mice. All mice used were on a C57BL/6 background.

extract_protocol: Total RNA was extracted from the aortas of mice using the RNeasy Kit (Qiagen, Valencia, CA). RNA quantity was determined by the NanoDrop ND-2000 (Thermo Scientific, Wilmington, DE). The RNA integrity was determined by the RNA 28S/18S ratio using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male mice Wild-type mice, Apolipoprotein E (ApoE) gene knockout mice, and ApoE/caspase-1 double gene deficient mice were fed high fat diet (catalog #88137, Harlan Teklad) for 3 weeks starting from 8-week of age to induce early hyperlipidemia.  At 11 week-old, mice were sacrificed and aortas were collected for microarray analysis.

value: aorta

value: male

tag: genotype

value: ApoE Knockout

value: 11 weeks


title: ApoE knockout aorta, biological replicate 2

tag: tissue


title: ApoE knockout aorta, biological replicate 4


title: Pre atorvastatin treatment MN25

status: Public on Jun 23 2015

city: Lund

first: Siker

last: Kimbung

address: Scheelevägen 2

department: Department of Oncology and Pathology, Clinical Sciences, Lund

country: Sweden

institute: Lund University

description: Core needle biopsy taken before commencement of 2 weeks atorvastatin treatment

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: Primary breast cancer

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: RNeasy protocol (Qiagen)

tag: treatment

value: no treatment (baseline)

tag: subject

value: breast cancer tumor biopsy


title: ApoE knockout aorta, biological replicate 1

tag: strain


title: EGFP-negative 2

scan_protocol: Samples were processed by the Boston Children’s Hospital Molecular Genetics Core Facility for hybridization and analysis using Affymetrix Zv9 microarray chips.

value: EGFP-negative


title: Post atorvastatin treatment FF25

description: Surgical biopsy following completion of 2 weeks atorvastatin treatment

value: 2 weeks atorvastatin


title: Post atorvastatin treatment FF43


title: Pre atorvastatin treatment FF33


title: EGFP-negative 3


title: EGFP-positive 1


title: Pre atorvastatin treatment MN10


title: EGFP-positive 3


title: EGFP-negative 1


title: ApoE knockout aorta, biological replicate 3


title: Pre atorvastatin treatment FF19


title: Pre atorvastatin treatment FF26


title: Pre atorvastatin treatment MN48


title: Post atorvastatin treatment FF10


title: Post atorvastatin treatment MN26


title: Pre atorvastatin treatment MN33


title: Post atorvastatin treatment FF3


title: Post atorvastatin treatment FF48


title: Post atorvastatin treatment MN19


title: Pre atorvastatin treatment MN43


title: Pre atorvastatin treatment MN11


title: Post atorvastatin treatment FF11


title: Post atorvastatin treatment FF24


title: Post atorvastatin treatment FF28


title: Post atorvastatin treatment FF6


title: Pre atorvastatin treatment MN29


title: Pre atorvastatin treatment MN6


title: Pre atorvastatin treatment MN2


title: Pre atorvastatin treatment MN1


title: Pre atorvastatin treatment MN17


title: Pre atorvastatin treatment MN28


title: Pre atorvastatin treatment MN44


title: Post atorvastatin treatment FF2


title: Pre atorvastatin treatment MN50


title: Post atorvastatin treatment FF17


title: Pre atorvastatin treatment MN24


title: Post atorvastatin treatment FF50


title: Pre atorvastatin treatment MN4


title: Pre atorvastatin treatment MN22


title: Post atorvastatin treatment FF22


title: Post atorvastatin treatment FF44


title: Post atorvastatin treatment FF1


title: Pre atorvastatin treatment MN39


title: osteosarcoma_jwrna_tissue_sarcoma_osteosarcoma

status: Public on May 28 2015

type: SRA

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

department: Pathology

institute: University of Michigan

description:
Sample name: MCTP_SAMPLE_276
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence alignment was performed using the Tuxedo pipeline: Bowtie2 (Bowtie2/2.0.2) and Tophat2 (TopHat/2.0.4)(Kim et al., 2013). We supplied TopHat with the set of transcript models annotated in the Homo sapiens Ensembl database version 69. The option fr-firststrand was used for the strand specific RNA-seq libraries while all other parameters were used with default values. When provided with ssRNA-seq data TopHat2 annotates aligned reads with the tag XS indicating the strand of origin in the DNA.
We used Ensembl v69 as the reference transcriptome to reconstruct the longest annotation for each gene based on the transcript and exon information provided by this assembly. We only included transcript isoforms that satisfied the following criteria: gene and transcript biotypes were annotated with the same type; transcript isoform annotation level was manual or automatic followed by manual revision (annotation levels 1 or 2) and transcript isoform was not reported as a problematic in the Encode-Gencode attributes table (e.g: transcript biotype is retained_intron, to be experimentally confirmed, or disruptive_domain).  Moreover, each transcript isoform used for our gene models was annotated with their “isoform expression rank” across the tissue cohorts, and their support level (tsl) provided by the Genecode project. Tsl equal to 1 indicates that all splice junctions of that transcript are supported by at least one non-suspect mRNA; any other number suggests that the transcript is supported by suspicious ESTs. These final gene models were used as the reference loci, or features, for downstream analysis.
The final gene models in the summarized transcriptome were used to compute strand specific expression. Paired-end reads mapping to the forward or opposite strand of a feature were counted in order to quantify the raw amount of forward and opposite transcription on a particular locus.  In order to determine what DNA strand a read pair was originated from, we first used the reads’ XS tag, provided by TopHat2, to identify the strand for each read in the pair. Then, we use the fact that in our ssRNA-seq protocol the second read is complementary to original mRNA and therefore the second read has to be on the same strand than the feature, while the first read on the opposite strand. These criteria unambiguously define a read pair DNA strand of origin. We discard all pairs in which one or both reads map to multiple locations in the genome, and all read pairs in which any of the reads was improperly mapped or did not have the XS flag provided by TopHat2 to indicate the strand of origin.
Genome_build: hg19
Supplementary_files_format_and_content: Feature (e.g. gene) raw read count over sense and antisense strands.  Processed data files linked to SuperSeries record.

extract_protocol:
Total RNA from frozen tissues or cell lines were isolated using miRNeasy mini kit (Qiagen Valencia, CA) while RNA was isolated from FFPE sections using FFPE RNAeasy kit (Qiagen).  For RNA from frozen sections and cell lines only samples with RNA integrity number (RIN) >8.0, upon 2100 Bioanalyzer analysis (Agilent Santa Clara, CA) were subjected to RNA sequencing.
Transcriptome libraries were prepared following a modified protocol previously described for generating strand specific RNASeq libraries 8.  Briefly 2.5 μg of total RNA was subjected to polyA selection using oligodT beads (Invitrogen, Carlsbad, CA).  Purified polyA RNA was fragmented and reverse transcribed using Superscipt-II (Invitrogen, Carlsbad CA).  Second strand synthesis was performed with DNA Ploymerase I (New England Biolabs, Ipswich, MA) in the presence of dNTP mix containing dUTP instead of dTTP.  The product was then subjected to end repair, A base addition and adaptor ligation steps.  Libraries were next size selected in the range of 350 bps after resolving in a 3% Nusieve 3:1 (Lonza, Basel, Switzerland) agarose gel and DNA recovered using QIAEX II gel extraction reagent (Qiagen, Valencia, CA). Libraries were barcoded during the 14-cycle PCR amplification with Phusion DNA polymerase (New England Biolabs, Ipswich, MA) and purified using AMPure XP beads (Beckman Coulter, Brea, CA).

value: not collected

value: MCTP

value: tissue

tag: disease

value: cancer

value: OSTEOSARCOMA


title: osteosarcoma_soas2_cell_line_sarcoma_osteosarcoma

description:
Sample name: MCTP_SAMPLE_279
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

tag: gender

value: metastatic


title: Post atorvastatin treatment FF42


title: osteosarcoma_os99_cell_line_sarcoma_osteosarcoma

description:
Sample name: MCTP_SAMPLE_278
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Post atorvastatin treatment FF4


title: rare_hc1_cell_line_rare_cancer_hairy_cell_leukemia

description:
Sample name: MCTP_SAMPLE_358
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: RARE


title: rare_L428_cell_line_rare_cancer_hodgkins_lymphoma

description:
Sample name: MCTP_SAMPLE_359
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: HODGKINS


title: rare_snuc_cell_line_rare_sinonasal_undifferentiated_carcinoma

description:
Sample name: MCTP_SAMPLE_369
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: rare_bewo_cell_line_rare_cancer_choriocarcinoma

description:
Sample name: MCTP_SAMPLE_356
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: CHORIO


title: osteosarcoma_mg63_cell_line_sarcoma_osteosarcoma

description:
Sample name: MCTP_SAMPLE_277
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Pre atorvastatin treatment MN41


title: rare_tfk1_cell_line_rare_cancer_bile_duct_carcinoma

description:
Sample name: MCTP_SAMPLE_371
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: rare_egi1_cell_line_rare_cancer_bile_duct_carcinoma

description:
Sample name: MCTP_SAMPLE_357
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Post atorvastatin treatment FF41


title: Post atorvastatin treatment FF39


title: prca_rwpe_cell_line_prostate_benign

description:
Sample name: MCTP_SAMPLE_339
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: benign

value: BENIGN


title: pt_vcap_2_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_375
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: prostate

value: PRCA


title: pt_vcap_1_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_374
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: pt_vcap_3_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_376
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: osteosarcoma_hu09_cell_line_sarcoma_osteosarcoma

description:
Sample name: MCTP_SAMPLE_275
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: pt_lncap_3_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_71
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_PE01_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_295
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: ovarian

value: OVARIAN


title: ovarian_UC101_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_301
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_peo23_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_297
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_pea1_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_296
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_TOV21_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_300
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_TOV112D_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_299
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_UH01_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_302
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: pt_lncap_1_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_69
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: pt_lncap_2_cell_line_prostate_adenocarcinoma

description:
Sample name: MCTP_SAMPLE_70
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_RMG1_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_298
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_ovtoko_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_294
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_ovsayo_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_293
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Post atorvastatin treatment FF15

description: Surgical biopsy following completion of 2 weeks atorvastatin treatment

value: breast cancer tumor biopsy


title: Post atorvastatin treatment FF16

value: 2 weeks atorvastatin


title: ovarian_ovcar3_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_290
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: not collected


title: Pre atorvastatin treatment MN16

description: Core needle biopsy taken before commencement of 2 weeks atorvastatin treatment

value: no treatment (baseline)


title: ovarian_ovmana_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_292
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: MCTP


title: ovarian_ovas_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_289
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp

value: cancer


title: ovarian_ovacr5_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_288
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_oc316_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_287
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: ovarian_OAW28_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_286
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp


title: Pre atorvastatin treatment MN42


title: ovarian_igrov1_cell_line_ovarian_carcinoma

description:
Sample name: MCTP_SAMPLE_285
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Sense_Strand.tsv.gz
processed data file: MCTP_ssRNASeq_Cohort_Feature_Read_Counts_Antisense_Strand.tsv.gz
Processed data files linked to SuperSeries record.
Strand-specific RNA sequencing (ssRNASeq). Illumina HiSeq 2000, pair-end reads of 101bp