title: eosinophil

first: Ning

last: Lu

address: No. 15, Da Tun Road, Chaoyang District

department: Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 30
CEL file 21499.CEL not available

hyb_protocol: Following fragmentation, 15μg cRNA were hybridized for 16hs at 45°C on Affymetrix GeneChip U133 plus 2.0 arrays. Arrays were stained with a streptavidin-phycoerythrin conjugate (Molecular Probes) and visualized with a GeneArray scanner.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The scanned images were aligned and analyzed using the GeneChip software Microarray Suite 5.0 (Affymetrix) according to the manufacturer’s instructions. The signal intensities were normalized to the mean intensity of all the genes represented on the array, and global scaling (scaling to all probe sets) was applied before performing comparison analysis. Genes with variable expression levels were selected based on the following criteria: genes should be expressed (have presence calls) in at least one of the three samples and σi/μi ratio should be >0.65, where σi and μi are the standard deviation and mean of the hybridization intensity values of each particular gene across all samples, respectively.

source_name: freshly isolated eosinophil

label_protocol: Biotinylated cRNA samples were generated with the Bioarray High-Yield RNA Transcript Labeling kit (ENZO Diagnostics), and purified with RNeasy mini columns (Qiagen) according to the manufacture’s protocol.

extract_protocol: Total RNA of each samples was extracted by using RNeasy kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol:
[subsets purification protocol] CD4+ T cells were enriched from blood buffy coats by means of the CD4+ T cell isolation kit (Stem cell, 15022 or 15062) according to manufacturer’s instructions. Enriched CD4+ T cells were stained with FITC-labeled lineage cocktail of antibodyCD8 (HIT8a, dilution 1:100), CD14 (MφP9, dilution 1:100), CD16 (3G8, dilution 1:100), CD19 (HIB19, dilution 1:100), CD20 (2H7, dilution 1:100), CD56 (B159, dilution 1:100), CD11c (B-Ly6, dilution 1:100), TCRγ/δ (11F2, dilution 1:100) from BD Biosciences; CD25 (VT-072, dilution 1:100) from Biolegend; PE-CD45RO (UCHL1, dilution 1:200), APC-cy7-CD4 (RPA-T4, dilution 1:200), PerCP-Cy5.5-CD45RA (HI100, dilution 1:100), CD11c-APC (B-ly6, dilution 1:100) from BD Biosciences;, Biotin-CRTH2 (BM16, 1:200 dilution) from Milteney Biotec, and then washed, revealed with strepavidn-PE-cy7 from ebiosciences. Stained cells were sorted into fractions of CD45RA+CD4+ naive T, CD45RO+CRTH2+CD4+ Th2 memory, CD45RO+CRTH2-CD4+ Th1 memory,and CD4+CD11c+DCs by using a FACS Aria (BD Biosciences) with purity >99%. pDC was enriched firstly by adding lineage cocktail mAbs of anti-CD3 (SP34-2, dilution 1:100), CD14 (MφP9, dilution 1:100), CD11b (M1/70, dilution 1:100), CD19 (HIB19, dilution 1:100), CD57 (NK-1, dilution 1:100), CD235a (GA-R2 (HIR2), dilution 1:100) from BD Biosciences, following by adding Anti-Mouse IgG MicroBeads (Milteney Biotec, 130-048-401) and going through LD columns (Milteney Biotec, 30-042-901). Enriched pDC was stained with antibodies of APC-cy7-CD4 (RPA-T4, dilution 1:200), BV421-BDCA2 (V24-785, dilution 1:200), CD11c-APC (B-ly6, dilution 1;100), and FITC-lineage anti-(CD3, CD14, CD11b, CD19, CD57, CD235a) from BD Biosciences and were sorted into fraction of CD4+BDCA2+ pDC. Eosinophils was enriched by two layer percoll gradient centrifugation of buffy coats blood first, then purified by adding CD15 microbeads (Milteney Biotec,130-046-601) following run through LD columns. CD15 depleted cells was collected and centrifuged. Basophils were isolatedby using EasySep™ Human Basophil Enrichment Kit (Stem cells, 19069) according to manufacturer’s instructions. Mast cells were generated from human CD34+ stem cells. . The following peripheral blood cell subsets were freshly sorted as: CD16+ monocytes, and CD16+ monocyte-derived DCs (monocytes cultured for 6 days with GM-CSF and IL-4), CD68+CD16+ neutrophils, CD16+CD56+ NK cells, CD19+ B cells, and CD3+CD8+ T cells.
Purified PBMC subsets were cultured with medium or medium together with cytokines or agonist mAbs accordingly.

tag: cells

value: PBMC

tag: cell subset

value: eosinophil


title: LUZ19M 10minRep1

status: Public on Jan 19 2018

type: SRA

city: Leuven

first: Bob

last: Blasdel

state: Vlaams-Brabant

address: Kasteelpark Arenberg 21, bus 2462

country: Belgium

institute: KU Leuven

description: Non-ribosomal RNA

library_source: transcriptomic

data_processing:
After trimming, sequencing reads were aligned separately to both the phage and host genomes with the CLC Genomics workbench v7.5.1 (QIAGEN Bioinformatics, Aarhus, Denmark)
Alignments were then summarized into count tables of Total Gene Reads that map to phage or host gene features respectively. Each statistical comparison presented was performed using the DESeq2 R/Bioconductor package to normalize host transcript populations to host transcript populations, before testing for differential expression as described by Blasdel et al. (2017).
The core analysis compares directional host total gene read counts for four phage negative controls sampled at a point immediately before infection to samples representing the synchronized late infections of LUZ19, YuA, PEV2 and 14-1. The DESeq2 test for the statistical significance of differential expression between the negative controls and phage-infected samples here is used to specifically highlight gene features that are differentially expressed in common between the different phage infections. As the four phages used have radically different metabolisms, genome contents, and methods for coopting host mechanisms, they are unlikely to all mediate differential expression of any given host gene in the same way. Thus, any differential expression of host genes that is common to all of the independent infections is likely to be mediated by the one biological entity all of the infections have in common, the host.
Given that there are two biological entities within the infected cell whose transcripts are sequenced together, and which change in total abundance relative to each other, meaningfully assessing differential expression for host genes becomes non-intuitively complex. Indeed, we observe a global depletion of all host transcripts relative to the total (phage and host) transcript population present in the cell due to the influx of phage transcripts. Therefore, two approaches could theoretically be used to measure the change in the abundance of a host transcript during a phage infection. We could measure changes (1) relative to either only other host transcripts or (2) relative to the total transcript population in the cell, including new phage transcripts. We have here adopted the first, asking which host transcripts are up or down regulated relative to other host transcripts by normalizing host transcripts before infection to host transcripts after infection. This has the effect of artificially enriching host reads in the phage infected condition by normalizing away the influx of phage transcripts, so as to compare it to the uninfected condition as if those phage transcripts were not present. The answer to this question focuses on how the host transcripts are being being targeted for either increased transcription or decreased degradation by at least one of the two biological entities in the cell, by ignoring the replacement of host transcripts with phage transcripts. Analyzing the change in a transcript's abundance relative to the total transcript population could not be addressed analysis of multiple phage infections, since depletion of host transcripts relative to the total happens at different rates during different phage infections. This effectively prevents us from elucidating a transcript's differential ability to compete for ribosome activity through changes relative abundance. For example, as was reported for prophage transcripts by Blasdel et al. (2017) during phage infection, a transcript could be targeted for increased transcription even while the stronger degradation of all non-phage transcripts reduces its abundance relative to the total transcript population in the cell.
Genome_build: Pseudomonas aeruginosa PAO1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000006765.1)
Supplementary_files_format_and_content: Total gene read counts, Results of differential expression analysis

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: Cell Lysate

growth_protocol: The Pseudomonas aeruginosa strain PAO1 was used as a host for phages LUZ19, YuA, PEV2, 14-1, and PhiKZ. Cultures were grown to an OD600 0.3 (1.2 x 10^8 / mL) in Lysogeny broth (10 g/L Tryptone, 5 g/L Yeast extract, 5 g/L NaCl) and infected at a multiplicity of infection of 50 to ensure synchronous infection. P. aeruginosa strain PAK was used as a host for phages PAK_P3 and PAK_P4.

extract_protocol:
At time points after the addition of phage chosen to reflect each phase of infection, cells were immediately halted with stop solution (1%, 9% ethanol, 90% sample Blasdel (2018), pelleted, and re-suspended in TRIzol to lyse cells as well as inactivate RNAses and start an organic extraction. The resulting nucleic acid was digested with TURBO DNAse to remove DNA, rRNA was removed with the Ribo-Zero kit.
Stranded cDNA was prepared with the TruSeq Stranded mRNA Library Prep Kit ahead of sequencing according to manufacturers instructions

treatment_protocol: RNA-Sequencing was performed on four phage-negative controls taken immediately before infection. Samples were also taken from synchronized infections by phages LUZ19, YuA, PEV2, and 14-1 to represent early, middle and late transcription as described by Blasdel et al. (2017, 2018). Briefly, synchronicity was controlled for by ensuring that fewer than 5% of host cells still survived before the early time point was taken.

tag: phage

value: Infected by LUZ19

tag: time point

tag: phase of infection

value: Middle


title: Neutrophil

type: RNA

city: Beijing

country: China

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 11
CEL file 20327.CEL not available

label: biotin

organism: Homo sapiens

source_name: freshly isolated Neutrophil

value: Neutrophil


title: HCC009_non-tumor tissue_SNP

type: genomic

first: Gangqiao

last: Zhou

address: No. 27, Taiping Road, Haidian District

institute: Beijing Institute of Radiation Medicine

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
From raw.CEL file, Copy-number estimation using Robust Multichip Analysis (CRMA) was used to pre-process the probe signal intensities. The procedure included that signal intensities were calibrated for offset and crosstalk between alleles, and normalized for probe sequence effects. After summarizing to probe-set level signals, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, taking paired tumor-adjacent tissue as a reference for every tumor tissue. Then segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm2 with default parameters in the R package “DNA-copy” (http://www.r-project.org/).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: adjacent non-tumor liver tissues of HCC patient

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by an Affymetrix service facility (CapitalBio Corporation, China).

extract_protocol: Genomic DNA was extracted from frozen tissues using proteinase K digestion and subsequent phenol/chlororform extraction. DNA concentration and purity were determined using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: For all tumors and non-tumor tissues, samples were snap frozen and stored at -80°C. Tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis in all tumor samples.

tag: subject id

tag: subject status

value: hepatocellular carcinoma (HCC) patient

tag: gender

value: male

tag: age

tag: tnm staging


title: sample collected from patient 5C at 3 months after transplantation [Accommodation_PRAGUE_C5]

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: For all samples a total of 750 ng of labeled cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package.  Please note that only probes with detectable signal intensity in at least five samples were included, resulting in 20,370 data rows. The probes with no signal were excluded from the non_normalized data matrix as well.

source_name: renal graft biopsy

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 200 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The small portion (2mm) of the  the renal graft biopsy was immediately placed in RNA later (Ambion Corporation, Austin, TX), snap frozen and stored at -80 °C until RNA extraction. RNA was isolated from renal biopsies using the RNeasy Micro Kit (Qiagen, Hilden, Germany).Quality and integrity of PAXgene RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring absorbance at 260 nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Whole renal transcriptome was evaluated in 3-months protocol biopsies with isolated C4d staining in otherwise stable ABO incompatible (ABOi) and HLA incompatible DSA positive kidney grafts (HLAi) as well as in C4d negative HLA compatible grafts with normal histological findings (controls) with the aim to elucidate the mechanism of accommodation.

tag: patient id

tag: type of  transplantation (aboincompatible=0, hlaincompatible=1, abocompatible with stable graft function and no dsa=3)

tag: donor specific antibodies positivity 1= yes, 0= no

tag: tissue

value: renal graft biopsy


title: sample collected from patient 3C at 3 months after transplantation [Accommodation_PRAGUE_C3]


title: sample collected from patient 6C at 3 months after transplantation [Accommodation_PRAGUE_C6]


title: B cells

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 2
CEL file 3791.CEL not available

source_name: freshly isolated CD19+B cells

value: CD19+B cells


title: sample collected from patient 2C at 3 months after transplantation [Accommodation_PRAGUE_C2]


title: basophil

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 29
CEL file 21498.CEL not available

source_name: freshly isolated basophil

value: basophil


title: LUZ19E 5minRep2

description: Non-ribosomal RNA

value: Early


title: LUZ19E 5minRep3

description: Non-ribosomal RNA


title: sample collected from patient 4C at 3 months after transplantation [Accommodation_PRAGUE_C4]


title: CR Th2 T Cell (TTH)

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 15
CEL file 21112.CEL not available

source_name: freshly isolated CRTH2+ memory Th2 cells

value: CRTH2+ memory Th2 cells


title: CD8 T cells

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 1
CEL file 3789.CEL not available

source_name: freshly isolated CD8+T cells

value: CD8+T cells


title: mast cell (CBMC)

description:
Gene expression data from activated CD34+ stem cells
Sample name: 31
CEL file 3786.CEL not available

source_name: derived from human CD34+ stem cells

value: CD34+ stem cell derived

value: derived from human CD34+ stem cells


title: LUZ19E 5minRep1

description: Non-ribosomal RNA


title: sample collected from patient 1C at 3 months after transplantation [Accommodation_PRAGUE_C1]


title: HCC006_non-tumor tissue_SNP

value: female


title: HCC007_non-tumor tissue_SNP


title: sample collected from patient 7B at 3 months after transplantation [Accommodation_PRAGUE_B7]


title: HCC010_non-tumor tissue_SNP


title: Effector Memory T Cell (TEM)

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 14
CEL file 21111.CEL not available

source_name: freshly isolated CD45Ro+ CCR7- effector memory T cells

value: CD45Ro+ CCR7- effector memory T cells


title: sample collected from patient 5B at 3 months after transplantation [Accommodation_PRAGUE_B5]


title: sample collected from patient 6B at 3 months after transplantation [Accommodation_PRAGUE_B6]


title: HCC005_non-tumor tissue_SNP


title: Naïve T Cell (TN)

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 13
CEL file 21110.CEL not available

source_name: freshly isolated CD4+CD45RA+CD45RO- Naïve T cells

value: PBMC

value: CD4+CD45RA+CD45RO- Naïve T cells


title: HCC004_non-tumor tissue_SNP


title: HCC001_non-tumor tissue_SNP


title: HCC008_non-tumor tissue_SNP


title: sample collected from patient 4B at 3 months after transplantation [Accommodation_PRAGUE_B4]


title: HCC003_non-tumor tissue_SNP


title: IPC med

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 66
CEL file 25588.CEL not available

source_name: freshly isolated BDCA2+ pDC

value: BDCA2+ pDC


title: Central Memory T Cell (TCM)

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 16
CEL file 21113.CEL not available

source_name: freshly isolated CD45Ro+ CCR7+ Centrol memory T cells

value: CD45Ro+ CCR7+ Centrol memory T cells


title: HCC002_non-tumor tissue_SNP


title: NK cells fresh

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 28
CEL file 21125.CEL not available

source_name: freshly isolated CD56+NK cells

value: CD56+NK cells


title: sample collected from patient 2B at 3 months after transplantation [Accommodation_PRAGUE_B2]


title: sample collected from patient 3B at 3 months after transplantation [Accommodation_PRAGUE_B3]


title: HCC030_tumor tissue_SNP

source_name: tumor liver tissues of HCC patient

value: hepatocellular carcinoma (HCC) patient


title: IPC fresh

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 9
CEL file 20325.CEL not available


title: sample collected from patient 11A at 3 months after transplantation [Accommodation_PRAGUE_A11]


title: sample collected from patient 1B at 3 months after transplantation [Accommodation_PRAGUE_B1]


title: mono-DC old

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 34
CEL file 3690.CEL not available

source_name: freshly isolated monocytes

value: monocytes


title: mono-DC new

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 33
CEL file 21145.CEL not available


title: HCC031_tumor tissue_SNP

value: male


title: HCC029_tumor tissue_SNP


title: CD16- monocytes

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 3
CEL file 3792.CEL not available

source_name: freshly isolated CD16-monocytes


title: HCC025_tumor tissue_SNP


title: HCC027_tumor tissue_SNP


title: HCC026_tumor tissue_SNP


title: CD11c DC fresh (MDN)

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 17
CEL file 21114.CEL not available

source_name: freshly isolated CD4+CD11c+mDC


title: CD16+ monocytes

description:
Gene expression data from freshly purified human PBMC subsets
Sample name: 4
CEL file 3793.CEL not available

source_name: freshly isolated CD16+ monocytes

value: CD16+ monocytes


title: HCC028_tumor tissue_SNP


title: sample collected from patient 10A at  3 months after transplantation [Accommodation_PRAGUE_A10]

value: renal graft biopsy


title: sample collected from patient 8A at 3 months after transplantation [Accommodation_PRAGUE_A8]


title: HCC023_tumor tissue_SNP


title: sample collected from patient 7A at 3 months after transplantation [Accommodation_PRAGUE_A7]


title: HCC022_tumor tissue_SNP


title: sample collected from patient 5A at 3 months after transplantation [Accommodation_PRAGUE_A5]


title: HCC021_tumor tissue_SNP


title: sample collected from patient 9A at  3 months after transplantation [Accommodation_PRAGUE_A9]


title: HCC019_tumor tissue_SNP


title: HCC020_tumor tissue_SNP


title: sample collected from patient 4A at 3 months after transplantation [Accommodation_PRAGUE_A4]


title: HCC024_tumor tissue_SNP


title: HCC018_tumor tissue_SNP


title: sample collected from patient 3A at 3 months after transplantation [Accommodation_PRAGUE_A3]


title: sample collected from patient 1A at 3 months after transplantation [Accommodation_PRAGUE_A1]


title: sample collected from patient 6A at 3 months after transplantation [Accommodation_PRAGUE_A6]


title: sample collected from patient 2A at 3 months after transplantation [Accommodation_PRAGUE_A2]


title: CD166(-+)_2

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

country: South Korea

institute: POSTECH

description: Gene expression in hESC-derived unsorted differentiated cells (ALCAM-/+) [rep2]

hyb_protocol: According to the standard Agilent protocols, the RNA was reverse-transcribed, amplified and then hybridized onto the array.

scan_protocol: Agilent Technologies G2600D SG13094295

data_processing: Scanned signal intensity was log2-transformed. The log2-transformed data for two comparisons (K129R versus WT, K171R versus WT) were then quantile-normalized. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011a).

source_name: hESC-derived unsorted differentiated cells (ALCAM-/+), replicate 2

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Adherent colonies of hESC line H9 (WA-09), hESC line Royan H5 and derivatives (rH5-ISL1-Hygro) were maintained on mouse embryonic fibroblasts in knockout serum replacement (KOSR, Invitrogen, 10828-028) containing hESC medium as described previously

extract_protocol: Total RNA was isolated from four types of cells using WelPrepTM (Welgene, Daegu, Korea), and the integrity of the total RNA was checked using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Differentiation of hESC and hiPSC lines into cardiac progenitor cells was based on sequential treatment of Activin A (1 day) and BMP4 (4 days).

tag: cell type


title: 14-1L 12minRep2

description: Non-ribosomal RNA

source_name: Cell Lysate

value: Infected by 14-1

value: Late


title: HCC014_tumor tissue_SNP


title: HCC016_tumor tissue_SNP


title: 14-1L 12minRep1

description: Non-ribosomal RNA


title: HCC015_tumor tissue_SNP


title: CD166(-+)_1

description: Gene expression in hESC-derived unsorted differentiated cells (ALCAM-/+) [rep1]

source_name: hESC-derived unsorted differentiated cells (ALCAM-/+), replicate 1


title: HCC011_tumor tissue_SNP


title: CD166(+)_2

description: Gene expression in hESC-derived ALCAM+ cells [rep2]

source_name: hESC-derived ALCAM+ cells, replicate 2

value: hESC-derived ALCAM+ cells


title: CD166(-)_2

description: Gene expression in hESC-derived ALCAM- cells [rep2]

source_name: hESC-derived ALCAM- cells, replicate 2

value: hESC-derived ALCAM- cells


title: 14-1M 6minRep2

description: Non-ribosomal RNA

value: Middle


title: 14-1M 6minRep1

description: Non-ribosomal RNA


title: CD166(+)_1

description: Gene expression in hESC-derived ALCAM+ cells [rep1]

source_name: hESC-derived ALCAM+ cells, replicate 1


title: HCC017_tumor tissue_SNP


title: HCC013_tumor tissue_SNP


title: PEV2L 15minRep2

description: Non-ribosomal RNA

value: Infected by PEV2


title: HCC010_tumor tissue_SNP


title: YuAL 25minRep1

description: Non-ribosomal RNA

value: Infected by YuA


title: PEV2M 10minRep2

description: Non-ribosomal RNA


title: PEV2E 5minRep2

description: Non-ribosomal RNA

value: Early


title: HCC007_tumor tissue_SNP


title: HCC012_tumor tissue_SNP


title: HCC008_tumor tissue_SNP


title: HCC006_tumor tissue_SNP

value: female


title: YuAM 15minRep1

description: Non-ribosomal RNA


title: HCC005_tumor tissue_SNP


title: HCC004_tumor tissue_SNP


title: hESC_1

description: Gene expression in hESC cells [rep1]

source_name: hESC, replicate 1

value: hESC


title: HCC009_tumor tissue_SNP


title: YuAE 5minRep1

description: Non-ribosomal RNA


title: CD166(-)_1

description: Gene expression in hESC-derived ALCAM- cells [rep1]

source_name: hESC-derived ALCAM- cells, replicate 1


title: Negative_Control0minRep4

description: Non-ribosomal RNA

value: Infected by no phage


title: Negative_Control0minRep1

description: Non-ribosomal RNA


title: Negative_Control0minRep2

description: Non-ribosomal RNA


title: HCC002_tumor tissue_SNP


title: Negative_Control0minRep3

description: Non-ribosomal RNA


title: hESC_2

description: Gene expression in hESC cells [rep2]

source_name: hESC, replicate 2


title: HCC003_tumor tissue_SNP


title: HCC001_tumor tissue_SNP


title: AcH4 Human Aortic Vascular Smooth Muscle Cells 3

city: Toronto

first: Philip

middle: A

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

country: Canada

institute: University of Toronto

description: HuAoVSMC pan-AcH4 versus rabbit serum ChIP-chip analysis using the custom 1M ultra high resolution tiling array

hyb_protocol: Cy5-labelled pan-AcH4 and corresponding Cy3-labelled rabbit serum ChIP samples were hybridized to custom 1M tiling arrays in accordance to manufacturer's ChIP-chip hybridization recommendations using the Agilent microarray hybridization chamber system.

scan_protocol: Microarrays were washed and scanned using the Agilent G2565C DNA Scanner.

data_processing: Agilent Feature Extraction software (Agilent) was used to analyze acquired array images. Quantified data files from Agilent Feature Extraction software (Agilent) were then collected into a single directory. Each file contained sense and corresponding antisense tiled probes to genomic regions surrounding a predefined list of genes with either EC-enriched expression, roles in EC physiology, or roles as control genes.  Mean expression measurements  (cy5 and cy3 channels) for each of the probes were extracted and sorted into an ascending chromosomal order as defined by the mid-point of the probe location in a format acceptable for input into the Tilemap command line software using custom scripts written in PERL.  Preprocessing of the data consisted of quantile normalization followed by taking the log base 2.  Bar files were then created for input to the Tilemapv2 program to find pulled down fragment peaks using the moving average (MA) mode.  The MA algorithm uses a modified t-statistic averaged over a sliding 400 bp window of adjacent probes. False Discovery Rate (FDR) calculations are based on a left tail distribution estimate of the MA test statistics.  We used an MA cutoff of 3.0 for peak selection.  Based on the average probe spacing on the custom Agilent arrays, a window size of 3 was chosen for the tilemap configuration parameter file.  Various choices for the configuration of tilemap were tested during the course of experiments to optimize peak finding using both real and simulated data.

label_protocol: ChIP samples were amplified using the whole genome amplification kit (Sigma) and labelled according to maufacturer's ChIP-chip labeling recommendations (Agilent Tecnologies). Pan-AcH4 and corresponding normal rabbit serum ChIP samples were labelled with cyanine 5-dUTP and cyanine 3-dUTP respectively with the Agilent Genomic DNA labeling kit PLUS.

growth_protocol:
HuAoVSMC (ScienCell; https://www.sciencellonline.com/human-aortic-smooth-muscle-cells.html) were cultured according to provider's instructions using their recommended complete human smooth muscle cell medium. All biological replicates were used at passage 3-4.
See protocols in SAMPLES

extract_protocol: Chromatin immunoprecipitation was conducted using the Chromatin Immunoprecipitation kit (Millipore, 17-295) according to the manufacturer's instructions. Briefly, 1x 106 cells were used per ChIP reaction. Cultured cells were fixed in 1% formaldehyde at 37 °C in 5% CO2 for 10 minutes by adding formaldehyde directly to the medium. Cells were washed twice in cold 1x PBS and lysed with a SDS-based lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris, pH 8.1). Sonication of lysates was performed on ice using a Sonics and Materials Vibra-Cell sonicator with a 3-mm tip set at 30% maximum power with 10 s pulses and a 30s rest interval between every 5 pulses. Sonication was conducted to solubilize chromatin and fragment chromatin to a size of 500-1000 bp. Chromatin was pre-cleared with salmon-sperm DNA/protein A-agaraose for 1 h . Pre-cleared chromatin samples were incubated with 5 μl of pan-AcH4 (Millipore) or normal rabbit serum (Santa Cruz) overnight with agitation at 4 °C.  Salmon sperm DNA protein A-agarose (Millipore) was added and allowed to bind for 60 min at 4 °C before extensive washing. Samples were eluted in 1% SDS, 0.1M NaHCO3 and formaldehyde cross-links were reversed overnight at 65 °C. ChIP samples were then subjected to proteinase K digestion and purified using the QIAquick PCR purification kit (QIAGEN) into 10 mM Tris, pH 8.5.

tag: cell line

value: HuAoVSMC

tag: antibody

value: rabbit serum

tag: tag

value: normal rabbit serum control ChIP


title: AcH4 Human Aortic Vascular Smooth Muscle Cells 1


title: wt-Zn versus wt+Zn, rep2

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

country: Spain

institute: CENIT SUPPORT SYSTEMS

description: Analysis used WT under zinc growing conditions as control samples for comparison to the experimental absence of zinc

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data analysis was carried out using Flexarray version 1.6.1. The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalized values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats with all replicates combined. Data was compiled from two zinc-limiting growing conditions and two zinc repleted cultures each with a dye-swap replicate, thus providing two biological repeats within four technical repeats.

organism: Aspergillus fumigatus

source_name: WT mycelium growing under alkaline zinc-limiting conditions

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Culture in zinc-limiting and zinc-replete media

extract_protocol: RNA was obtained with the QIAGEN RNeasy mini Kit (cat. 74904) according to manufacturer instructions

tag: genotype

value: wild type strain

tag: growth protocol

value: alkaline zinc-limiting conditions

value: mycelium

source_name: WT mycelium growing under alkaline zinc conditions

value: alkaline zinc conditions


title: AcH4 Human Umbilical Vein Endothelial Cells 2

description: HUVEC pan-AcH4 versus rabbit serum ChIP-chip analysis using the custom 1M ultra high resolution tiling array

source_name: Human umbilical vein endothelial cells

growth_protocol:
HUVECs were isolated from umbilical cords of male and female births. HUVECs were cultured in supplemented M199 medium for 2 passages and all biological replicates were used at passage 3-4.
See protocols in SAMPLES

value: HUVEC


title: dzafA-Zn versus dzafA+Zn, rep2

description: Analysis used zafA null strain under zinc growing conditions as control samples for comparison to the experimental absence of zinc

source_name: zafA null strain growing under alkaline zinc-limiting conditions

value: zafA null strain

source_name: zafA null strain mycelium growing under alkaline zinc conditions


title: dzafA-Zn versus dzafA+Zn, rep1


title: wt-Zn versus dzafA-Zn, rep2

description: Analysis used WT strain under zinc-limiting growing conditions as control samples for comparison to the zafA null strain under zinc-limiting growing conditions


title: AcH4 Human Umbilical Vein Endothelial Cells 3


title: wt-Zn versus dzafA-Zn, rep1


title: AcH3 Human Aortic Vascular Smooth Muscle Cells 2

description: HuAoVSMC pan-AcH3 versus rIgG ChIP-chip analysis using the custom 1M ultra high resolution tiling array

hyb_protocol: Cy5-labelled pan-AcH3 and corresponding Cy3-labelled rIgG ChIP samples were hybridized to custom 1M tiling arrays in accordance to manufacturer's ChIP-chip hybridization recommendations using the Agilent microarray hybridization chamber system.

label_protocol: pan-AcH3 and rIgG ChIP samples were amplified using the whole genome amplification kit (Sigma) and labelled according to maufacturer's ChIP-chip labeling recommendations (Agilent Tecnologies). Pan-AcH3 and corresponding rigG samples were labelled with cyanine 5-dUTP and cyanine 3-dUTP respectively with the Agilent Genomic DNA labeling kit PLUS.

growth_protocol: HuAoVSMC (ScienCell; https://www.sciencellonline.com/human-aortic-smooth-muscle-cells.html) were cultured according to provider's instructions using their recommended complete human smooth muscle cell medium. All biological replicates were used at passage 3-4.

extract_protocol: Chromatin immunoprecipitation was conducted using the Chromatin Immunoprecipitation kit (Millipore, 17-295) according to the manufacturer's instructions. Briefly, 1x 106 cells were used per ChIP reaction. Cultured cells were fixed in 1% formaldehyde at 37 °C in 5% CO2 for 10 minutes by adding formaldehyde directly to the medium. Cells were washed twice in cold 1x PBS and lysed with a SDS-based lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris, pH 8.1). Sonication of lysates was performed on ice using a Sonics and Materials Vibra-Cell sonicator with a 3-mm tip set at 30% maximum power with 10 s pulses and a 30s rest interval between every 5 pulses. Sonication was conducted to solubilize chromatin and fragment chromatin to a size of 500-1000 bp. Chromatin was pre-cleared with salmon-sperm DNA/protein A-agaraose for 1 h . Pre-cleared chromatin samples were incubated with 5 μg of pan-AcH3 (Millipore) or rabbit control IgG (Santa Cruz) overnight with agitation at 4 °C.  Salmon sperm DNA protein A-agarose (Millipore) was added and allowed to bind for 60 min at 4 °C before extensive washing. Samples were eluted in 1% SDS, 0.1M NaHCO3 and formaldehyde cross-links were reversed overnight at 65 °C. ChIP samples was then subjected to proteinase K digestion and purified using the QIAquick PCR purification kit (QIAGEN) into 10 mM Tris, pH 8.5.

value: rabbit IgG isotype control ChIP


title: AcH3 Human Umbilical Vein Endothelial Cells 1

description: HUVEC pan-AcH3 versus rIgG ChIP-chip analysis using the custom 1M ultra high resolution tiling array

growth_protocol: HUVECs were isolated from umbilical cords of male and female births. HUVECs were cultured in supplemented M199 medium for 2 passages and all biological replicates were used at passage 3-4.


title: AcH4 Human Aortic Vascular Smooth Muscle Cells 2


title: AcH4 Human Umbilical Vein Endothelial Cells 1


title: AcH3 Human Aortic Vascular Smooth Muscle Cells 1


title: HBO1 siRNA treated HUVEC 4

description: Gene expression after 72 h of siRNA treatment

hyb_protocol: Cy3-Labeled cRNA was hybridized to Custom Human LncRNA Array v3.0 (8x 60K, Arraystar) using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 8 out of 8 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: HUVEC, HBO1 siRNA, 72h, biological replicate 4

label_protocol: The Agilent Quick Amp Labeling Kit (Agilent Technologoies) was used to simultaneously amplify and label RNA with Cy3 according to manufacturer's instructions.

extract_protocol: RNA was extracted from siRNA-treated HUVECs using guanidinium-acid-phenol reagents that are based on the research of Chomczynski and Sacchi, 1987. A known amount of exogenous luciferase RNA was introduced at the beginning of the extraction to assess for RNA extraction and first strand cDNA synthesis efficiency.

treatment_protocol: Each biological replicate was subjected to either control siRNA or HBO1 siRNA (40 nM) for 72 hrs before extraction.

value: Human umbilical vein endothelial cells

tag: treatment

value: HBO1 siRNA treated


title: AcH3 Human Umbilical Vein Endothelial Cells 2


title: HBO1 siRNA treated HUVEC 3

source_name: HUVEC, HBO1 siRNA, 72h, biological replicate 3


title: Control siRNA treated HUVEC 4

source_name: HUVEC, control siRNA, 72h, biological replicate 4

value: Control siRNA treated


title: Control siRNA treated HUVEC 3

source_name: HUVEC, control siRNA, 72h, biological replicate 3


title: wt-Zn versus wt+Zn, rep1


title: HBO1 siRNA treated HUVEC 2

source_name: HUVEC, HBO1 siRNA, 72h, biological replicate 2


title: C57_DRG_6day_1

status: Public on Jan 18 2018

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

description:
Sample name: C57_DRG_20_144
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadStation.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

organism: Mus musculus

source_name: DRG, SNI, 144h

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

growth_protocol: Experiments were performed in adult (9-10 weeks old) male C57BL/6J mice (Jackson Laboratory, Maine, USA).

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

treatment_protocol: Mice were anesthetized with isoflurane (2-4%) and SNI surgery performed; the tibial and common peroneal branches of the sciatic nerve were tightly ligated with a silk suture and transected distally while the sural nerve was left intact (PMIDs 10924808, 16542774).

tag: strain/background

value: Male

value: adult

value: Dorsal root ganglia (DRG)

value: spared nerve injury (SNI)

tag: timepoint (days post sni)


title: C57_DRG_10day_1

description:
Sample name: C57_DRG_26_240
Replicate 1

source_name: DRG, SNI, 240h


title: C57_DRG_8day_2

description:
Sample name: C57_DRG_50_192
Replicate 2

source_name: DRG, SNI, 192h


title: C57_DRG_5day_2

description:
Sample name: C57_DRG_43_120
Replicate 2

source_name: DRG, SNI, 120h


title: C57_DRG_10day_2

description:
Sample name: C57_DRG_51_240
Replicate 2


title: C57_DRG_8day_3

description:
Sample name: C57_DRG_76_192
Replicate 3


title: C57_DRG_9day_2

description:
Sample name: C57_DRG_77_216
Replicate 2

source_name: DRG, SNI, 216h


title: C57_DRG_9day_1

description:
Sample name: C57_DRG_25_216
Replicate 1


title: Control siRNA treated HUVEC 2

source_name: HUVEC, control siRNA, 72h, biological replicate 2


title: Control siRNA treated HUVEC 1

source_name: HUVEC, control siRNA, 72h, biological replicate 1


title: C57_DRG_7day_2

description:
Sample name: C57_DRG_49_168
Replicate 2

source_name: DRG, SNI, 168h


title: C57_DRG_5day_3

description:
Sample name: C57_DRG_69_120
Replicate 3


title: C57_DRG_6day_2

description:
Sample name: C57_DRG_46_144
Replicate 2


title: C57_DRG_6day_3

description:
Sample name: C57_DRG_72_144
Replicate 3


title: C57_DRG_7day_3

description:
Sample name: C57_DRG_75_168
Replicate 3


title: HBO1 siRNA treated HUVEC 1

source_name: HUVEC, HBO1 siRNA, 72h, biological replicate 1


title: C57_DRG_7day_1

description:
Sample name: C57_DRG_23_168
Replicate 1


title: C57_DRG_4day_1

description:
Sample name: C57_DRG_40_96
Replicate 1

source_name: DRG, SNI, 96h


title: C57_DRG_5day_1

description:
Sample name: C57_DRG_17_120
Replicate 1


title: C57_DRG_8day_1

description:
Sample name: C57_DRG_24_192
Replicate 1


title: C57_DRG_3day_3

description:
Sample name: C57_DRG_62_72
Replicate 3

source_name: DRG, SNI, 72h


title: C57_DRG_3day_1

description:
Sample name: C57_DRG_10_72
Replicate 1


title: C57_DRG_2day_3

description:
Sample name: C57_DRG_59_48
Replicate 3

source_name: DRG, SNI, 48h


title: C57_DRG_3day_2

description:
Sample name: C57_DRG_36_72
Replicate 2


title: C57_DRG_2day_2

description:
Sample name: C57_DRG_33_48
Replicate 2


title: C57_DRG_4day_2

description:
Sample name: C57_DRG_66_96
Replicate 2


title: C57_DRG_2day_1

description:
Sample name: C57_DRG_7_48
Replicate 1


title: C57_DRG_1day_3

description:
Sample name: C57_DRG_56_24
Replicate 3

source_name: DRG, SNI, 24h


title: C57_DRG_1day_1

description:
Sample name: C57_DRG_4_24
Replicate 1


title: C57_DRG_1day_2

description:
Sample name: C57_DRG_30_24
Replicate 2


title: C57_DRG_16hour_2

description:
Sample name: C57_DRG_29_16
Replicate 2

source_name: DRG, SNI, 16h


title: C57_DRG_8hour_1

description:
Sample name: C57_DRG_2_8
Replicate 1

source_name: DRG, SNI, 8h


title: C57_DRG_16hour_1

description:
Sample name: C57_DRG_3_16
Replicate 1


title: C57_DRG_naive_5

description:
Sample name: C57_DRG_53_0
Replicate 5

source_name: DRG, naïve, 0h


title: C57_DRG_naive_7

description:
Sample name: C57_DRG_79_0
Replicate 7


title: C57_DRG_naive_2

description:
Sample name: C57_DRG_13_0
Replicate 2


title: C57_DRG_8hour_2

description:
Sample name: C57_DRG_28_8
Replicate 2


title: C57_DRG_8hour_3

description:
Sample name: C57_DRG_54_8
Replicate 3


title: C57_DRG_16hour_3

description:
Sample name: C57_DRG_55_16
Replicate 3


title: C57_DRG_naive_3

description:
Sample name: C57_DRG_27_0
Replicate 3


title: C57_DRG_naive_6

description:
Sample name: C57_DRG_65_0
Replicate 6


title: C57_DRG_naive_1

description:
Sample name: C57_DRG_1_0
Replicate 1


title: C57_DRG_naive_4

description:
Sample name: C57_DRG_39_0
Replicate 4


title: FNPHE3

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: One µg of purified cRNA was fragmented to uniform size and applied to Agilent Sheep Gene Expression Microarray, 8 x 15K (Design ID 019921, Agilent Technologies) in hybridization buffer. The arrays were hybridized at 65° C for 17 hours in a shaking incubator and washed at 37° C for 1 min. Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies).  Annotations are based on the Agilent eArray annotation file dated January 2010 and manual annotation by blasting the probe sequence against NCBI database.

organism: Ovis aries

source_name: Near-term Sheep Fetus Cereberal Artery Phenylephrine Treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, <1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  Following second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the labeled cRNA was assayed by spectrophotometry and Agilent Bioanalyzer.

treatment_protocol: Microarray analysis was conducted by utilizing the commercial services of GenUs Biosystems (Northbrook, Illinois). In previous studies, we have described this technique in detail 2-4. Briefly, MCA segments were homogenized and lysed in Trizol (Ambion, Austin, TX) and total RNA was isolated using standard procedure followed by purification over spin columns (Ambion). Nanodrop 2000 Spectrophotometer was used to measure total RNA concentration and purity at optical density 260 and 280. Quality and degradation were assessed using an Agilent Bioanalyzer with RNA 6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA). RNA with integrity number >8 were used for preparing labeled cRNA by amplifying the Poly(A)+ RNA population within the total RNA sample. About 1 µg of total RNA was primed with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence and reverse transcribed.  Following second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  Labeled cRNA quality and quantity was assayed by spectrophotometry and Agilent Bioanalyzer. One µg of purified cRNA was fragmented to uniform size and applied to Agilent Sheep Gene Expression Microarray, 8 x 15K (Design ID 019921, Agilent Technologies) in hybridization buffer. Hybridization of the arrays was conducted at 65° C for 17 hours in a shaking incubator. Following hybridization, the array chips were washed at 37° C for 1 min, then rinsed and dried. Following this the array chips were scanned at 5 µm resolution with an Agilent G2565 Microarray Scanner (Agilent Technologies). The scanned images were processed with Agilent Feature Extraction software and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies). Annotations are based on the Agilent eArray annotation file dated January 2010.

value: Phenylephrine Treated

value: Cerebral Artery

value: Nearterm Fetus - 146 Days Old


title: FN2

source_name: Near-term Sheep Fetus Cereberal Artery Untreated

value: untreated


title: WHCO1 cells vehicle control 24h rep1

city: Cape Town

first: Alexis

last: Bick

state: Western Cape

address: Anzio Road, Observatory

department: Division of Medical Biochemistry and Structural Biology

country: South Africa

institute: University of Cape Town

description:
WHCO1_Un_1
replicate 1

hyb_protocol: cRNA samples (1.5μg) were resuspended in RNase-free water to a final volume of 10μl, after which 20μl of Hybridization Buffer (HYB) was added to each cRNA sample. The Hyb chamber gaskets were inserted into the BeadChip Hyb chamber and 200μl Humidity Control Buffer (HCB) was loaded into each of the humidifying buffer reservoirs. BeadChips (Illumina WG6-v3 Gene Expression BeadChips, Illumina, San Diego, CA, USA) were placed into the chamber inserts. Samples were heated at 65°C for 5 min and then loaded onto the BeadChips. The sealed Hyb chamber containing the BeadChips was then incubated overnight at 58°C on a rocking platform. BeadChips were submerged in E1BC Wash Solution and their coverseals were removed, after which both chips were inserted into a submerged slide rack. The slide rack was then transferred into a Hybex waterbath containing preheated High-Temp Wash Buffer (55°C) and chips were incubated at 55°C for 10 min. The slide rack was transferred into 250ml E1BC Wash buffer, agitated and shaken on an orbital shaker for 5 min at the highest possible speed at room temperature. The slide rack was transferred into 250ml 100% ethanol, agitated and shaken on an orbital shaker for 10 min at room temperature. The rack was transferred into 250ml fresh Wash E1BC solution, agitated and shaken on an orbital shaker for 2 min at room temperature. Block E1 buffer (8ml) was added to two wash trays; BeadChips were placed into the trays and blocked for 10 min at medium speed on a rocker. For detection, 4ml Block E1 buffer containing 4μl streptavidin-Cy3 (from 1mg/ml in RNase-free water stock solution) was added to two fresh wash trays. BeadChips were placed face-up into the wash trays, which were covered and rocked at medium speed for 10 min. BeadChips were transferred back to the slide rack submerged in 250ml Wash E1BC solution, agitated then shaken on an orbital shaker for 5 min at room temperature. The rack of BeadChips was centrifuged at 25°C for 4 min. Dry BeadChips were stored in the dark.

scan_protocol: Dry BeadChips were scanned with the Illumina BeadArray Reader (a sub-micron resolution scanner that can scan the 3 μm high-density features in Illumina WG-6 BeadChips). Signal intensities were recorded as iDAT files (image data) for each chip. iDAT files were converted into data tables by Illumina BeadStudio/GenomeStudio version 3 Gene Expression Module software (www.illumina.com).

data_processing:
Samples were classified into two groupsets (WHCO1 and EPC-2) and two groups within those groupsets (BaP and Un, the reference group). This allowed the generation of data manifest tables containing probe and gene lists and their associated signal intensities. Clusters (dendrograms) were generated in GenomeStudio using the Correlation method to determine which samples are most similar based on the expression levels of genes within them. Absolute correlation, Manhattan and Euclidian methods were also used for comparison. Outliers were determined from the clusters and were removed before further analysis. A differential expression analysis was run with the following parameters: average normalization, no background subtraction, Benjamini and Hochberg false discovery rate calculation and the Mann-Whitney method of calculating false discovery rate. Data were filtered for detection p-value <0.05, which corresponds to a 5% false positive rate. No background subtraction was carried out, since this resulted in negative signal values for some genes. Any remaining negative signal values were truncated to 1. Average signal values were then filtered using 2% trimmed mean scaling in order to set the target average intensity of both chips to 500. This method removes highest and lowest 2% expressed genes. Fold change was calculated by averaging BaP and Un values within each cell line and dividing average BaP by average Un. Using the Illumina BeadChip, the minimum statistically significant detectable fold-change is 1.35-fold for single replicates. We chose 2-fold as a cut-off since this is widely used. Lastly, genes were again eliminated if signal was not detected in all samples where the gene was supposedly up- or down-regulated.
Sample: GenomeStudio-generated average fluorescent signal intensity; Detection Pval: p-value calculated by GenomeStudio from negative probes in the chip that measure non-specific hybridization

source_name: WHCO1 cells vehicle control 24h

label_protocol: RNA samples were amplified and labeled with biotin using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA). Briefly, RNA was reverse transcribed to synthesize first strand cDNA, after which second strand cDNA was synthesized with the simultaneous removal of RNA. cDNA was purified and used to transcribe cRNA, which was purified and yield analyzed spectrophotometrically. The protocol is as follows: RNA (500ng) from each sample was prepared with nuclease-free water to 11μl total volume. Reverse transcriptase master mix (1μl T7 oligo(dT) primer, 2μl 10x first strand buffer, 4μl dNTP mix, 1μl RNase inhibitor and 1μl ArrayScript reverse transcriptase per reaction) was added to each sample to bring the volume to 20μl. Samples were incubated at 42°C for 2h and then briefly centrifuged and placed on ice. Second strand master mix (63μl nuclease-free water, 10μl second strand buffer, 4μl dNTP mix, 2μl DNA polymerase and 1μl RNase H per reaction) was added to each sample to bring the volume to 100μl. Samples were incubated at 16°C for 2h then placed on ice. cDNA binding buffer (250μl) was added to each sample and the mixture was passed through a cDNA filter cartridge (Ambion, Austin, TX, USA) by centrifugation at 10 000 x g for 1 min. The flowthrough was discarded and 500μl wash buffer containing 100% ethanol was added to each cartridge. Samples were centrifuged at 10 000 x g for 1 min and flow-through was discarded. Filter cartridges were transferred to cDNA elution tubes. Preheated nuclease-free water (50-55°C, 10μl) was added to the filter cartridges; samples were incubated at room temperature for 2 min then centrifuged for 1.5 min at 10 000 x g. A second aliquot of 9μl nuclease-free water was added and samples were centrifuged again, leaving eluted double-stranded cDNA in the tube. An in vitro transcription (IVT) master mix was prepared at room temperature (2.5μl T7 10X reaction buffer, 2.5μl T7 enzyme mix and 2.5μl biotin-NTP mix) and 7.5μl was mixed with each cDNA sample. Tubes were incubated at 37°C for 14h in a hybridization oven to maintain constant temperature. Reactions were stopped by the addition of 75μl nuclease-free water, bringing the final volume to 100μl. cRNA binding buffer (350μl) was added to each sample, followed by 250μl 100% ethanol and mixing by pipetting. Samples were immediately placed onto cRNA filter cartridges (Ambion, Austin, TX, USA) and centrifuged at 10 000 x g for 1 min. Flow-through was discarded and 650μl wash buffer was added to each cartridge. Samples were centrifuged at 10 000 x g for 1 min and flow-through was discarded. cRNA was eluted by the addition of 100μl preheated nuclease-free water (50-60°C) and centrifugation for 1.5 min at 10 000 x g. Purified cRNA was concentrated by precipitation by the addition of one tenth volume of 5M NH4OAc and 2.5 volumes of 100% ethanol and left at -20°C for 30 min. Samples were microcentrifuged at top speed at room temperature for 15 min. Supernatants were discarded and pellets were washed with 500μl 70% cold ethanol by centrifugation. Pellets were air-dried and resuspended in 50μl RNasefree water. cRNA yield was assessed using the Nanodrop 1000A spectrophotometer at 260nm.

growth_protocol: Cell culture in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum, 100 units/ml penicillin and 100 μg/ml streptomycin (WHCO1) or keratinocyte serum-free medium supplemented with 50 μg/ml bovine pituitary extract, 1 ng/ml epidermal growth factor, 100 U/ml penicillin and 100 μg/ml streptomycin (EPC-2). Cells were cultured in a humidifed incubator containing 5% CO2.

extract_protocol: Total RNA extraction: Cells were washed twice with ice cold 1 x PBS, after which 1ml of the TRIzol lysis reagent (Invitrogen, Carlsbad, CA, USA) was added to each dish. Cells were aspirated and transferred to an eppendorf tube. After 5 min at room temperature, 200 μl chloroform was added and each sample was mixed vigorously. After 3 min at room temperature, samples were centrifuged at 12000 x g for 15 min at 4°C. The top aqueous layer was transferred to a new tube and an equal volume of isopropanol was added. After 10 min at room temperature, samples were centrifuged at 12000 x g for 10 min at 4°C and the supernatant was discarded. Pellets were washed twice by the addition of 500 μl 75% ethanol, vortexing and centrifugation at 7500 x g for 5 min at 4°C. Samples were left to dry at room temperature, dissolved in 25 μl DEPC-treated water and stored at -80°C.

treatment_protocol: Treatment with 0.1% DMSO (vehicle control) or 10 μM benzo[a]pyrene in DMSO for 24 hours

value: Esophagus

value: Esophageal squamous cell carcinoma cell line WHCO1

tag: cell line origin

value: Cancer

tag: donor gender

tag: donor nationality

value: South African

value: control


title: FN3

tag: age


title: FNPHE4


title: WHCO1 cells vehicle control 24h rep2

description:
WHCO1_Un_2
replicate 2


title: WHCO1 cells BaP-treated 24 h rep2

description:
WHCO1_BaP_2
replicate 2

source_name: WHCO1 cells BaP-treated 24 h

value: BaP


title: FNPHE2


title: EPC-2 cells BaP-treated 24 h rep2

description:
EPC-2_BaP_2
replicate 2

source_name: EPC-2 cells BaP-treated 24 h

value: Immortalized normal esophageal cell line EPC-2

value: Normal

value: Japanese


title: FN4


title: EPC-2 cells vehicle control 24h rep2

description:
EPC-2_Un_2
replicate 2

source_name: EPC-2 cells vehicle control 24h

value: Male


title: WHCO1 cells BaP-treated 24 h rep1

description:
WHCO1_BaP_1
replicate 1


title: EPC-2 cells vehicle control 24h rep1

description:
EPC-2_Un_1
replicate 1


title: EPC-2 cells BaP-treated 24 h rep1

description:
EPC-2_BaP_1
replicate 1


title: ANPHE3

source_name: Adult Sheep Cerebral Artery Phenylephrine Treated

value: Adult Sheep 2 Years Old


title: FNPHE1


title: ANPHE4


title: ANPHE1


title: AN4

source_name: Adult Sheep Cerebral Artery Untreated


title: 96DPHE4

source_name: Premature Sheep Fetus Cerebral Artery Phenylephrine Treated

value: Fetus - 96 Days Old


title: ANPHE2


title: AN1


title: FN1


title: 96DPHE2


title: 96DPHE3


title: 96DPHE1


title: AN2


title: AN3


title: MELCYT, sample 1100 [validation set]

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
SAMPLE 1100
Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

tag: methylation class

value: MELCYT

tag: material


title: 96D3

source_name: Premature Sheep Fetus Cerebral Artery Untreated

value: Cerebral Artery


title: MB, SHH CHL AD, sample 1099 [validation set]

description:
SAMPLE 1099
Methylation data from brain tumor sample.

value: MB, SHH CHL AD


title: 96D2

value: untreated


title: 96D4


title: GBM, MID, sample 1094 [validation set]

description:
SAMPLE 1094
Methylation data from brain tumor sample.

value: GBM, MID


title: GBM, MES, sample 1093 [validation set]

description:
SAMPLE 1093
Methylation data from brain tumor sample.

value: GBM, MES


title: NBNPHE3

source_name: New Born Lamb Cerebral Artery Phenylephrine Treated

value: Phenylephrine Treated

value: New Born - 12 hours old


title: DMG, K27, sample 1102 [validation set]

description:
SAMPLE 1102
Methylation data from brain tumor sample.

value: DMG, K27


title: MB, SHH CHL AD, sample 1103 [validation set]

description:
SAMPLE 1103
Methylation data from brain tumor sample.


title: EPN, PF A, sample 1101 [validation set]

description:
SAMPLE 1101
Methylation data from brain tumor sample.

value: EPN, PF A


title: GBM, RTK II, sample 1090 [validation set]

description:
SAMPLE 1090
Methylation data from brain tumor sample.

value: GBM, RTK II


title: 96D1


title: MNG, sample 1104 [validation set]

description:
SAMPLE 1104
Methylation data from brain tumor sample.

value: MNG


title: NBN3

source_name: New Born Lamb Cerebral Artery Untreated


title: GBM, MES, sample 1089 [validation set]

description:
SAMPLE 1089
Methylation data from brain tumor sample.


title: GBM, MID, sample 1088 [validation set]

description:
SAMPLE 1088
Methylation data from brain tumor sample.


title: NBNPHE4


title: NBN4


title: NBNPHE2


title: NBNPHE1


title: NBN2


title: O IDH, sample 1098 [validation set]

description:
SAMPLE 1098
Methylation data from brain tumor sample.

value: O IDH


title: O IDH, sample 1097 [validation set]

description:
SAMPLE 1097
Methylation data from brain tumor sample.


title: NBN1


title: GBM, MES, sample 1095 [validation set]

description:
SAMPLE 1095
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 1078 [validation set]

description:
SAMPLE 1078
Methylation data from brain tumor sample.

value: GBM, RTK I


title: MB, G3, sample 1080 [validation set]

description:
SAMPLE 1080
Methylation data from brain tumor sample.

value: MB, G3


title: Jam3-WT LICs

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

institute: Tongji hospital

description: Gene expression of Jam3 WT LICs

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: leukemia-initiating cells from three AML mouse

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

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: WT and Jam3-null AML cells with MLL-AF9-YFP gene expression  were purified by flow cytometry staining with Mac-1+c-Kit+

value: Bone marrow

tag: gender

value: female

tag: genotype/variation

value: Jam3-WT LICs


title: Jam3-null LICs

description: Gene expression of Jam3 null LICs

tag: tissue

value: Jam3-null LICs


title: MB, SHH INF, sample 1091 [validation set]

description:
SAMPLE 1091
Methylation data from brain tumor sample.

value: brain tumor

value: MB, SHH INF


title: GBM, G34, sample 1096 [validation set]

description:
SAMPLE 1096
Methylation data from brain tumor sample.

value: GBM, G34


title: GBM, RTK II, sample 1092 [validation set]

description:
SAMPLE 1092
Methylation data from brain tumor sample.


title: A IDH, sample 1067 [validation set]

description:
SAMPLE 1067
Methylation data from brain tumor sample.

value: A IDH


title: A IDH, sample 1068 [validation set]

description:
SAMPLE 1068
Methylation data from brain tumor sample.


title: MNG, sample 1086 [validation set]

description:
SAMPLE 1086
Methylation data from brain tumor sample.


title: MNG, sample 1087 [validation set]

description:
SAMPLE 1087
Methylation data from brain tumor sample.


title: DMG, K27, sample 1084 [validation set]

description:
SAMPLE 1084
Methylation data from brain tumor sample.


title: A IDH, sample 1076 [validation set]

description:
SAMPLE 1076
Methylation data from brain tumor sample.


title: O IDH, sample 1079 [validation set]

description:
SAMPLE 1079
Methylation data from brain tumor sample.


title: A IDH, sample 1064 [validation set]

description:
SAMPLE 1064
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 1083 [validation set]

description:
SAMPLE 1083
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 1065 [validation set]

description:
SAMPLE 1065
Methylation data from brain tumor sample.

value: MB, SHH CHL AD


title: A IDH, sample 1077 [validation set]

description:
SAMPLE 1077
Methylation data from brain tumor sample.


title: MNG, sample 1085 [validation set]

description:
SAMPLE 1085
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1072 [validation set]

description:
SAMPLE 1072
Methylation data from brain tumor sample.


title: GBM, MES, sample 1066 [validation set]

description:
SAMPLE 1066
Methylation data from brain tumor sample.

value: GBM, MES


title: GBM, MID, sample 1059 [validation set]

description:
SAMPLE 1059
Methylation data from brain tumor sample.

value: GBM, MID


title: PITUI, sample 1082 [validation set]

description:
SAMPLE 1082
Methylation data from brain tumor sample.

value: PITUI


title: GBM, MID, sample 1070 [validation set]

description:
SAMPLE 1070
Methylation data from brain tumor sample.


title: SCHW, sample 1069 [validation set]

description:
SAMPLE 1069
Methylation data from brain tumor sample.

value: SCHW


title: LGG, PA MID, sample 1071 [validation set]

description:
SAMPLE 1071
Methylation data from brain tumor sample.

value: LGG, PA MID


title: GBM, RTK II, sample 1057 [validation set]

description:
SAMPLE 1057
Methylation data from brain tumor sample.

value: GBM, RTK II


title: A IDH, sample 1081 [validation set]

description:
SAMPLE 1081
Methylation data from brain tumor sample.


title: GBM, MES, sample 1075 [validation set]

description:
SAMPLE 1075
Methylation data from brain tumor sample.


title: MB, G4, sample 1056 [validation set]

description:
SAMPLE 1056
Methylation data from brain tumor sample.

value: MB, G4


title: GBM, RTK I, sample 1062 [validation set]

description:
SAMPLE 1062
Methylation data from brain tumor sample.

value: GBM, RTK I


title: MB, SHH CHL AD, sample 1061 [validation set]

description:
SAMPLE 1061
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 1073 [validation set]

description:
SAMPLE 1073
Methylation data from brain tumor sample.

value: LGG, PA PF


title: GBM, RTK II, sample 1047 [validation set]

description:
SAMPLE 1047
Methylation data from brain tumor sample.


title: A IDH, HG, sample 1048 [validation set]

description:
SAMPLE 1048
Methylation data from brain tumor sample.

value: A IDH, HG


title: LGG, PA PF, sample 1054 [validation set]

description:
SAMPLE 1054
Methylation data from brain tumor sample.


title: LGG, PA/GG ST, sample 1051 [validation set]

description:
SAMPLE 1051
Methylation data from brain tumor sample.

value: LGG, PA/GG ST


title: A IDH, sample 1050 [validation set]

description:
SAMPLE 1050
Methylation data from brain tumor sample.


title: O IDH, sample 1058 [validation set]

description:
SAMPLE 1058
Methylation data from brain tumor sample.

value: O IDH


title: PXA, sample 1045 [validation set]

description:
SAMPLE 1045
Methylation data from brain tumor sample.

value: brain tumor

value: PXA


title: A IDH, HG, sample 1055 [validation set]

description:
SAMPLE 1055
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1060 [validation set]

description:
SAMPLE 1060
Methylation data from brain tumor sample.


title: GBM, MES, sample 1049 [validation set]

description:
SAMPLE 1049
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 1046 [validation set]

description:
SAMPLE 1046
Methylation data from brain tumor sample.


title: MNG, sample 1041 [validation set]

description:
SAMPLE 1041
Methylation data from brain tumor sample.

value: MNG


title: LGG, PA/GG ST, sample 1043 [validation set]

description:
SAMPLE 1043
Methylation data from brain tumor sample.


title: GBM, MES, sample 1037 [validation set]

description:
SAMPLE 1037
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1044 [validation set]

description:
SAMPLE 1044
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1032 [validation set]

description:
SAMPLE 1032
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 1031 [validation set]

description:
SAMPLE 1031
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1035 [validation set]

description:
SAMPLE 1035
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 1039 [validation set]

description:
SAMPLE 1039
Methylation data from brain tumor sample.


title: GBM, MES, sample 1033 [validation set]

description:
SAMPLE 1033
Methylation data from brain tumor sample.


title: EPN, RELA, sample 1042 [validation set]

description:
SAMPLE 1042
Methylation data from brain tumor sample.

value: EPN, RELA


title: GBM, MES, sample 1030 [validation set]

description:
SAMPLE 1030
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1034 [validation set]

description:
SAMPLE 1034
Methylation data from brain tumor sample.


title: A IDH, sample 1025 [validation set]

description:
SAMPLE 1025
Methylation data from brain tumor sample.

value: A IDH


title: A IDH, HG, sample 1038 [validation set]

description:
SAMPLE 1038
Methylation data from brain tumor sample.


title: LGG, PA MID, sample 1040 [validation set]

description:
SAMPLE 1040
Methylation data from brain tumor sample.


title: ANA PA, sample 1021 [validation set]

description:
SAMPLE 1021
Methylation data from brain tumor sample.

value: ANA PA


title: O IDH, sample 1020 [validation set]

description:
SAMPLE 1020
Methylation data from brain tumor sample.


title: EPN, PF A, sample 1018 [validation set]

description:
SAMPLE 1018
Methylation data from brain tumor sample.

value: EPN, PF A


title: DMG, K27, sample 1027 [validation set]

description:
SAMPLE 1027
Methylation data from brain tumor sample.

value: DMG, K27


title: EPN, RELA, sample 1023 [validation set]

description:
SAMPLE 1023
Methylation data from brain tumor sample.


title: GBM, MES, sample 1029 [validation set]

description:
SAMPLE 1029
Methylation data from brain tumor sample.

value: GBM, MES


title: LGG, PA/GG ST, sample 1016 [validation set]

description:
SAMPLE 1016
Methylation data from brain tumor sample.


title: GBM, MES, sample 1022 [validation set]

description:
SAMPLE 1022
Methylation data from brain tumor sample.


title: A IDH, sample 1024 [validation set]

description:
SAMPLE 1024
Methylation data from brain tumor sample.


title: A IDH, HG, sample 1019 [validation set]

description:
SAMPLE 1019
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1017 [validation set]

description:
SAMPLE 1017
Methylation data from brain tumor sample.


title: DMG, K27, sample 1015 [validation set]

description:
SAMPLE 1015
Methylation data from brain tumor sample.


title: A IDH, HG, sample 1012 [validation set]

description:
SAMPLE 1012
Methylation data from brain tumor sample.


title: ANA PA, sample 1011 [validation set]

description:
SAMPLE 1011
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 1006 [validation set]

description:
SAMPLE 1006
Methylation data from brain tumor sample.


title: GBM, MES, sample 1014 [validation set]

description:
SAMPLE 1014
Methylation data from brain tumor sample.


title: A IDH, sample 1013 [validation set]

description:
SAMPLE 1013
Methylation data from brain tumor sample.


title: GBM, MES, sample 1008 [validation set]

description:
SAMPLE 1008
Methylation data from brain tumor sample.


title: A IDH, sample 1028 [validation set]

description:
SAMPLE 1028
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1002 [validation set]

description:
SAMPLE 1002
Methylation data from brain tumor sample.


title: MNG, sample 1005 [validation set]

description:
SAMPLE 1005
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 1004 [validation set]

description:
SAMPLE 1004
Methylation data from brain tumor sample.


title: EPN, PF B, sample 999 [validation set]

description:
SAMPLE 999
Methylation data from brain tumor sample.

value: EPN, PF B


title: GBM, MES, sample 1007 [validation set]

description:
SAMPLE 1007
Methylation data from brain tumor sample.


title: O IDH, sample 1010 [validation set]

description:
SAMPLE 1010
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 1009 [validation set]

description:
SAMPLE 1009
Methylation data from brain tumor sample.

value: GBM, RTK II


title: GBM, RTK II, sample 1026 [validation set]

description:
SAMPLE 1026
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 998 [validation set]

description:
SAMPLE 998
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 995 [validation set]

description:
SAMPLE 995
Methylation data from brain tumor sample.


title: GBM, MID, sample 1001 [validation set]

description:
SAMPLE 1001
Methylation data from brain tumor sample.

value: GBM, MID


title: EPN, PF A, sample 994 [validation set]

description:
SAMPLE 994
Methylation data from brain tumor sample.


title: MB, G4, sample 1000 [validation set]

description:
SAMPLE 1000
Methylation data from brain tumor sample.

value: MB, G4


title: DMG, K27, sample 992 [validation set]

description:
SAMPLE 992
Methylation data from brain tumor sample.


title: EPN, PF A, sample 989 [validation set]

description:
SAMPLE 989
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 991 [validation set]

description:
SAMPLE 991
Methylation data from brain tumor sample.

value: MB, SHH CHL AD


title: GBM, RTK II, sample 986 [validation set]

description:
SAMPLE 986
Methylation data from brain tumor sample.


title: A IDH, sample 997 [validation set]

description:
SAMPLE 997
Methylation data from brain tumor sample.


title: A IDH, sample 982 [validation set]

description:
SAMPLE 982
Methylation data from brain tumor sample.


title: GBM, MES, sample 993 [validation set]

description:
SAMPLE 993
Methylation data from brain tumor sample.


title: GBM, MES, sample 988 [validation set]

description:
SAMPLE 988
Methylation data from brain tumor sample.


title: DMG, K27, sample 985 [validation set]

description:
SAMPLE 985
Methylation data from brain tumor sample.


title: A IDH, sample 1003 [validation set]

description:
SAMPLE 1003
Methylation data from brain tumor sample.


title: LGG, DNT, sample 990 [validation set]

description:
SAMPLE 990
Methylation data from brain tumor sample.

value: LGG, DNT


title: GBM, MYCN, sample 983 [validation set]

description:
SAMPLE 983
Methylation data from brain tumor sample.

value: GBM, MYCN


title: GBM, RTK II, sample 980 [validation set]

description:
SAMPLE 980
Methylation data from brain tumor sample.


title: GBM, MES, sample 974 [validation set]

description:
SAMPLE 974
Methylation data from brain tumor sample.


title: O IDH, sample 996 [validation set]

description:
SAMPLE 996
Methylation data from brain tumor sample.

value: O IDH


title: MB, G4, sample 987 [validation set]

description:
SAMPLE 987
Methylation data from brain tumor sample.

value: brain tumor


title: A IDH, sample 984 [validation set]

description:
SAMPLE 984
Methylation data from brain tumor sample.


title: MELAN, sample 969 [validation set]

description:
SAMPLE 969
Methylation data from brain tumor sample.

value: MELAN


title: SCHW, sample 970 [validation set]

description:
SAMPLE 970
Methylation data from brain tumor sample.

value: SCHW


title: O IDH, sample 967 [validation set]

description:
SAMPLE 967
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 965 [validation set]

description:
SAMPLE 965
Methylation data from brain tumor sample.

value: LGG, PA PF


title: A IDH, sample 962 [validation set]

description:
SAMPLE 962
Methylation data from brain tumor sample.

value: A IDH


title: GBM, RTK II, sample 976 [validation set]

description:
SAMPLE 976
Methylation data from brain tumor sample.


title: DMG, K27, sample 981 [validation set]

description:
SAMPLE 981
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 972 [validation set]

description:
SAMPLE 972
Methylation data from brain tumor sample.


title: GBM, MYCN, sample 979 [validation set]

description:
SAMPLE 979
Methylation data from brain tumor sample.


title: GBM, MES, sample 977 [validation set]

description:
SAMPLE 977
Methylation data from brain tumor sample.


title: MNG, sample 957 [validation set]

description:
SAMPLE 957
Methylation data from brain tumor sample.

value: MNG


title: GBM, RTK II, sample 978 [validation set]

description:
SAMPLE 978
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 975 [validation set]

description:
SAMPLE 975
Methylation data from brain tumor sample.


title: MNG, sample 951 [validation set]

description:
SAMPLE 951
Methylation data from brain tumor sample.


title: GBM, MES, sample 971 [validation set]

description:
SAMPLE 971
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 968 [validation set]

description:
SAMPLE 968
Methylation data from brain tumor sample.


title: GBM, RTK III, sample 944 [validation set]

description:
SAMPLE 944
Methylation data from brain tumor sample.

value: GBM, RTK III


title: O IDH, sample 966 [validation set]

description:
SAMPLE 966
Methylation data from brain tumor sample.


title: A IDH, sample 941 [validation set]

description:
SAMPLE 941
Methylation data from brain tumor sample.


title: A IDH, sample 950 [validation set]

description:
SAMPLE 950
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 964 [validation set]

description:
SAMPLE 964
Methylation data from brain tumor sample.


title: MNG, sample 958 [validation set]

description:
SAMPLE 958
Methylation data from brain tumor sample.


title: GBM, MES, sample 939 [validation set]

description:
SAMPLE 939
Methylation data from brain tumor sample.


title: O IDH, sample 940 [validation set]

description:
SAMPLE 940
Methylation data from brain tumor sample.


title: MNG, sample 959 [validation set]

description:
SAMPLE 959
Methylation data from brain tumor sample.


title: GBM, RTK III, sample 938 [validation set]

description:
SAMPLE 938
Methylation data from brain tumor sample.


title: GBM, MES, sample 973 [validation set]

description:
SAMPLE 973
Methylation data from brain tumor sample.


title: A IDH, sample 949 [validation set]

description:
SAMPLE 949
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 948 [validation set]

description:
SAMPLE 948
Methylation data from brain tumor sample.


title: GBM, MID, sample 946 [validation set]

description:
SAMPLE 946
Methylation data from brain tumor sample.


title: DMG, K27, sample 947 [validation set]

description:
SAMPLE 947
Methylation data from brain tumor sample.

value: DMG, K27


title: A IDH, HG, sample 943 [validation set]

description:
SAMPLE 943
Methylation data from brain tumor sample.

value: A IDH, HG


title: PLEX, AD, sample 953 [validation set]

description:
SAMPLE 953
Methylation data from brain tumor sample.

value: PLEX, AD


title: GBM, RTK II, sample 929 [validation set]

description:
SAMPLE 929
Methylation data from brain tumor sample.

value: GBM, RTK II


title: O IDH, sample 937 [validation set]

description:
SAMPLE 937
Methylation data from brain tumor sample.


title: A IDH, HG, sample 928 [validation set]

description:
SAMPLE 928
Methylation data from brain tumor sample.


title: GBM, MES, sample 927 [validation set]

description:
SAMPLE 927
Methylation data from brain tumor sample.

value: GBM, MES


title: GBM, RTK II, sample 963 [validation set]

description:
SAMPLE 963
Methylation data from brain tumor sample.


title: A IDH, sample 942 [validation set]

description:
SAMPLE 942
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 934 [validation set]

description:
SAMPLE 934
Methylation data from brain tumor sample.


title: GBM, RTK III, sample 936 [validation set]

description:
SAMPLE 936
Methylation data from brain tumor sample.


title: GBM, MES, sample 930 [validation set]

description:
SAMPLE 930
Methylation data from brain tumor sample.


title: MNG, sample 925 [validation set]

description:
SAMPLE 925
Methylation data from brain tumor sample.


title: MNG, sample 932 [validation set]

description:
SAMPLE 932
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 924 [validation set]

description:
SAMPLE 924
Methylation data from brain tumor sample.


title: ETMR, sample 922 [validation set]

description:
SAMPLE 922
Methylation data from brain tumor sample.

value: ETMR


title: GBM, MES, sample 921 [validation set]

description:
SAMPLE 921
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 933 [validation set]

description:
SAMPLE 933
Methylation data from brain tumor sample.


title: O IDH, sample 923 [validation set]

description:
SAMPLE 923
Methylation data from brain tumor sample.


title: HGNET, MN1, sample 914 [validation set]

description:
SAMPLE 914
Methylation data from brain tumor sample.

value: HGNET, MN1


title: MNG, sample 945 [validation set]

description:
SAMPLE 945
Methylation data from brain tumor sample.


title: LGG, PA/GG ST, sample 931 [validation set]

description:
SAMPLE 931
Methylation data from brain tumor sample.

value: LGG, PA/GG ST


title: GBM, RTK II, sample 916 [validation set]

description:
SAMPLE 916
Methylation data from brain tumor sample.


title: A IDH, sample 917 [validation set]

description:
SAMPLE 917
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 911 [validation set]

description:
SAMPLE 911
Methylation data from brain tumor sample.


title: A IDH, sample 915 [validation set]

description:
SAMPLE 915
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 920 [validation set]

description:
SAMPLE 920
Methylation data from brain tumor sample.

value: MB, SHH CHL AD


title: MNG, sample 935 [validation set]

description:
SAMPLE 935
Methylation data from brain tumor sample.


title: GBM, MID, sample 908 [validation set]

description:
SAMPLE 908
Methylation data from brain tumor sample.

value: GBM, MID


title: GBM, RTK I, sample 909 [validation set]

description:
SAMPLE 909
Methylation data from brain tumor sample.

value: brain tumor

value: GBM, RTK I


title: DLGNT, sample 905 [validation set]

description:
SAMPLE 905
Methylation data from brain tumor sample.

value: DLGNT


title: PLEX, PED A , sample 926 [validation set]

description:
SAMPLE 926
Methylation data from brain tumor sample.

value: PLEX, PED A


title: MNG, sample 899 [validation set]

description:
SAMPLE 899
Methylation data from brain tumor sample.


title: O IDH, sample 900 [validation set]

description:
SAMPLE 900
Methylation data from brain tumor sample.

value: O IDH


title: GBM, RTK I, sample 897 [validation set]

description:
SAMPLE 897
Methylation data from brain tumor sample.


title: GBM, MID, sample 896 [validation set]

description:
SAMPLE 896
Methylation data from brain tumor sample.


title: PITAD, FSH LH, sample 910 [validation set]

description:
SAMPLE 910
Methylation data from brain tumor sample.

value: PITAD, FSH LH


title: ETMR, sample 907 [validation set]

description:
SAMPLE 907
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 913 [validation set]

description:
SAMPLE 913
Methylation data from brain tumor sample.


title: GBM, MES, sample 893 [validation set]

description:
SAMPLE 893
Methylation data from brain tumor sample.


title: O IDH, sample 903 [validation set]

description:
SAMPLE 903
Methylation data from brain tumor sample.


title: ANA PA, sample 895 [validation set]

description:
SAMPLE 895
Methylation data from brain tumor sample.

value: ANA PA


title: ANA PA, sample 904 [validation set]

description:
SAMPLE 904
Methylation data from brain tumor sample.


title: A IDH, sample 902 [validation set]

description:
SAMPLE 902
Methylation data from brain tumor sample.

value: A IDH


title: GBM, MES, sample 885 [validation set]

description:
SAMPLE 885
Methylation data from brain tumor sample.


title: GBM, MES, sample 901 [validation set]

description:
SAMPLE 901
Methylation data from brain tumor sample.


title: O IDH, sample 886 [validation set]

description:
SAMPLE 886
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 889 [validation set]

description:
SAMPLE 889
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 894 [validation set]

description:
SAMPLE 894
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 891 [validation set]

description:
SAMPLE 891
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 887 [validation set]

description:
SAMPLE 887
Methylation data from brain tumor sample.


title: GBM, MID, sample 898 [validation set]

description:
SAMPLE 898
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 892 [validation set]

description:
SAMPLE 892
Methylation data from brain tumor sample.


title: GBM, MES, sample 884 [validation set]

description:
SAMPLE 884
Methylation data from brain tumor sample.


title: O IDH, sample 888 [validation set]

description:
SAMPLE 888
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 881 [validation set]

description:
SAMPLE 881
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 878 [validation set]

description:
SAMPLE 878
Methylation data from brain tumor sample.


title: MNG, sample 874 [validation set]

description:
SAMPLE 874
Methylation data from brain tumor sample.

value: MNG


title: A IDH, HG, sample 875 [validation set]

description:
SAMPLE 875
Methylation data from brain tumor sample.

value: A IDH, HG


title: MNG, sample 866 [validation set]

description:
SAMPLE 866
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 883 [validation set]

description:
SAMPLE 883
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 877 [validation set]

description:
SAMPLE 877
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 863 [validation set]

description:
SAMPLE 863
Methylation data from brain tumor sample.

value: GBM, RTK II


title: GBM, MES, sample 880 [validation set]

description:
SAMPLE 880
Methylation data from brain tumor sample.

value: GBM, MES


title: ANA PA, sample 890 [validation set]

description:
SAMPLE 890
Methylation data from brain tumor sample.


title: ANA PA, sample 872 [validation set]

description:
SAMPLE 872
Methylation data from brain tumor sample.


title: MB, G4, sample 862 [validation set]

description:
SAMPLE 862
Methylation data from brain tumor sample.

value: MB, G4


title: GBM, MES, sample 871 [validation set]

description:
SAMPLE 871
Methylation data from brain tumor sample.


title: LGG, DNT, sample 868 [validation set]

description:
SAMPLE 868
Methylation data from brain tumor sample.

value: LGG, DNT


title: ANA PA, sample 882 [validation set]

description:
SAMPLE 882
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 870 [validation set]

description:
SAMPLE 870
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 867 [validation set]

description:
SAMPLE 867
Methylation data from brain tumor sample.


title: SCHW, MEL, sample 856 [validation set]

description:
SAMPLE 856
Methylation data from brain tumor sample.

value: SCHW, MEL


title: GBM, MID, sample 864 [validation set]

description:
SAMPLE 864
Methylation data from brain tumor sample.


title: O IDH, sample 869 [validation set]

description:
SAMPLE 869
Methylation data from brain tumor sample.


title: A IDH, sample 873 [validation set]

description:
SAMPLE 873
Methylation data from brain tumor sample.


title: LGG, PA PF, sample 876 [validation set]

description:
SAMPLE 876
Methylation data from brain tumor sample.

value: LGG, PA PF


title: A IDH, HG, sample 860 [validation set]

description:
SAMPLE 860
Methylation data from brain tumor sample.


title: MB, SHH INF, sample 879 [validation set]

description:
SAMPLE 879
Methylation data from brain tumor sample.

value: MB, SHH INF


title: A IDH, sample 858 [validation set]

description:
SAMPLE 858
Methylation data from brain tumor sample.

value: brain tumor


title: GBM, RTK II, sample 865 [validation set]

description:
SAMPLE 865
Methylation data from brain tumor sample.


title: A IDH, sample 861 [validation set]

description:
SAMPLE 861
Methylation data from brain tumor sample.


title: O IDH, sample 859 [validation set]

description:
SAMPLE 859
Methylation data from brain tumor sample.


title: O IDH, sample 857 [validation set]

description:
SAMPLE 857
Methylation data from brain tumor sample.


title: DMG, K27, sample 855 [validation set]

description:
SAMPLE 855
Methylation data from brain tumor sample.

value: DMG, K27


title: MNG, sample 853 [validation set]

description:
SAMPLE 853
Methylation data from brain tumor sample.


title: SCHW, sample 854 [validation set]

description:
SAMPLE 854
Methylation data from brain tumor sample.

value: SCHW


title: MELAN, sample 849 [validation set]

description:
SAMPLE 849
Methylation data from brain tumor sample.

value: MELAN


title: MB, G3, sample 841 [validation set]

description:
SAMPLE 841
Methylation data from brain tumor sample.

value: MB, G3


title: MNG, sample 852 [validation set]

description:
SAMPLE 852
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 845 [validation set]

description:
SAMPLE 845
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 843 [validation set]

description:
SAMPLE 843
Methylation data from brain tumor sample.


title: LGG, PA MID, sample 847 [validation set]

description:
SAMPLE 847
Methylation data from brain tumor sample.

value: LGG, PA MID


title: GBM, G34, sample 848 [validation set]

description:
SAMPLE 848
Methylation data from brain tumor sample.

value: GBM, G34


title: DMG, K27, sample 846 [validation set]

description:
SAMPLE 846
Methylation data from brain tumor sample.


title: GBM, MID, sample 844 [validation set]

description:
SAMPLE 844
Methylation data from brain tumor sample.

value: GBM, MID


title: O IDH, sample 851 [validation set]

description:
SAMPLE 851
Methylation data from brain tumor sample.

value: O IDH


title: SCHW, sample 850 [validation set]

description:
SAMPLE 850
Methylation data from brain tumor sample.


title: MB, G3, sample 840 [validation set]

description:
SAMPLE 840
Methylation data from brain tumor sample.


title: GBM, MES, sample 842 [validation set]

description:
SAMPLE 842
Methylation data from brain tumor sample.


title: A IDH, HG, sample 839 [validation set]

description:
SAMPLE 839
Methylation data from brain tumor sample.

value: A IDH, HG


title: EPN, PF A, sample 833 [validation set]

description:
SAMPLE 833
Methylation data from brain tumor sample.

value: EPN, PF A


title: O IDH, sample 832 [validation set]

description:
SAMPLE 832
Methylation data from brain tumor sample.


title: GBM, G34, sample 838 [validation set]

description:
SAMPLE 838
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 834 [validation set]

description:
SAMPLE 834
Methylation data from brain tumor sample.

value: GBM, RTK II


title: A IDH, sample 831 [validation set]

description:
SAMPLE 831
Methylation data from brain tumor sample.

value: A IDH


title: ANA PA, sample 836 [validation set]

description:
SAMPLE 836
Methylation data from brain tumor sample.

value: ANA PA


title: O IDH, sample 835 [validation set]

description:
SAMPLE 835
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 837 [validation set]

description:
SAMPLE 837
Methylation data from brain tumor sample.

value: GBM, RTK I


title: O IDH, sample 830 [validation set]

description:
SAMPLE 830
Methylation data from brain tumor sample.


title: MB, SHH CHL AD, sample 826 [validation set]

description:
SAMPLE 826
Methylation data from brain tumor sample.

value: MB, SHH CHL AD


title: A IDH, sample 825 [validation set]

description:
SAMPLE 825
Methylation data from brain tumor sample.


title: PXA, sample 828 [validation set]

description:
SAMPLE 828
Methylation data from brain tumor sample.

value: PXA


title: A IDH, HG, sample 829 [validation set]

description:
SAMPLE 829
Methylation data from brain tumor sample.

value: brain tumor


title: PXA, sample 827 [validation set]

description:
SAMPLE 827
Methylation data from brain tumor sample.


title: LGG, PA/GG ST, sample 823 [validation set]

description:
SAMPLE 823
Methylation data from brain tumor sample.

value: LGG, PA/GG ST


title: CHORDM, sample 821 [validation set]

description:
SAMPLE 821
Methylation data from brain tumor sample.

value: CHORDM


title: MB, SHH CHL AD, sample 818 [validation set]

description:
SAMPLE 818
Methylation data from brain tumor sample.


title: MB, G3, sample 824 [validation set]

description:
SAMPLE 824
Methylation data from brain tumor sample.


title: DMG, K27, sample 812 [validation set]

description:
SAMPLE 812
Methylation data from brain tumor sample.

value: DMG, K27


title: GBM, MES, sample 822 [validation set]

description:
SAMPLE 822
Methylation data from brain tumor sample.

value: GBM, MES


title: LGG, PA PF, sample 816 [validation set]

description:
SAMPLE 816
Methylation data from brain tumor sample.

value: LGG, PA PF


title: CNS NB, FOXR2, sample 820 [validation set]

description:
SAMPLE 820
Methylation data from brain tumor sample.

value: CNS NB, FOXR2


title: O IDH, sample 815 [validation set]

description:
SAMPLE 815
Methylation data from brain tumor sample.


title: O IDH, sample 819 [validation set]

description:
SAMPLE 819
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 817 [validation set]

description:
SAMPLE 817
Methylation data from brain tumor sample.


title: ATRT, TYR, sample 811 [validation set]

description:
SAMPLE 811
Methylation data from brain tumor sample.

value: ATRT, TYR


title: GBM, RTK II, sample 813 [validation set]

description:
SAMPLE 813
Methylation data from brain tumor sample.


title: EPN, RELA, sample 810 [validation set]

description:
SAMPLE 810
Methylation data from brain tumor sample.

value: EPN, RELA


title: GBM, RTK II, sample 808 [validation set]

description:
SAMPLE 808
Methylation data from brain tumor sample.


title: GBM, RTK I, sample 809 [validation set]

description:
SAMPLE 809
Methylation data from brain tumor sample.


title: GBM, RTK II, sample 801 [validation set]

description:
SAMPLE 801
Methylation data from brain tumor sample.


title: MB, WNT, sample 796 [validation set]

description:
SAMPLE 796
Methylation data from brain tumor sample.

value: MB, WNT


title: A IDH, HG, sample 803 [validation set]

description:
SAMPLE 803
Methylation data from brain tumor sample.

value: A IDH, HG


title: GBM, MES, sample 804 [validation set]

description:
SAMPLE 804
Methylation data from brain tumor sample.


title: EPN, PF B, sample 799 [validation set]

description:
SAMPLE 799
Methylation data from brain tumor sample.

value: EPN, PF B


title: ANA PA, sample 798 [validation set]

description:
SAMPLE 798
Methylation data from brain tumor sample.


title: O IDH, sample 797 [validation set]

description:
SAMPLE 797
Methylation data from brain tumor sample.

value: O IDH


title: GBM, MYCN, sample 814 [validation set]

description:
SAMPLE 814
Methylation data from brain tumor sample.

value: GBM, MYCN


title: O IDH, sample 795 [validation set]

description:
SAMPLE 795
Methylation data from brain tumor sample.


title: A IDH, sample 794 [validation set]

description:
SAMPLE 794
Methylation data from brain tumor sample.

value: A IDH


title: LGG, MYB, sample 793 [validation set]

description:
SAMPLE 793
Methylation data from brain tumor sample.

value: LGG, MYB


title: EPN, PF A, sample 791 [validation set]

description:
SAMPLE 791
Methylation data from brain tumor sample.

value: EPN, PF A


title: GBM, RTK II, sample 787 [validation set]

description:
SAMPLE 787
Methylation data from brain tumor sample.

value: brain tumor

value: GBM, RTK II


title: O IDH, sample 789 [validation set]

description:
SAMPLE 789
Methylation data from brain tumor sample.


title: GBM, MES, sample 786 [validation set]

description:
SAMPLE 786
Methylation data from brain tumor sample.


title: MNG, sample 800 [validation set]

description:
SAMPLE 800
Methylation data from brain tumor sample.

value: MNG


title: A IDH, sample 807 [validation set]

description:
SAMPLE 807
Methylation data from brain tumor sample.


title: ETMR, sample 779 [validation set]

description:
SAMPLE 779
Methylation data from brain tumor sample.

value: ETMR


title: LGG, PA MID, sample 780 [validation set]

description:
SAMPLE 780
Methylation data from brain tumor sample.

value: LGG, PA MID