title: H1-6-only-1

value: hepatoma cells

value: mono-culture


title: LSWT11 leaf RNA [Sample_1295_LIB13590_LDI11332]

status: Public on Jan 31 2023

type: SRA

city: Norwich

first: Martin

last: Vickers

state: Norfolk

address: Colney Ln

country: United Kingdom

institute: John Innes Centre

description: part of multi-tissue transcriptome, used for read counting

library_source: transcriptomic

data_processing:
FastQC
Kontaminant pipeline (removing contaminants using sortmerna v2.0)
Trimmed sequence reads (trim_galore v 0.4.1)
read mapping using Kallisto
Assembly: Rbp1.0 grasspea assembly that is published with manuscript
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Lathyrus sativus

source_name: juvenile whole leaf

extract_protocol:
Rneasy Plant Mini Kit Qiagen
TruSeq RNA

tag: tissue

value: juvenile whole leaf

tag: genotype

tag: treatment

tag: time

value: 3 weeks after imbibing


title: P5Tx_Liver

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

description:
Single-cell RNA-Seq
mRNA

data_processing:
To distinguish the human cancer cells from the mouse TME cells, we aligned the sequencing data of each sample to GRCh37 (hg19) and GRCm38 (mm10) reference genomes separately using the Cell Ranger Single-Cell Software Suite (v-2.0.1, 10X Genomics), and estimated the unique molecular identifiers (UMIs) with the default parameters.
We then merged the UMI files of the 4 samples (P5Tx Liver, P5Tx Tumor, P60Tx Liver and P60Tx Tumor) for both human cancer cells and mouse TME cells with an in-house script. Thereafter, we introduced the Seurat (v-3.2.2, PMID: 31178118) R package to remove the low-quality cells following these criteria: human cancer cells expressed < 1000 or > 8000 genes or mitochondrial gene content > 15% of total UMIs; mouse TME cells expressed <200 or >3000 genes or mitochondrial gene content > 10% of total UMIs.
To normalize the data, we divided the UMI count of each gene by the total UMI counts of the cell and scaled the library size to 1,000,000, followed by a natural log plus 1 transformation (“NormalizeData”). Then the normalized data was further scaled so that the mean expression across cells is 0 and the variance is 1 (“ScaleData”). The principle component analysis (PCA) was employed for dimensionality reduction (“RunPCA”). To determine the number of components to choose, we implemented a resampling test inspired by the JackStraw procedure (“JackStraw” and “ScoreJackStraw”) and picked the first 15 principal components which explained sufficient observed variance. Thereafter, to identify the clusters from the reduced dimensional space, we constructed a k-nearest neighborhood (KNN) graph based on the Euclidean distance in PCA space and refined the edge weights among cells based on the shared overlap in local neighborhoods (“FindNeighbors”). We then applied the modularity optimization technique named Louvain algorithm to iteratively group cell together with a resolution parameter of 0.5 (“FindClusters”). Finally, the Uniform Manifold Approximation and Projection (UMAP) was used to visualize the clustering results (“DimPlot”).
Genome_build: mm10/hg19
Supplementary_files_format_and_content: *.tar.gz: Tar archives include Cell Ranger count matrix for single cells in each sample; barcodes.tsv, genes.tsv, matrix.mtx.

organism:
Homo sapiens
Mus musculus

source_name: Liver tissue from model established in postnatal day 5

extract_protocol:
The liver tissue and bulk tumors were minced and then enzymatically digested in advanced DMEM/F-12 (Thermo Fisher Scientific, Waltham, MA), containing 10 U/mL Papain (Worthington, Lakewood, NJ), 1 mmol/L N-acetyl cysteine (Sigma-Aldrich, St. Louis, MO), 12mg/mL DNase I (Sigma-Aldrich). The mixture was incubated at 37°C for about 30 min for the enzymatic digestion. The additional mechanical digestion was performed by gently pipetting up and down. Thereafter, the cell suspensions were passed through a 100-μm strainer and washed twice with 5ml of cold Advance DMEM/F12 and centrifugated at 300g for 5min at 4°C.
The single cells dissociated from liver and tumor tissues were processed by the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) as per the manufacturer’s protocol. Briefly, the single cells were washed once with PBS plus 0.04% BSA and counted with Luna-FL Fluorescence Cell Counter (VitaScientific). Then the cells were added to each lane of the chip and partitioned into Gel Beads in emulsion in the Chromium Controller. The cells were lysed, barcoded and reversely transcribed, followed by amplification, fragmentation, adaptor attachment and indexing. The libraries were sequenced by Novaseq 6000 (Illumina).

treatment_protocol: Around 37.5 thousand HepG2 cells suspended in 1.5 ul of Matrigel were injected to each liver of five-day-old (P5) and sixty-day-old NSG mice.

tag: mouse strain

value: NOD scid gamma mouse

tag: mouse age at model establishment

value: Liver tissue


title: NC3

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

country: China

institute: CAS

data_processing:
The StringTie software and  Hisat2 is used to proofread gene transcriptome data.
Fragments per kilobase million are calculated by R software ballgown at the gene and transcript levels.
Differential expression analysis of RNAs using edgeR was performed.
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: microglial cells

growth_protocol: BV2 microglial cells were cultured in Dulbecco’s modified Eagle medium high glucose media containing 10% fetal bovine serum.

extract_protocol:
Total RNA in the BV2 cells was isolated using TRIzol reagent. The quality and quantity of the RNA was assessed using a NanoDrop ND-1000 spectrophotometer.
Total RNA was removed using the Ribo-Zero Magnetic Gold Kit. The processed product RNA was constructed with KAPA Stranded RNA-Seq Library Prep Kit. The constructed library was tested by Agilent 2100 Bioanalyzer and the library was quantified using quantitative PCR.

treatment_protocol: Half the cells of this subline provided the negative control group (Ad-NC). The other half were then infected with adenovirus for 48 hours to give the experimental group (Ad-shGCH1).

value: negative control


title: H1-6-LSEC-3

city: Osaka

first: Hoang

middle: Huu

last: Truong

state: Select a State or Province

address: 1-4-3 Asahi-machi, Abeno-ku, Osaka-City, Osaka, Japan

department: Hepatology

country: Japan

institute: Graduate School of Medicine, Osaka City University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage. Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM(Transcripts Per Kilobase Million).
IIn groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: mm10
Supplementary files format and content: Expression_Profile.mm10.table.xlsx

source_name: Liver

growth_protocol: 5× 10^5 LSECs were cultured in completed LSECs medium in the bottom of 12 wells insert-plate, 1× 10^5 Hepa1-6 cells were cultured in DMEM supplemented with 10% FBS, 1% Penicillin/streptomycin in the 3um-insert.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E.

treatment_protocol: Next day,  removed the medium in both cell types, wash 3 times by DMEM solution, then co-cultured using DMEM supplemented with 2% FBS, 1% penicillin/ streptomycin. After 24 hours, mRNA was extracted.

value: Liver

tag: cell line

tag: cell type

value: hepatoma cells, primary LSECs

tag: culture conditions

value: co-culture


title: LSWT11 seedling shoot tip RNA [Sample_1348_LIB11624_LDI11331]

source_name: seedling shoot tip

value: seedling shoot tip

value: 10 days after imbibing


title: HC_2_m6A_seq

city: hefei

first: Jun

last: Wu

state: Anhui

address: Meishan Road 81

institute: Anhui medical university

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: Version GRCh38.p10
Supplementary_files_format_and_content: txt,tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.
Immunoprecipitated m6A RNA fragments for m6A-seq (IP), total RNA for RNA-Seq (Input).

value: peripheral blood

value: peripheral blood mononuclear cell

tag: disease state

value: healthy control


title: HC_1_m6A_seq


title: LSWT11 seedling root tip RNA [Sample_1295_LIB13589_LDI11330]

source_name: seedling radicle

value: seedling radicle


title: NC2


title: SLE_3_m6A_seq

value: systemic lupus erythematosus patient


title: SLE_2_m6A_seq


title: T2


title: LSWT11 root RNA [Sample_1295_LIB11627_LDI11333]

source_name: juvenile whole root

value: juvenile whole root


title: T3


title: LSWT11 seedling shoot tip RNA [Sample_1295_LIB11624_LDI11331]


title: T1


title: SLE_1_m6A_seq


title: LSWT11 flower RNA [Sample_1295_LIB11628_LDI11334]

source_name: open flower

value: open flower

value: 3 months after imbibing


title: T2DM_ischemic_gastrocnemius_3

status: Public on Jan 30 2023

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: Ischemic gastrocnemius muscle of type 2 diabetic mice collected at day-7 post FAL

extract_protocol:
Tissues were snap frozen in liquid nitrogen and Total RNA was isolated from both normoxic adductor and ischemic gastrocnemius muscles using RNeasy Fibrous Tissue Mini Kit (QIAGEN Finland, Helsinki, Finland) according to manufacturer's instructions.
Total RNA was enriched for Poly (A)+ RNA with MicroPoly (A) Purist Kit (Ambion, Austin, TX, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with Antarctic phosphatase (New England Biolabs, Ipswich, MA, USA) followed by heat-inactivation. Dephosphorylation reactions were mixed with 2 x Novex TBE-Urea sample buffer (Invitrogen), briefly denatured and loaded on a Novex denaturing 15% polyacrylamide TBE-urea gel according to the manufacturer’s instructions. Fragments of 50-300 nucleotides in length were gel purified .  Also the poly (A)+ tailing and cDNA synthesis was performed the next day. However, for reverse transcription oligos with custom barcodes (underlined) were used: 5’phosCA/TG/AC/GTGATCGTCGGACTGTAGAACTCT/idSp/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’. After cDNA synthesis, exonuclease was used to catalyze the removal of excess oligos. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of ~150-200 bps were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 8 cycles. The final product was ran on Novex 10%TBE gel, gel purified as above and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA). The library was sequenced for 50 cycles on the Illumina HiSeq 2000 according to the manufacturer’s instructions.

treatment_protocol: Unilateral hindlimb ischemia was induced by ligating the femoral artery distal to the origin of the profunda femoral artery. Thus arteriogenesis will predominate in the adductor muscles and angiogenesis predominates in the gastrocnemius and tibilais muscles.

tag: strain background

tag: mouse status

value: type 2 diabetic

tag: time point

value: at day-7 post FAL

value: Ischemic gastrocnemius muscle


title: T2DM_ischemic_gastrocnemius_2


title: Control_ischemic_gastrocnemius_6

source_name: Ischemic gastrocnemius muscle of control mice collected at day-7 post FAL

value: control


title: T2DM_ischemic_gastrocnemius_6


title: Control_ischemic_gastrocnemius_5


title: NC1

value: negative control


title: T2DM_ischemic_gastrocnemius_5


title: Control_ischemic_gastrocnemius_3


title: MAHA_1DS

description: part of transcriptome drough response experiment

source_name: whole shoot

value: whole shoot

value: Mahateora

value: NIAB field, simulated drought

value: 3 months after planting


title: T2DM_ischemic_gastrocnemius_1


title: SNI Contralateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 1

type: RNA

city: Boston

first: Isaac

middle: Ming-Cheng

last: Chiu

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

description: FACS purified Nav1.8Tg-Tomato positive cells from pooled contralateral DRG samples following sciatic nerve transection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr on Affymetrix mouse Gene ST version 1.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix CEL files were analyzed with the Robust Mutli-array Average (RMA) algorithm as the normalization method with quantile normalization, background correction, and median scalin. using the GenePattern (http://www.broadinstitute.org/cancer/software/genepattern) software platform.

label: Biotin

source_name: Contralateral DRG (L4-L6) from Nav1.8Tg-TdTomato mice after sciatic nerve transection

label_protocol: 100 ng total RNA was amplified using the GeneChip WT cDNA synthesis and amplification kit (Affymetrix).  cDNA synthesis, biotinylation of cRNA, fragmentation, and labeling was according to standard Affymetrix protocols.

growth_protocol: Nav1.8-Cre Transgenic mice (also known as SNS-Cre mice) were bred with Rosa26-TdTomato (ai14 line from Jackson Labs) reporter mice to generate Nav1.8-Cre Tg/TdTomato reporter progeny.  Adult mice (7-14 week old) were used for this experiment.

extract_protocol: RNA was extraced by sequential Qiazol extraction and Qiagen Rneasy micro column purification with genomic dna digest.

treatment_protocol: Nav1.8-Cre Tg/TdTomato mice underwent CFA intraplantar injection or sciatic nerve transection on the left side (ispilateral). At day 1 post CFA injection or day 5 post-sciatic nerve transection, mice were euthanized. Following euthanasia, ipsilateral or contralateral lumbar L4-L6 dorsal root ganglia (DRG) were dissected from mice having underwent various treatments, digested with Collagenase/Dispase enzyme mixtures for cell dissociation.  Lumbar DRG were pooled from 3 mice per microarray sample.  TdTomato high expressing cells were purified by flow cytometry.

value: DRG facs purified Nav1.8 lineage neurons


title: T2DM_ischemic_gastrocnemius_4


title: CFA Contralateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 3

description: FACS purified Nav1.8Tg-Tomato positive cells from pooled contralateral DRG samples following CFA intraplantar inflammation

source_name: Contralateral DRG (L4-L6) from CFA injected Nav1.8Tg-TdTomato mice


title: T2DM_Adductor_3

source_name: Adductor muscle of type 2 diabetic mice collected at day-7 post FAL

value: Adductor muscle


title: CFA Contralateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 2


title: CFA Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 3

description: FACS purified Nav1.8Tg-Tomato positive cells from pooled ipsilateral DRG samples following CFA intraplantar inflammation

source_name: Ipsilateral DRG (L4-L6) from CFA injected Nav1.8Tg-TdTomato mice


title: SNI Contralateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 2


title: SNI Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 1

description: FACS purified Nav1.8Tg-Tomato positive cells from pooled ipsilateral DRG samples following sciatic nerve transection

source_name: Ipsilateral DRG (L4-L6) from Nav1.8Tg-TdTomato mice after sciatic nerve transection


title: CFA Contralateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 1


title: SNI Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 3


title: Control_ischemic_gastrocnemius_1


title: SNI Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 2


title: CFA Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 1


title: T2DM_Adductor_1


title: T2DM_Adductor_4


title: Control_ischemic_gastrocnemius_4


title: Control_ischemic_gastrocnemius_2


title: T2DM_Adductor_5


title: mnp-20-0959

type: genomic

city: Heidelberg

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Pilocytic Astrocytoma

tag: "patient age (years)"

tag: "patient gender"

value: female

tag: "tumor location"

value: cerebellum


title: Control_Adductor_5

source_name: Adductor muscle of control mice collected at day-7 post FAL

tag: tissue


title: Control_Adductor_1


title: Control_Adductor_2


title: mnp-20-0476

value: Diffuse midline glioma, H3 K27-mutated

value: male

value: spinal cord


title: mnp-20-1016

value: Ependymoma, WHO grade III

value: cerebellum, fourth ventricle


title: mnp-20-1488

value: Glioblastoma (GBM)

value: primary somatosensory cortex, primary motor cortex


title: CFA Ipsilateral DRG (lumbar) Nav1.8Tg-TdTomato , biological replicate 2


title: mnp-20-1401

value: CNS Ewing family tumor

value: cerebellum, parietal lobe


title: T2DM_Adductor_2

value: type 2 diabetic

value: at day-7 post FAL


title: Control_Adductor_3

value: control


title: mnp-20-0448


title: mnp-20-0035

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-1202

value: FFPE tissue

value: Pilocytic Astrocytoma


title: mnp-20-0341

value: CNS sarcoma

value: parietal lobe


title: Control_Adductor_4

value: Adductor muscle


title: mnp-20-0778

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: female


title: mnp-20-0031

value: cerebellum, fourth ventricle


title: T2DM_Adductor_6


title: mnp-20-1353

value: Astroblastoma


title: mnp-20-1300

value: Choroid plexus carcinoma

value: plexus choroideus


title: mnp-20-1313

value: Descriptive diagnosis

value: primary motor cortex, basal ganglia


title: mnp-20-0206

value: Anaplastic astrocytoma

value: male

value: cerebellum


title: mnp-20-0625


title: mnp-20-0838

value: Ganglioglioma


title: mnp-20-0030

value: FFPE tissue

value: occipital lobe


title: Control_Adductor_6

value: control

value: at day-7 post FAL


title: mnp-20-1466

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: temporal lobe


title: mnp-20-0646


title: mnp-20-0297

value: Choroid plexus papilloma

value: female

value: fourth ventricle


title: mnp-20-0870

value: Teratoma

value: pineal region


title: mnp-20-1346

value: Glioblastoma (GBM)


title: mnp-20-1339

value: Anaplastic pilocytic astrocytoma

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0474

value: Pilocytic Astrocytoma

value: male


title: mnp-20-1301

value: cerebellum


title: mnp-20-1573

value: FFPE tissue

value: cerebellum, fourth ventricle, pons


title: mnp-20-1576


title: mnp-20-1597

value: pons, medulla oblongata


title: mnp-20-1305

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-0458

value: Descriptive diagnosis

value: frontal lobe


title: mnp-20-0220

value: female

value: spinal cord


title: mnp-20-0550

value: CNS Ewing family tumor

value: parietal lobe


title: mnp-20-0843

value: Medulloblastoma, SHH

value: fourth ventricle


title: mnp-20-1181


title: mnp-20-1011

value: CNS tumor with BCOR internal tandem duplication

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1326

value: Pilocytic Astrocytoma

value: male

value: brain stem


title: mnp-20-0394

value: FFPE tissue

value: cerebellum


title: mnp-20-0316

value: Diffuse astrocytoma, IDH-mutated


title: mnp-20-1161

value: Glioblastoma (GBM)

value: temporal lobe, occipital lobe, parietal lobe


title: mnp-20-0248

value: Diffuse astrocytoma

value: pineal region


title: mnp-20-0580

value: Ganglioglioma


title: mnp-20-1003

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0697

value: Anaplastic pilocytic astrocytoma

value: hypothalamus


title: mnp-20-0862

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-0496

value: Pineoblastoma


title: mnp-20-1248


title: mnp-20-1362

value: female

value: parietal lobe, occipital lobe, frontal lobe


title: mnp-20-1594

value: Pilocytic Astrocytoma

value: male

value: supratentorial midline


title: mnp-20-0883

value: FFPE tissue

value: cerebellum


title: mnp-20-0782

value: parietal lobe, occipital lobe


title: mnp-20-1178

value: Diffuse midline glioma, H3 K27-mutated

value: thalamus


title: mnp-20-0750

value: Glioblastoma (GBM)

value: frontal lobe


title: mnp-20-1492


title: mnp-20-1380

value: Anaplastic astrocytoma

value: temporal lobe


title: mnp-20-0703


title: mnp-20-1548

value: Hemangioblastoma


title: mnp-20-0378

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: temporal lobe, occipital lobe


title: mnp-20-1459

value: Medulloblastoma, non-WNT/SHH

value: female

value: cerebellum, fourth ventricle


title: mnp-20-1101

value: male

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0919

value: FFPE tissue

value: fourth ventricle


title: mnp-20-1382


title: mnp-20-0460

value: Anaplastic ganglioglioma

value: occipital lobe


title: mnp-20-0401

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: mnp-20-0340

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: third ventricle


title: mnp-20-1061

value: Chondrosarcoma


title: mnp-20-0649

value: frontal lobe


title: mnp-20-0637

value: Pilocytic Astrocytoma

value: hypothalamus


title: mnp-20-1036

value: CNS sarcoma


title: mnp-20-1217

value: female

value: orbital frontal cortex


title: mnp-20-0932

value: medulla oblongata


title: mnp-20-0561

value: Germinoma

value: male

value: hypothalamus, pineal region


title: mnp-20-1242

value: FFPE tissue

value: cerebellum, fourth ventricle


title: mnp-20-0326

value: Medulloblastoma, WNT

value: fourth ventricle


title: mnp-20-1557

value: Glioblastoma (GBM)


title: mnp-20-0913

value: Adamantinomatous craniopharyngioma

value: pituitary gland


title: mnp-20-0635

value: occipital lobe


title: mnp-20-0250

value: Pineoblastoma

value: pineal region


title: mnp-20-1453

value: Pilocytic Astrocytoma


title: mnp-20-1472

value: Glioblastoma, H3 G34-mutated


title: mnp-20-0202

value: Diffuse midline glioma, H3 K27-mutated

value: female


title: mnp-20-1591


title: mnp-20-1408


title: mnp-20-0269

value: Descriptive diagnosis

value: cerebellum


title: mnp-20-1513

value: CNS sarcoma


title: mnp-20-1592

value: FFPE tissue

value: Ganglioglioma

value: medulla oblongataial prefrontal cortex


title: mnp-20-0092


title: mnp-20-1392

value: male

value: temporal lobe


title: mnp-20-1092

value: cerebellum, fourth ventricle


title: mnp-20-0886


title: mnp-20-0949

value: supratentorial midline


title: mnp-20-1159

value: Medulloblastoma, SHH


title: mnp-20-1146


title: mnp-20-0149

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0379


title: mnp-20-1460


title: mnp-20-1431


title: mnp-20-0344

value: CNS tumor with BCOR internal tandem duplication


title: mnp-20-0659

value: Pilocytic Astrocytoma


title: mnp-20-0555

value: Non-neoplastic tissue

value: fourth ventricle


title: mnp-20-0368

value: Adamantinomatous craniopharyngioma

value: female

value: pituitary gland


title: mnp-20-1265

value: cerebellum, fourth ventricle, pons


title: mnp-20-0818

value: FFPE tissue

value: Anaplastic astrocytoma

value: cerebellum, brain stem


title: mnp-20-0691

value: male


title: mnp-20-1293

value: Descriptive diagnosis


title: mnp-20-0391

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0052

value: pons


title: mnp-20-0634

value: orbital frontal cortex


title: mnp-20-0661

value: Medulloblastoma, WNT

value: cerebellum, fourth ventricle


title: mnp-20-1349

value: Pilocytic Astrocytoma

value: supratentorial midline


title: mnp-20-0050

value: spinal cord


title: mnp-20-1368

value: Ependymoma, WHO grade III

value: female

value: cerebellum


title: mnp-20-0764

value: FFPE tissue


title: mnp-20-0245

value: Meningioma, WHO grade I


title: mnp-20-0084


title: mnp-20-1585


title: mnp-20-1525

value: Choroid plexus carcinoma

value: parietal lobe


title: mnp-20-0939

value: male

value: basal ganglia


title: mnp-20-1520

value: brain stem


title: mnp-20-0321

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0867

value: Descriptive diagnosis

value: hypothalamus, basal ganglia


title: mnp-20-0823

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-1352


title: mnp-20-0603

value: Anaplastic pilocytic astrocytoma

value: frontal lobe, temporal lobe


title: mnp-20-0504

value: Pilocytic Astrocytoma

value: female

value: cerebellum, fourth ventricle


title: mnp-20-1007

value: FFPE tissue

value: Rhabdoid tumor

value: spinal cord


title: mnp-20-1236

value: male

value: hypothalamus


title: mnp-20-0169

value: cerebellum


title: mnp-20-1001

value: Angiocentric neuroepithelial tumor (ANET)


title: mnp-20-0192

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-1002


title: mnp-20-0439

value: Non-Langerhans cell histiocytosis

value: temporal lobe


title: mnp-20-0175


title: mnp-20-1199

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0565

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0435

value: Meningioma, WHO grade I


title: mnp-20-1148

value: Ganglioglioma

value: inferior temporal cortex


title: mnp-20-1448

value: Descriptive diagnosis


title: mnp-20-0403

value: FFPE tissue

value: Atypical choroid plexus papilloma

value: fourth ventricle


title: mnp-20-1108

value: Pilocytic Astrocytoma

value: female


title: mnp-20-0934

value: temporal lobe, occipital lobe


title: mnp-20-0366

value: Non-neoplastic tissue

value: male


title: mnp-20-1266

value: Medulloblastoma, SHH

value: cerebellum


title: mnp-20-1469


title: mnp-20-1241

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-1194

value: Glioblastoma (GBM)


title: mnp-20-1494

value: hypothalamus


title: mnp-20-0114

value: orbital frontal cortex


title: mnp-20-0902

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-0958

value: FFPE tissue

value: medulla oblongata, pons


title: mnp-20-0360

value: fourth ventricle, cerebellum


title: mnp-20-0512

value: Pilocytic Astrocytoma

value: spinal cord


title: mnp-20-0398

value: fourth ventricle


title: mnp-20-0516

value: Ganglioglioma

value: female


title: mnp-20-1272

value: Anaplastic astrocytoma

value: male


title: mnp-20-1288

value: cerebellum


title: mnp-20-0609

value: Pilomyxoid astrocytoma (PMA)


title: mnp-20-0947


title: mnp-20-0837

value: Glioblastoma (GBM)

value: parietal lobe


title: mnp-20-1231

value: Germ cell tumor

value: pineal region


title: mnp-20-0350

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0668

value: FFPE tissue

value: CNS tumor with BCOR internal tandem duplication


title: mnp-20-1091

value: cerebellum, fourth ventricle


title: mnp-20-0819

value: Pilocytic Astrocytoma


title: mnp-20-0193

value: Adamantinomatous craniopharyngioma

value: hypothalamus


title: mnp-20-1521

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1507

value: fourth ventricle


title: mnp-20-0725

value: Atypical meningioma, WHO grade II

value: female

value: third ventricle


title: mnp-20-1500

value: Diffuse astrocytoma

value: male

value: frontal lobe


title: mnp-20-1395

value: Atypical choroid plexus papilloma

value: parietal lobe


title: mnp-20-0207

value: orbital frontal cortex


title: mnp-20-0133

value: FFPE tissue


title: mnp-20-0877

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: mnp-20-1590

value: Pleomorphic xanthoastrocytoma (PXA)

value: frontal lobe, temporal lobe


title: mnp-20-0848

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: temporal lobe


title: mnp-20-0613

value: Glioblastoma (GBM)


title: mnp-20-1113


title: mnp-20-0552

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-0914

value: Pineoblastoma


title: mnp-20-1057

value: Pilocytic Astrocytoma

value: female

value: cerebellum, fourth ventricle


title: mnp-20-0628

value: frontal lobe


title: mnp-20-0644

value: Anaplastic astrocytoma

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-1234

value: FFPE tissue

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: male


title: mnp-20-1560

value: cerebellum


title: mnp-20-0303

value: cerebellum, brain stem


title: mnp-20-0971

value: Papillary glioneuronal tumor (PGNT)


title: mnp-20-0210

value: Non-neoplastic tissue

value: pons


title: mnp-20-0279

value: CNS tumor with BCOR internal tandem duplication

value: parietal lobe, occipital lobe


title: mnp-20-0091

value: cerebellum, pons, medulla oblongata


title: mnp-20-0153

value: Glioblastoma, IDH-mutated


title: mnp-20-0881

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0188

value: Embryonal tumor with multilayered rosettes (ETMR)

value: parietal lobe


title: mnp-20-0940

value: Pineoblastoma

value: pineal region


title: mnp-20-1375

value: FFPE tissue

value: Pilocytic Astrocytoma

value: female

value: occipital lobe


title: mnp-20-1286

value: Ganglioglioma

value: inferior temporal cortex


title: mnp-20-0361

value: male

value: spinal cord


title: mnp-20-0036

value: frontal lobe


title: mnp-20-0587

value: cerebellum, fourth ventricle


title: mnp-20-1225

value: temporal lobe


title: mnp-20-0729

value: cerebellum


title: mnp-20-0832

value: frontal lobe, temporal lobe


title: mnp-20-1069


title: mnp-20-0568

value: Glioblastoma (GBM)


title: mnp-20-0657

value: Pleomorphic xanthoastrocytoma (PXA)

value: parietal lobe


title: mnp-20-0983

value: Diffuse midline glioma, H3 K27-mutated

value: medulla oblongata


title: mnp-20-0605

value: FFPE tissue

value: pons


title: mnp-20-0966

value: Atypical choroid plexus papilloma


title: mnp-20-0154

value: Medulloblastoma, non-WNT/SHH

value: female


title: mnp-20-1593

value: Pilocytic Astrocytoma

value: male


title: mnp-20-1006

value: cerebellum, fourth ventricle, pons


title: mnp-20-1289

value: Schwannoma

value: cerebellum, pons, fourth ventricle


title: mnp-20-1531

value: fourth ventricle


title: mnp-20-0075

value: Medulloblastoma, WNT

value: cerebellum, fourth ventricle


title: mnp-20-1523

value: cerebellum


title: mnp-20-0406

value: Meningioma, WHO grade I


title: mnp-20-0842

value: orbital frontal cortex


title: mnp-20-1205


title: mnp-20-0371

value: Glioblastoma, IDH-mutated

value: frontal lobe


title: mnp-20-1280

value: FFPE tissue


title: mnp-20-1050


title: mnp-20-0183


title: mnp-20-0302

value: CNS Neuroblastoma

value: frontal lobe, temporal lobe


title: mnp-20-1000

value: Descriptive diagnosis

value: female


title: mnp-20-0400

value: Pilocytic Astrocytoma

value: male

value: occipital lobe


title: mnp-20-0281

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1039

value: Atypical choroid plexus papilloma

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1424

value: pons


title: mnp-20-0602

value: Anaplastic astrocytoma

value: temporal lobe, basal ganglia


title: mnp-20-0422

value: medulla oblongata


title: mnp-20-1041

value: primary motor cortex


title: mnp-20-0319

value: fourth ventricle


title: mnp-20-1165

value: FFPE tissue


title: mnp-20-0111

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: fourth ventricle, cerebellum


title: mnp-20-0384

value: Anaplastic oligodendroglioma

value: orbital frontal cortex


title: mnp-20-1285


title: mnp-20-0098

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: female

value: ventrolateral prefrontal cortex


title: mnp-20-1197

value: Medulloblastoma, non-WNT/SHH

value: male

value: cerebellum, fourth ventricle


title: mnp-20-0748

value: Pilocytic Astrocytoma


title: mnp-20-0122

value: Glioblastoma (GBM)

value: parietal lobe


title: mnp-20-0370

value: Ganglioglioma

value: cerebellum


title: mnp-20-0790


title: mnp-20-1495


title: mnp-20-0255

value: fourth ventricle


title: mnp-20-1506

value: FFPE tissue

value: cerebellum, fourth ventricle, pons


title: mnp-20-0922


title: mnp-20-1008


title: mnp-20-0929


title: mnp-20-0667

value: Anaplastic astrocytoma, IDH-mutated

value: temporal lobe


title: mnp-20-1473


title: mnp-20-0986

value: Anaplastic astrocytoma

value: thalamus


title: mnp-20-1292

value: Medulloblastoma, SHH


title: mnp-20-0317

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0652

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-0346

value: male


title: mnp-20-0601

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: ventrolateral prefrontal cortex


title: mnp-20-1058

value: Anaplastic pilocytic astrocytoma


title: mnp-20-0692

value: Pleomorphic xanthoastrocytoma (PXA)


title: mnp-20-0049

value: Germinoma

value: third ventricle


title: mnp-20-0001

value: FFPE tissue

value: Adamantinomatous craniopharyngioma

value: female

value: hypothalamus


title: mnp-20-1212


title: mnp-20-1017

value: Medulloblastoma, WNT

value: cerebellum, fourth ventricle


title: mnp-20-0338

value: CNS Neuroblastoma

value: temporal lobe


title: mnp-20-0396

value: Glioblastoma (GBM)

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-1418

value: Pilocytic Astrocytoma

value: male


title: mnp-20-1331

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1399

value: Anaplastic astrocytoma, IDH-mutated

value: parietal lobe


title: mnp-20-1195

value: cerebellum, fourth ventricle, pons


title: mnp-20-0721


title: mnp-20-1112

value: Medulloblastoma, SHH


title: mnp-20-0533

value: FFPE tissue

value: Diffuse midline glioma, H3 K27-mutated


title: mnp-20-0640


title: mnp-20-1028

value: Ganglioglioma

value: female

value: pons


title: mnp-20-0454

value: cerebellum


title: mnp-20-0462

value: Hemangioblastoma

value: medulla oblongata


title: mnp-20-0664

value: pituitary gland


title: mnp-20-0642

value: Descriptive diagnosis

value: thalamus


title: mnp-20-1270

value: male


title: mnp-20-0780

value: thalamus, hippocampus


title: mnp-20-0152

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-0708

value: Pilocytic Astrocytoma


title: mnp-20-0455

value: Subependymal giant cell astrocytoma (SEGA)

value: parietal lobe


title: mnp-20-0118

value: FFPE tissue

value: fourth ventricle


title: mnp-20-0899

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0769

value: Adamantinomatous craniopharyngioma

value: hypothalamus


title: mnp-20-0404

value: Glioblastoma (GBM)

value: frontal lobe


title: mnp-20-0087

value: female


title: mnp-20-0930

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0355

value: Schwannoma


title: mnp-20-0658

value: male

value: cerebellum


title: mnp-20-0836

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-0872

value: Atypical teratoid/rhabdoid tumor (AT/RT)


title: mnp-20-1474

value: parietal lobe, occipital lobe


title: mnp-20-1045

value: FFPE tissue

value: Chordoma


title: mnp-20-0418

value: Meningioma, WHO grade I


title: mnp-20-0127

value: Choroid plexus papilloma

value: fourth ventricle


title: mnp-20-0150

value: Medulloblastoma, NOS


title: mnp-20-0272

value: occipital lobe


title: mnp-20-0542

value: Anaplastic astrocytoma

value: frontal lobe


title: mnp-20-1596

value: Descriptive diagnosis

value: supratentorial midline


title: mnp-20-1378

value: Pituitary adenoma

value: male

value: pituitary gland


title: mnp-20-0445

value: Rosette-forming glioneuronal tumor (RGNT)

value: cerebellum, fourth ventricle


title: mnp-20-1139

value: Ganglioglioma

value: orbital frontal cortex


title: mnp-20-1316

value: FFPE tissue

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-0010

value: Pineoblastoma

value: female

value: pineal region


title: mnp-20-0134

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0172

value: Pilocytic Astrocytoma

value: cerebellum


title: mnp-20-0728

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1154

value: Adamantinomatous craniopharyngioma

value: hypothalamus


title: mnp-20-1546

value: male


title: mnp-20-1435


title: mnp-20-0215

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1328

value: Papillary glioneuronal tumor (PGNT)


title: mnp-20-1345

value: Ganglioglioma


title: mnp-20-0447

value: cerebellum, fourth ventricle


title: mnp-20-1334

value: FFPE tissue

value: cerebellum, fourth ventricle, pons


title: mnp-20-0543


title: mnp-20-1376


title: mnp-20-0363

value: Medulloblastoma, WNT


title: mnp-20-0757

value: thalamus


title: mnp-20-0452

value: Anaplastic oligodendroglioma

value: female

value: temporal lobe


title: mnp-20-0622

value: Pilocytic Astrocytoma

value: pons


title: mnp-20-0233

value: Diffuse midline glioma, H3 K27-mutated


title: mnp-20-0551

value: Glioblastoma (GBM)

value: parietal lobe


title: mnp-20-1497

value: male


title: mnp-20-1341

value: cerebellum


title: mnp-20-0900


title: mnp-20-0564


title: mnp-20-1530

value: Pineal parenchymal tumor of intermediate differentiation (PPTID)

value: pineal region


title: mnp-20-1055

value: Medulloblastoma, SHH


title: mnp-20-0863

value: FFPE tissue

value: Oligodendroglioma, IDH-mutated

value: frontal lobe


title: mnp-20-0699

value: Descriptive diagnosis

value: occipital lobe


title: mnp-20-0631

value: Schwannoma

value: female

value: cerebellum, fourth ventricle, pons


title: mnp-20-0595

value: spinal cord


title: mnp-20-1048

value: cerebellum, fourth ventricle


title: mnp-20-1198

value: Ganglioglioma

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1167

value: Embryonal tumor with multilayered rosettes (ETMR)

value: male


title: mnp-20-1377


title: mnp-20-0259

value: Glioblastoma (GBM)


title: mnp-20-0655

value: Astroblastoma

value: temporal lobe


title: mnp-20-0890

value: FFPE tissue

value: Germinoma

value: hypothalamus


title: mnp-20-0265

value: Anaplastic astrocytoma

value: frontal lobe


title: mnp-20-0709

value: basal ganglia


title: mnp-20-0059

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1040


title: mnp-20-1123

value: Medulloblastoma, SHH


title: mnp-20-1487

value: female


title: mnp-20-1137

value: Pilocytic Astrocytoma


title: mnp-20-0416


title: mnp-20-0226


title: mnp-20-0575

value: Pineoblastoma

value: pineal region


title: mnp-20-0065

value: cerebellum, fourth ventricle


title: mnp-20-0734

value: Non-neoplastic tissue


title: mnp-20-1344


title: mnp-20-0951

value: male


title: mnp-20-0376


title: mnp-20-0121

value: brain stem, fourth ventricle


title: mnp-20-0759

value: cerebellum, fourth ventricle, pons


title: mnp-20-1356

value: FFPE tissue

value: cerebellum, third ventricle


title: mnp-20-0334

value: Atypical meningioma, WHO grade II

value: cerebellum, pons, fourth ventricle


title: mnp-20-1140

value: Glioblastoma (GBM)

value: temporal lobe, occipital lobe


title: mnp-20-1127

value: cerebellum


title: mnp-20-1428


title: mnp-20-0208

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1422

value: Ganglioglioma

value: female

value: primary somatosensory cortex


title: mnp-20-0331

value: Pilocytic Astrocytoma


title: mnp-20-0258

value: orbital frontal cortex


title: mnp-20-0538

value: Descriptive diagnosis

value: temporal lobe


title: mnp-20-1164

value: Medulloblastoma, NOS

value: male

value: fourth ventricle


title: mnp-20-0593

value: FFPE tissue

value: cerebellum, fourth ventricle


title: mnp-20-0852


title: mnp-20-1475


title: mnp-20-0332

value: Subependymal giant cell astrocytoma (SEGA)

value: parietal lobe


title: mnp-20-1340

value: cerebellum, third ventricle


title: mnp-20-0126

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: cerebellum


title: mnp-20-1269

value: Meningioma, WHO grade II

value: spinal cord


title: mnp-20-0288

value: Pleomorphic xanthoastrocytoma (PXA)

value: female


title: mnp-20-0874

value: Diffuse astrocytoma


title: mnp-20-1228

value: Pilocytic Astrocytoma

value: hypothalamus


title: mnp-20-1227

value: Glioblastoma (GBM)


title: mnp-20-1033

value: male


title: mnp-20-1111

value: Non-neoplastic tissue

value: temporal lobe


title: mnp-20-0766

value: FFPE tissue

value: Atypical meningioma, WHO grade II

value: third ventricle


title: mnp-20-0927

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-0377

value: Medulloblastoma, WNT

value: cerebellum, fourth ventricle, pons


title: mnp-20-1118

value: Atypical choroid plexus papilloma

value: parietal lobe


title: mnp-20-1143

value: female

value: orbital frontal cortex


title: mnp-20-0570

value: Rosette-forming glioneuronal tumor (RGNT)

value: pons


title: mnp-20-0327


title: mnp-20-1443

value: cerebellum


title: mnp-20-0720

value: Pilocytic Astrocytoma

value: male


title: mnp-20-1330

value: Paraganglioma

value: hypothalamus


title: mnp-20-1274

value: FFPE tissue

value: Ganglioglioma

value: occipital lobe


title: mnp-20-0517

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1541

value: cerebellum, fourth ventricle


title: mnp-20-0271

value: Medulloblastoma, SHH


title: mnp-20-0179

value: Diffuse midline glioma, H3 K27-mutated

value: spinal cord


title: mnp-20-1282

value: Anaplastic astrocytoma

value: frontal lobe, temporal lobe


title: mnp-20-1504

value: female


title: mnp-20-0799

value: Schwannoma


title: mnp-20-0792

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: fourth ventricle


title: mnp-20-0592

value: Pilocytic Astrocytoma

value: orbital frontal cortex


title: mnp-20-0536

value: male


title: mnp-20-0695

value: FFPE tissue

value: cerebellum


title: mnp-20-1501


title: mnp-20-0518


title: mnp-20-0176

value: Chordoma


title: mnp-20-0417


title: mnp-20-1021

value: Atypical choroid plexus papilloma

value: third ventricle


title: mnp-20-1483


title: mnp-20-1412

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-0072

value: Non-neoplastic tissue


title: mnp-20-0151

value: High-grade glioma, NOS

value: occipital lobe


title: mnp-20-0246

value: Anaplastic astrocytoma

value: female


title: mnp-20-0456

value: Anaplastic astrocytoma, IDH-mutated

value: temporal lobe, occipital lobe


title: mnp-20-0356

value: Glioblastoma (GBM)


title: mnp-20-0405

value: Pilocytic Astrocytoma


title: mnp-20-0023

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: male

value: hypothalamus


title: mnp-20-1550

value: FFPE tissue

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-1278

value: fourth ventricle


title: mnp-20-1304

value: Atypical meningioma, WHO grade II


title: mnp-20-0389

value: Ganglioglioma


title: mnp-20-0330

value: Diffuse midline glioma, H3 K27-mutated

value: spinal cord


title: mnp-20-1157

value: cerebellum, fourth ventricle


title: mnp-20-1162

value: pons


title: mnp-20-1097

value: Pleomorphic xanthoastrocytoma (PXA)

value: female

value: temporal lobe


title: mnp-20-1365

value: Medulloblastoma, WNT


title: mnp-20-0683

value: Pilocytic Astrocytoma

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1229

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: male


title: mnp-20-0576

value: FFPE tissue

value: medulla oblongata


title: mnp-20-1020

value: Embryonal tumor with multilayered rosettes (ETMR)

value: orbital frontal cortex


title: mnp-20-1509

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-0791

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-1381

value: cerebellum, fourth ventricle


title: mnp-20-0737

value: Atypical choroid plexus papilloma


title: mnp-20-0739


title: mnp-20-0906

value: Ganglioglioma

value: frontal lobe


title: mnp-20-0071

value: Choroid plexus papilloma

value: third ventricle


title: mnp-20-0916

value: female


title: mnp-20-0282

value: Pilocytic Astrocytoma


title: mnp-20-0638

value: cerebellum


title: mnp-20-1215


title: mnp-20-1141

value: male


title: mnp-20-0335

value: FFPE tissue

value: Germinoma


title: mnp-20-0797


title: mnp-20-1388

value: parietal lobe


title: mnp-20-0213


title: mnp-20-0722


title: mnp-20-0907


title: mnp-20-1096

value: Medulloblastoma, WNT


title: mnp-20-1556

value: spinal cord


title: mnp-20-0380

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0590

value: Glioblastoma (GBM)

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1104

value: cerebellum, fourth ventricle


title: mnp-20-1493


title: mnp-20-0948


title: mnp-20-1425

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0308

value: fourth ventricle


title: mnp-20-1456

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: hypothalamus


title: mnp-20-0022

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0028


title: mnp-20-0814

value: Pilocytic Astrocytoma


title: mnp-20-1172

value: female

value: cerebellum, fourth ventricle, pons


title: mnp-20-0548

value: FFPE tissue

value: Pleomorphic xanthoastrocytoma (PXA)

value: male


title: mnp-20-0238

value: cerebellum, brain stem


title: mnp-20-1547

value: spinal cord


title: mnp-20-1275

value: Glioblastoma (GBM)

value: medulla oblongata


title: mnp-20-0858

value: thalamus


title: mnp-20-0783

value: cerebellum


title: mnp-20-1168

value: fourth ventricle


title: mnp-20-0105

value: Descriptive diagnosis


title: mnp-20-0048

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1094


title: mnp-20-0466


title: mnp-20-1396

value: cerebellum, third ventricle


title: mnp-20-1347

value: cerebellum, fourth ventricle


title: mnp-20-0835

value: Pilocytic Astrocytoma

value: basal ganglia


title: mnp-20-0660


title: mnp-20-0651

value: Pineocytoma

value: female

value: brain stem, cerebellum


title: mnp-20-1220

value: FFPE tissue

value: Non-neoplastic tissue

value: male

value: inferior temporal cortex


title: mnp-20-0110

value: Adamantinomatous craniopharyngioma

value: pituitary gland


title: mnp-20-0089

value: Medulloblastoma, SHH

value: cerebellum


title: mnp-20-0502

value: spinal cord


title: mnp-20-0892

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0081

value: Diffuse astrocytoma


title: mnp-20-0434

value: Pleomorphic xanthoastrocytoma (PXA)

value: parietal lobe


title: mnp-20-0845

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0009

value: Pilocytic Astrocytoma

value: orbital frontal cortex


title: mnp-20-0095

value: supratentorial midline


title: mnp-20-0135

value: FFPE tissue

value: female

value: cerebellum, fourth ventricle, pons


title: mnp-20-1213

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0130

value: male

value: hypothalamus


title: mnp-20-0066

value: fourth ventricle


title: mnp-20-0328

value: cerebellum


title: mnp-20-1297

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle


title: mnp-20-0686

value: Descriptive diagnosis


title: mnp-20-0937

value: Meningioma, WHO grade I

value: occipital lobe


title: mnp-20-1299

value: temporal lobe, occipital lobe


title: mnp-20-1407


title: mnp-20-0453

value: Medulloblastoma, WNT


title: mnp-20-1420

value: Pilocytic Astrocytoma


title: mnp-20-0719

value: FFPE tissue

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0976

value: female


title: mnp-20-0742


title: mnp-20-0960


title: mnp-20-1311

value: Anaplastic astrocytoma, IDH-mutated

value: frontal lobe


title: mnp-20-0608

value: Glioblastoma (GBM)

value: male

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0701

value: Ganglioglioma


title: mnp-20-0273

value: cerebellum


title: mnp-20-0209

value: Langerhans cell histiocytosis (LCH)

value: temporal lobe


title: mnp-20-0005

value: fourth ventricle


title: mnp-20-0140


title: mnp-20-0715

value: cerebellum, fourth ventricle, pons


title: mnp-20-0423

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-0752

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle


title: mnp-20-0224

value: FFPE tissue

value: Pilocytic Astrocytoma


title: mnp-20-0950

value: Anaplastic pilocytic astrocytoma

value: thalamus


title: mnp-20-0266

value: Oligodendroglioma, IDH-mutated

value: female


title: mnp-20-0413

value: male


title: mnp-20-1489

value: Diffuse midline glioma, H3 K27-mutated


title: mnp-20-0817

value: Glioblastoma (GBM)

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0671

value: Medulloblastoma, non-WNT/SHH

value: cerebellum


title: mnp-20-1142


title: mnp-20-1332


title: mnp-20-0020


title: mnp-20-1390


title: mnp-20-0197


title: mnp-20-0682


title: mnp-20-1366

value: hypothalamus


title: mnp-20-0397

value: Pilomyxoid astrocytoma (PMA)

value: basal ganglia


title: mnp-20-1070

value: Atypical choroid plexus papilloma

value: third ventricle


title: mnp-20-0444

value: FFPE tissue

value: cerebellum, fourth ventricle, medulla oblongata


title: mnp-20-1544

value: Embryonal tumor with multilayered rosettes (ETMR)

value: fourth ventricle, brain stem


title: mnp-20-0117

value: pons


title: mnp-20-0147

value: Ependymoma, WHO grade III

value: cerebellum, third ventricle


title: mnp-20-1554

value: Ganglioglioma

value: male

value: temporal lobe


title: mnp-20-0537

value: Non-neoplastic tissue

value: female

value: pituitary gland


title: mnp-20-1314

value: Pilocytic Astrocytoma

value: thalamus


title: mnp-20-1151

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle


title: mnp-20-1088

value: FFPE tissue

value: Diffuse midline glioma, H3 K27-mutated


title: mnp-20-1457


title: mnp-20-1218

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: parietal lobe, occipital lobe


title: mnp-20-1062

value: Glioblastoma (GBM)

value: occipital lobe


title: mnp-20-1276

value: Atypical choroid plexus papilloma

value: third ventricle


title: mnp-20-1371

value: Medulloblastoma, non-WNT/SHH

value: male


title: mnp-20-1208


title: mnp-20-0251

value: cerebellum


title: mnp-20-0815

value: Meningioma, WHO grade I

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-1130

value: Ganglioglioma

value: temporal lobe


title: mnp-20-1369

value: fourth ventricle


title: mnp-20-0353

value: Pilocytic Astrocytoma

value: cerebellum, fourth ventricle


title: mnp-20-0256

value: FFPE tissue

value: Anaplastic astrocytoma

value: female

value: thalamus


title: mnp-20-0684


title: mnp-20-0653


title: mnp-20-0755

value: Glioblastoma, IDH-mutated

value: frontal lobe


title: mnp-20-0505

value: Choroid plexus papilloma


title: mnp-20-0290


title: mnp-20-0805

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1535

value: Glioblastoma (GBM)

value: male

value: parietal lobe


title: mnp-20-0969

value: cerebellum


title: mnp-20-1387

value: Rosette-forming glioneuronal tumor (RGNT)

value: occipital lobe


title: mnp-20-1518

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-0055

value: Embryonal tumor with multilayered rosettes (ETMR)

value: inferior temporal cortex, brain stem


title: mnp-20-1051

value: FFPE tissue

value: Diffuse astrocytoma

value: temporal lobe


title: mnp-20-0510

value: Pilocytic Astrocytoma

value: female

value: pons


title: mnp-20-0626

value: parietal lobe, occipital lobe


title: mnp-20-1037

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-0809

value: male

value: fourth ventricle, cerebellum


title: mnp-20-0931


title: mnp-20-0513


title: mnp-20-0365

value: CNS Neuroblastoma

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0557

value: Descriptive diagnosis

value: temporal lobe, occipital lobe


title: mnp-20-0878

value: Pleomorphic xanthoastrocytoma (PXA)

value: occipital lobe


title: mnp-20-0252

value: FFPE tissue

value: Non-neoplastic tissue

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0428

value: Ganglioglioma

value: frontal lobe


title: mnp-20-1093

value: temporal lobe


title: mnp-20-1187

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-0700

value: Pilocytic Astrocytoma

value: pons


title: mnp-20-1138

value: Ependymoma, WHO grade III

value: female

value: parietal lobe


title: mnp-20-0975

value: Adamantinomatous craniopharyngioma

value: male

value: pituitary gland


title: mnp-20-1450

value: Descriptive diagnosis

value: parietal lobe, occipital lobe


title: mnp-20-1389

value: FFPE tissue

value: CNS Ewing family tumor


title: mnp-20-0583

value: cerebellum


title: mnp-20-0577

value: Anaplastic astrocytoma


title: mnp-20-1329


title: mnp-20-0314

value: Low-grade astrocytoma, NOS

value: parietal lobe, hippocampus


title: mnp-20-1394

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle


title: mnp-20-0286

value: Subependymal giant cell astrocytoma (SEGA)


title: mnp-20-1568


title: mnp-20-0760

value: Pilocytic Astrocytoma


title: mnp-20-0189

value: hypothalamus


title: mnp-20-0166

value: Glioblastoma (GBM)


title: mnp-20-0912

value: female

value: cerebellum, third ventricle, brain stem


title: mnp-20-0527

value: Anaplastic pilocytic astrocytoma

value: male

value: medulla oblongataial prefrontal cortex


title: mnp-20-0662

value: FFPE tissue


title: mnp-20-1254

value: Ganglioglioma

value: orbital frontal cortex


title: mnp-20-1268

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: mnp-20-0041

value: thalamus


title: mnp-20-0032


title: mnp-20-0962

value: Medulloblastoma, SHH

value: cerebellum


title: mnp-20-1312

value: Ependymoma, WHO grade III

value: brain stem


title: mnp-20-0866

value: cerebellum, fourth ventricle


title: mnp-20-0572

value: CNS Neuroblastoma


title: mnp-20-0145

value: female


title: mnp-20-0942

value: Adamantinomatous craniopharyngioma

value: pituitary gland


title: mnp-20-0880

value: temporal lobe


title: mnp-20-1415

value: Germinoma

value: male

value: pineal region


title: mnp-20-1147

value: FFPE tissue

value: Schwannoma

value: parietal lobe


title: mnp-20-1528

value: Atypical meningioma, WHO grade II

value: frontal lobe


title: mnp-20-0492

value: Choroid plexus papilloma


title: mnp-20-0146

value: Pilocytic Astrocytoma

value: cerebellum


title: mnp-20-1414

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0211


title: mnp-20-0139

value: cerebellum, fourth ventricle


title: mnp-20-0486

value: Atypical choroid plexus papilloma

value: female


title: mnp-20-0895

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1374

value: Glioblastoma (GBM)


title: mnp-20-1065


title: mnp-20-0600

value: CNS sarcoma


title: mnp-20-0283

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: male

value: thalamus, basal ganglia


title: mnp-20-1383

value: FFPE tissue

value: Rosette-forming glioneuronal tumor (RGNT)


title: mnp-20-1279

value: cerebellum, fourth ventricle, pons


title: mnp-20-0710


title: mnp-20-1458

value: Ganglioglioma

value: temporal lobe


title: mnp-20-0385

value: Pilocytic Astrocytoma

value: orbital frontal cortex


title: mnp-20-0829

value: occipital lobe


title: mnp-20-1309


title: mnp-20-1072

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: primary somatosensory cortex


title: mnp-20-0784

value: female


title: mnp-20-0999

value: Diffuse midline glioma, H3 K27-mutated

value: frontal lobe, temporal lobe


title: mnp-20-0539

value: Medulloblastoma, WNT

value: fourth ventricle


title: mnp-20-0589


title: mnp-20-0232

value: Anaplastic pilocytic astrocytoma

value: supratentorial midline


title: mnp-20-0162

value: FFPE tissue

value: medulla oblongata


title: mnp-20-1321

value: male


title: mnp-20-0136

value: cerebellum


title: mnp-20-1277

value: Anaplastic astrocytoma

value: parietal lobe


title: mnp-20-0278

value: thalamus


title: mnp-20-0992

value: Pilocytic Astrocytoma


title: mnp-20-0515

value: Glioblastoma (GBM)

value: spinal cord


title: mnp-20-0559

value: female


title: mnp-20-1582

value: Descriptive diagnosis


title: mnp-20-1075


title: mnp-20-0484


title: mnp-20-0184

value: Medulloblastoma, SHH


title: mnp-20-0612

value: brain stem, cerebellum


title: mnp-20-1601

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0621

value: Medulloblastoma, WNT

value: cerebellum, fourth ventricle


title: mnp-20-1317

value: FFPE tissue

value: frontal lobe


title: mnp-20-0429

value: Ganglioglioma


title: mnp-20-0306

value: Medulloblastoma, non-WNT/SHH

value: male


title: mnp-20-1463


title: mnp-20-1044


title: mnp-20-0008


title: mnp-20-0762

value: Choroid plexus papilloma

value: parietal lobe


title: mnp-20-0610

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0995

value: Diffuse midline glioma, H3 K27-mutated

value: pineal region


title: mnp-20-0298

value: female

value: occipital lobe


title: mnp-20-1128

value: Non-neoplastic tissue

value: hypothalamus


title: mnp-20-0125

value: Dysembryoplastic neuroepithelial tumor (DNET)


title: mnp-20-0068

value: Medulloblastoma, WNT

value: fourth ventricle


title: mnp-20-0525

value: FFPE tissue

value: Pilocytic Astrocytoma

value: cerebellum


title: mnp-20-0676

value: Anaplastic astrocytoma

value: thalamus


title: mnp-20-1256

value: male

value: spinal cord


title: mnp-20-1402

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0714

value: cerebellum, fourth ventricle


title: mnp-20-0788

value: Medulloblastoma, SHH


title: mnp-20-1076


title: mnp-20-0908

value: Glioblastoma (GBM)

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-1533

value: female

value: temporal lobe


title: mnp-20-0284

value: cerebellum, fourth ventricle, pons


title: mnp-20-0463


title: mnp-20-0534


title: mnp-20-1010

value: Atypical teratoid/rhabdoid tumor (AT/RT)


title: mnp-20-0011

value: hypothalamus


title: mnp-20-1320

value: FFPE tissue


title: mnp-20-1510


title: mnp-20-0830

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: mnp-20-0262

value: Pilocytic Astrocytoma

value: cerebellum


title: mnp-20-0928

value: male

value: fourth ventricle


title: mnp-20-0203

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-1439

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0412

value: Schwannoma


title: mnp-20-0745

value: Glioblastoma (GBM)


title: mnp-20-1430

value: brain stem


title: mnp-20-0678

value: cerebellum, fourth ventricle


title: mnp-20-1337

value: female


title: mnp-20-1529

value: Rosette-forming glioneuronal tumor (RGNT)


title: mnp-20-0276

value: Cribriform neuroepithelial tumor (CRINET)


title: mnp-20-0801

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-0611

value: FFPE tissue


title: mnp-20-1464


title: mnp-20-1129


title: mnp-20-0141

value: basal ganglia


title: mnp-20-0724

value: Ganglioglioma

value: spinal cord


title: mnp-20-0395

value: CNS sarcoma

value: parietal lobe, occipital lobe


title: mnp-20-0833

value: Pilocytic Astrocytoma

value: male


title: mnp-20-1027

value: cerebellum


title: mnp-20-0749

value: temporal lobe


title: mnp-20-0573

value: Glioblastoma (GBM)

value: orbital frontal cortex


title: mnp-20-0488


title: mnp-20-1110

value: medulla oblongata


title: mnp-20-0822

value: Schwannoma


title: mnp-20-0706


title: mnp-20-1496

value: Anaplastic astrocytoma

value: female


title: mnp-20-0672


title: mnp-20-0411

value: Germinoma

value: hypothalamus, thalamus


title: mnp-20-0369

value: FFPE tissue

value: Pineoblastoma

value: pineal region


title: mnp-20-0956

value: thalamus, hippocampus


title: mnp-20-0173

value: Ganglioglioma

value: frontal lobe


title: mnp-20-0243

value: Pilocytic Astrocytoma

value: male

value: third ventricle


title: mnp-20-1455

value: Glioblastoma (GBM)

value: frontal lobe, temporal lobe


title: mnp-20-1156

value: temporal lobe


title: mnp-20-0182

value: Low-grade astrocytoma, NOS

value: cerebellum, fourth ventricle


title: mnp-20-0747

value: inferior temporal cortex


title: mnp-20-1163

value: Atypical meningioma, WHO grade II

value: female

value: spinal cord


title: mnp-20-1436

value: FFPE tissue

value: fourth ventricle


title: mnp-20-0988


title: mnp-20-0694

value: cerebellum


title: mnp-20-1087

value: Anaplastic astrocytoma

value: thalamus, basal ganglia


title: mnp-20-0687

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0825

value: Ganglioglioma

value: male

value: brain stem


title: mnp-20-0723

value: Glioblastoma (GBM)

value: primary somatosensory cortex


title: mnp-20-1514


title: mnp-20-0985

value: Pilocytic Astrocytoma


title: mnp-20-1498

value: cerebellum, fourth ventricle


title: mnp-20-0348


title: mnp-20-1580

value: Low-grade astrocytoma, NOS

value: cerebellum, brain stem


title: mnp-20-1182

value: CNS sarcoma

value: primary somatosensory cortex, primary motor cortex, inferior parietal cortex, primary auditory cortex, posterior (caudal) superior temporal cortex


title: mnp-20-1190

value: FFPE tissue

value: frontal lobe


title: mnp-20-0046

value: Adamantinomatous craniopharyngioma

value: hypothalamus, third ventricle


title: mnp-20-0096

value: female

value: third ventricle


title: mnp-20-0438

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0180

value: fourth ventricle, cerebellum


title: mnp-20-0909


title: mnp-20-1173


title: mnp-20-1171

value: Schwannoma


title: mnp-20-0441


title: mnp-20-1066

value: spinal cord


title: mnp-20-1343

value: supratentorial midline


title: mnp-20-0856

value: Extraventricular neurocytoma

value: male

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0824

value: Anaplastic astrocytoma, IDH-mutated


title: mnp-20-1461

value: Pilocytic Astrocytoma

value: temporal lobe


title: mnp-20-0473

value: FFPE tissue

value: Anaplastic ganglioglioma


title: mnp-20-1570

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle


title: mnp-20-1519

value: Pineoblastoma

value: pineal region


title: mnp-20-0056

value: Medulloblastoma, SHH

value: female

value: cerebellum, fourth ventricle, pons


title: mnp-20-0221

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: parietal lobe


title: mnp-20-0102


title: mnp-20-1068

value: fourth ventricle


title: mnp-20-0156

value: Germinoma

value: male


title: mnp-20-1258

value: Low-grade astrocytoma, NOS


title: mnp-20-1364

value: Pilocytic Astrocytoma

value: supratentorial midline


title: mnp-20-1327

value: FFPE tissue

value: medulla oblongata


title: mnp-20-0223

value: inferior temporal cortex


title: mnp-20-1119

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: mnp-20-0620

value: Pleomorphic xanthoastrocytoma (PXA)

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0034

value: Medulloblastoma, non-WNT/SHH

value: cerebellum


title: mnp-20-0347

value: CNS Ewing family tumor

value: female

value: temporal lobe


title: mnp-20-0773

value: parietal lobe


title: mnp-20-1538

value: Medulloblastoma, SHH

value: male

value: cerebellum, fourth ventricle, pons


title: mnp-20-0062

value: CNS Ewing family tumor, CIC-altered

value: frontal lobe


title: mnp-20-1183

value: FFPE tissue

value: Ganglioglioma


title: mnp-20-0864

value: Descriptive diagnosis


title: mnp-20-0554

value: Pilocytic Astrocytoma

value: basal ganglia, thalamus


title: mnp-20-1348


title: mnp-20-1426

value: Germinoma

value: hypothalamus


title: mnp-20-0981

value: Schwannoma

value: spinal cord


title: mnp-20-0614

value: Polymorphous low-grade neuroepithelial tumor of the young (PLNTY)


title: mnp-20-1174

value: female


title: mnp-20-0993


title: mnp-20-0648

value: Glioblastoma (GBM)

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0443

value: Medulloblastoma, non-WNT/SHH

value: male

value: fourth ventricle


title: mnp-20-0743

value: cerebellum, fourth ventricle, pons


title: mnp-20-1537

value: FFPE tissue

value: pons


title: mnp-20-1410

value: cerebellum


title: mnp-20-0158

value: temporal lobe


title: mnp-20-0257

value: Pilocytic Astrocytoma

value: basal ganglia, thalamus, hypothalamus


title: mnp-20-1517

value: Medulloblastoma, SHH

value: cerebellum, fourth ventricle


title: mnp-20-1063

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0732

value: Germ cell tumor

value: frontal lobe


title: mnp-20-1442

value: Pineoblastoma

value: female

value: pineal region


title: mnp-20-0786

value: Medulloblastoma, non-WNT/SHH

value: male


title: mnp-20-0069

value: Diffuse midline glioma, H3 K27-mutated


title: mnp-20-0148

value: FFPE tissue

value: Medulloblastoma, WNT

value: fourth ventricle


title: mnp-20-1019

value: Ganglioglioma

value: cerebellum, fourth ventricle, pons


title: mnp-20-1480


title: mnp-20-0650

value: Dysembryoplastic neuroepithelial tumor (DNET)


title: mnp-20-0249

value: Pilocytic Astrocytoma


title: mnp-20-0165

value: Atypical choroid plexus papilloma

value: third ventricle


title: mnp-20-0414

value: temporal lobe, basal ganglia


title: mnp-20-0751

value: inferior temporal cortex


title: mnp-20-1222

value: cerebellum, fourth ventricle


title: mnp-20-1449

value: female

value: cerebellum


title: mnp-20-0074

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0490

value: male

value: cerebellum, brain stem


title: mnp-20-1393

value: FFPE tissue

value: Pineoblastoma

value: pineal region


title: mnp-20-1071

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-0393

value: cerebellum, pons, fourth ventricle


title: mnp-20-1014

value: Anaplastic astrocytoma

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-1131

value: spinal cord


title: mnp-20-0229

value: Ganglioglioma

value: pons, thalamus


title: mnp-20-0607

value: Pilocytic Astrocytoma

value: pons


title: mnp-20-1485

value: Descriptive diagnosis

value: female


title: mnp-20-0685

value: Medulloblastoma, SHH

value: male

value: cerebellum


title: mnp-20-1499

value: FFPE tissue

value: thalamus


title: mnp-20-1470

value: Ependymoma, WHO grade II

value: fourth ventricle


title: mnp-20-0124

value: Diffuse astrocytoma

value: supratentorial midline


title: mnp-20-0964

value: orbital frontal cortex


title: mnp-20-0656

value: Diffuse midline glioma, H3 K27-mutated

value: brain stem


title: mnp-20-1106

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: mnp-20-0333

value: Pilocytic Astrocytoma

value: occipital lobe


title: mnp-20-0143

value: Medulloblastoma, non-WNT/SHH


title: mnp-20-0362

value: Glioblastoma (GBM)

value: female

value: cerebellum, fourth ventricle


title: mnp-20-1082

value: Atypical choroid plexus papilloma

value: male

value: parietal lobe


title: mnp-20-1566

value: FFPE tissue

value: Descriptive diagnosis


title: mnp-20-1084

value: Medulloblastoma, WNT

value: fourth ventricle


title: mnp-20-0267


title: mnp-20-1385

value: Anaplastic astrocytoma

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-0506

value: cerebellum


title: mnp-20-0730


title: mnp-20-1542

value: temporal lobe


title: mnp-20-0581

value: Pilocytic Astrocytoma


title: mnp-20-0450


title: mnp-20-0670


title: mnp-20-0851


title: mnp-20-0483

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-1595

value: Malignant melanoma

value: occipital lobe


title: mnp-20-0980

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: female

value: frontal lobe


title: mnp-20-1221

value: male


title: SP1380 rofA mutant strain replikate 3

city: Parkville

first: Magnus

middle: Ganer

last: Jespersen

state: Victoria

address: 792 Elizabeth street

country: Australia

institute: The University of Melbourne

description: Bulk RNA-seq from SP1380 rofA mutant strain replikate 3

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against SP1448 (CP060267) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. Mutant stains compared to SP1448 wild-type
Assembly: CP060267
Supplementary files format and content: SP1448_count_file.tsv - Read counts in features for reads aligned to SP1448 reference
Supplementary files format and content: SP1448_WT_v_rofA.tsv - Differential gene expression between SP1448 rofA compared to SP1448 wild-type
Supplementary files format and content: SP1448_WT_v_ssrA.tsv - Differential gene expression between SP1448 ssRA compared to SP1448 wild-type

organism: Streptococcus pyogenes

source_name: Bacterial culture

growth_protocol: Bacteria were statically grown to late-logarithmic growth phase in Todd Hewitt broth supplemented with 1% yeast extract (THY) at 37˚C

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to late-logarithmic growth phase in THY. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions with an additional mechanical lysis step using Lysing Matrix B tubes (MP Biomedicals) on the FastPrep-2 5G bead beating grinder and lysis system (MP Biomedicals). To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNAseq analysis was performed at the Australian Centre for Ecogenomics (University of Queensland, Brisbane, Australia). cDNA libraries were prepared from total RNA using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Plus rRNA Depletion kit (Illumina). Sequencing of the cDNA libraries was performed on the NovaSeq 6000 System (Illumina) on a 2x150 bp SP flowcell run generating an average of 20 million reads per sample.

treatment_protocol: No treatment

value: Bacterial culture

value: SP1390 rofA

value: Bulk

tag: growth phase

value: Late logarithmic


title: SP1380 ssRA mutant strain replikate 3

description: Bulk RNA-seq from SP1380 ssRA mutant strain replikate 3

value: SP1390 ssRA


title: mnp-20-0254

value: FFPE tissue

value: occipital lobe, parietal lobe, frontal lobe, temporal lobe


title: SP1380 rofA mutant strain replikate 2

description: Bulk RNA-seq from SP1380 rofA mutant strain replikate 2


title: mnp-20-0639

value: cerebellum, fourth ventricle, pons


title: mnp-20-0970

value: Malignant peripheral nerve sheath tumor (MPNST)


title: SP1380 ssRA mutant strain replikate 1

description: Bulk RNA-seq from SP1380 ssRA mutant strain replikate 1


title: MCF-7_1

city: Kaunas

first: Monika

last: Pankevičiūtė-Bukauskienė

address: Sukilėlių pr. 15

department: Institute of Cardiology

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Raw data of the paired reads in fastq file format was then aligned on a genome sequence (the complete list of human transcripts obtained from Ensembl BioMart) using Bowtie2
Generated SAM files were analized by customized python scripts based on the HTSeq library. The expression of each gene was calculated in reads per kilobase per million reads (RPKM).
Student’s T-test was used to identify upregulated and downregulated genes comparing each cell line separately and values were corrected for multiple testing
Assembly: Reference sequence used for the alignment: the complete list of human transcripts from Ensembl BioMart
Supplementary files format and content: tab-delimited text files with ENSEMBL gene ID's, false discovery rates, corrections for multiple testing and differences between the average as well as volcano plots

source_name: Epithelial cell line from breast adenocarcinoma

growth_protocol: MCF-7 and BCC cells were cultured in Dulbecco's Modified Eagle Medium: Ham's F-12 (1:1; DMEM/F-12) medium, supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin (P/S). MCF-10A were cultured in DMEM/F-12 medium that was supplemented with 5% horse serum (hyclone), P/S, 10 µg/ml of human recombinant insulin, 100 ng/ml of cholera toxin, 20 ng/ml of recombinant human epidermal growth factor and 500 ng/ml of hydrocortisone. Cells were maintained at 37 °C in a humidified incubator with 5% CO2

extract_protocol:
The samples were sent to Zymo Research for Next-Gen RNA sequencing. The samples were prepared for shipment with DNA/RNA ShieldTM (Zymo Research, USA) by mixing 1 million cells with 500 µl of Shield stabilization solution.To remove rRNA, a method described by Bogdanova et al. (2011) was followed with some modifications.
RNA-Seq libraries were constructed from 500 ng of total RNA by using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research, USA) according to the manufacturer’s instructions. RNA sequencing was done on an Illumina NovaSeq (Illumina, USA) to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.

treatment_protocol: untreated

tag: background strain

tag: genotype

value: wild-type

tag: treatment

value: untreated


title: BCC_2

source_name: Primary breast cancer cell line

value: BCC


title: mnp-20-0287

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: BCC_1


title: SP1380 wild-type strain replikate 2

description: Bulk RNA-seq from SP1380 wild-type strain replikate 2

tag: cell line


title: SP1380 wild-type strain replikate 1

description: Bulk RNA-seq from SP1380 wild-type strain replikate 1

tag: cell type


title: MCF-7_3


title: MCF-10A_1

source_name: epithelial cell line from breast tissue


title: bulk RNA SP1380 rofA mutations replicate 3

description: Bulk RNA-seq from SP1380 rofA mutant strain

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against SP1380 (CP060269) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. SP1380 mutants compared invididually to SP1380 WT
Assembly: CP060269
Supplementary files format and content: SP1380_count_file.tsv - Tab seperated file - Count of SP1380 wildtype and mutants against SP1380 reference genome
Supplementary files format and content: SP1380_WT_v_ssrA.tsv - Tab seperated file - Differential gene expression results comparing SP1380 wild-type to ssRA mutant
Supplementary files format and content: SP1380_WT_v_rofA.tsv - Tab seperated file - Differential gene expression results comparing SP1380 wild-type to rofA mutant

value: SP1380 rofA


title: MCF-7_2


title: BCC_3


title: SP1380 rofA mutant strain replikate 1

description: Bulk RNA-seq from SP1380 rofA mutant strain replikate 1


title: SP1380 ssRA mutant strain replikate 2

description: Bulk RNA-seq from SP1380 ssRA mutant strain replikate 2


title: MCF-10A_2


title: MCF-10A_3


title: Patient104_Sample2

city: New York

first: Angelica

last: Galianese

state: New York

address: 615 W 164th Street, Apt 21C

institute: Columbia University

description: COUNTS_TABLE_RAW7: P104_S2

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples

source_name: nasopharyngeal samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: Patient104_Sample1

description: COUNTS_TABLE_RAW7: P104_S1


title: bulk RNA SP1380 ssRA mutant replicate 3

description: Bulk RNA-seq from SP1380 ssRA mutant strain

value: SP1380 ssRA


title: Patient104_Sample4

description: COUNTS_TABLE_RAW7: P104_S4


title: Patient103_Sample2

description: COUNTS_TABLE_RAW13: P103_S2


title: Patient104_Sample3

description: COUNTS_TABLE_RAW7: P104_S3


title: bulk RNA SP1380 wild-type replicate 3

description: Bulk RNA-seq from SP1380 wild type strain

value: Bacterial culture


title: bulk RNA SP1380 wild-type replicate 1


title: Bulk RNA-seq from 5448 with ssRA leader mutation grown in THY rep2

description: Bulk RNA-seq from late-logarithmic phase from 5448 with ssRA mutation in leader matching m1uk

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against 5448 (GCF_001021955.1) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. 5448 ssRA mutant compared to 5448 wild-type
Assembly: GCF_001021955.1
Supplementary files format and content: 5448_count_file.tsv - Tab seperated file - read counts against features of 5448 reference genome
Supplementary files format and content: 5448_WT_v_ssrA.tsv - Tab seperated file - differential gene expression between the mutant and wild type of 5448


title: Bulk RNA-seq from 5448 with ssRA leader mutation grown in THY rep1


title: Patient102_Sample1

description: COUNTS_TABLE_RAW13: P102_S1


title: Bulk RNA-seq from 5448 with ssRA leader mutation grown in THY rep3


title: Bulk RNA-seq from wild type 5448 grown in THY rep2

description: Bulk RNA-seq from late-logarithmic phase from wild type 5448 S. pyogenes


title: Patient101_Sample4

description: COUNTS_TABLE_RAW10: P101_S4


title: Patient104_Sample5

description: COUNTS_TABLE_RAW7: P104_S5


title: Patient103_Sample6

description: COUNTS_TABLE_RAW13: P103_S6


title: Bulk RNA-seq from wild type 5448 grown in THY rep1


title: Patient101_Sample2

description: COUNTS_TABLE_RAW10: P101_S2


title: bulk RNA SP1380 ssRA mutant replicate 1


title: SP1380 wild-type strain replikate 3

description: Bulk RNA-seq from SP1380 wild-type strain replikate 3


title: Patient103_Sample5

description: COUNTS_TABLE_RAW13: P103_S5


title: M1global HKU488 in THY broth bulk RNA-seq 2

description: Bulk RNA-seq from late-logarithmic phase from emm1 S. pyogenes M1global

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against 5448 (GCF_001021955.1) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. Isolates compared to WT 5448
Assembly: GCF_001021955.1
Supplementary files format and content: M1uk_raw_read_counts.tsv - count file for m1uk and m1global files aligned to 5448 reference genome
Supplementary files format and content: HKU488_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of HKU488 compared to 5448
Supplementary files format and content: SP1380_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1380 compared to 5448
Supplementary files format and content: SP1384_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1384 compared to 5448
Supplementary files format and content: SP1426_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1426 compared to 5448
Supplementary files format and content: SP1448_v_5448_DGE.tsv - Tab seperated file - Differential gene expression of SP1448compared to 5448


title: bulk RNA SP1380 rofA mutations replicate 1


title: Patient100_Sample8

description: COUNTS_TABLE_RAW13: P100_S8


title: Patient103_Sample1

description: COUNTS_TABLE_RAW13: P103_S1


title: bulk RNA SP1380 rofA mutations replicate 2


title: Patient101_Sample6

description: COUNTS_TABLE_RAW10: P101_S6


title: Patient100_Sample6

description: COUNTS_TABLE_RAW13: P100_S6


title: bulk RNA SP1380 wild-type replicate 2


title: M1global 5448 in THY broth bulk RNA-seq 3


title: Patient103_Sample3

description: COUNTS_TABLE_RAW13: P103_S3


title: Patient101_Sample5

description: COUNTS_TABLE_RAW10: P101_S5


title: HJ7JJBGXH_1#146360_CAGATC

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

organism: Equus caballus

source_name: chondrocytes

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Cat. 217004).
RealSeq Biofluids Plasma/Serum miRNA Library Kit

tag: biofluid

value: Plasma

tag: breed

value: Cob

tag: age

tag: Sex

value: Male

tag: disease state

value: Moderate-severe OA

value: chondrocytes


title: HJ7JJBGXH_1#146361_ACTTGA

value: Cross breed horse


title: M1uk SP1448 in THY broth bulk RNA-seq 3

description: Bulk RNA-seq from late-logarithmic phase from emm1 S. pyogenes M1uk

value: Bulk

value: Late logarithmic


title: bulk RNA SP1380 ssRA mutant replicate 2


title: HJ7JJBGXH_1#146359_GCCAAT

value: Icelandic pony

value: 7y 8m

value: Female


title: HJ7JJBGXH_1#146358_ACAGTG

value: Welsh pony


title: HJ7JJBGXH_1#146357_TGACCA

value: Irish Draught


title: Patient100_Sample2

description: COUNTS_TABLE_RAW13: P100_S2


title: M1global 5448 in THY broth bulk RNA-seq 2


title: Patient100_Sample3

description: COUNTS_TABLE_RAW13: P100_S3


title: M1uk SP1448 in THY broth bulk RNA-seq 2


title: Patient102_Sample2

description: COUNTS_TABLE_RAW13: P102_S2


title: M1uk SP1448 in THY broth bulk RNA-seq 1


title: Patient103_Sample4

description: COUNTS_TABLE_RAW13: P103_S4


title: M1global SP1426 in THY broth bulk RNA-seq 3


title: HJ7JJBGXH_1#146365_CTTGTA

value: Synovial fluid

value: Connemara cross


title: HJ7JJBGXH_1#146381_CCAACA

value: Sports Horse


title: M1global SP1426 in THY broth bulk RNA-seq 2

value: Bacterial culture


title: Patient99_Sample15

description: COUNTS_TABLE_RAW13: P99_S15

value: nasopharyngeal samples


title: M1global HKU488 in THY broth bulk RNA-seq 3


title: Patient101_Sample3

description: COUNTS_TABLE_RAW10: P101_S3


title: Patient101_Sample1

description: COUNTS_TABLE_RAW10: P101_S1


title: M1global SP1426 in THY broth bulk RNA-seq 1


title: HJ7JJBGXH_1#146356_TTAGGC

value: Plasma

value: Dutch warmblood

value: 5y 2m

value: Mild OA


title: HJ7JJBGXH_1#146380_CATTTT

value: Cob cross

value: Male

value: Moderate-severe OA

value: chondrocytes


title: HJ7JJBGXH_1#146364_GGCTAC


title: M1uk SP1384 in THY broth bulk RNA-seq 3

value: Bulk

value: Late logarithmic


title: HJ7JJBGXH_1#146376_CACGAT

value: Cob


title: Patient99_Sample12

description: COUNTS_TABLE_RAW13: P99_S12


title: Patient100_Sample5

description: COUNTS_TABLE_RAW13: P100_S5


title: HJ7JJBGXH_1#146354_ATCACG

value: Highland pony

value: Female


title: M1global HKU488 in THY broth bulk RNA-seq 1


title: HJ7JJBGXH_1#146369_CCGTCC

value: Synovial fluid

value: Irish sports horse


title: M1uk SP1384 in THY broth bulk RNA-seq 1

value: Bacterial culture


title: Patient99_Sample10

description: COUNTS_TABLE_RAW13: P99_S10

value: nasopharyngeal samples


title: Patient100_Sample7

description: COUNTS_TABLE_RAW13: P100_S7


title: Patient99_Sample13

description: COUNTS_TABLE_RAW13: P99_S13


title: M1global 5448 in THY broth bulk RNA-seq 1


title: HJ7JJBGXH_1#146362_GATCAG

value: Plasma


title: HJ7JJBGXH_1#146363_TAGCTT

value: Sports Horse


title: HJ7JJBGXH_1#146366_AGTCAA

value: Cross breed pony


title: HJ7JJBGXH_1#146355_CGATGT

value: Warmblood cross

value: Mild OA


title: Patient99_Sample14

description: COUNTS_TABLE_RAW13: P99_S14


title: M1uk SP1380 in THY broth bulk RNA-seq 2


title: HJ7JJBGXH_1#146371_ATGAGC


title: M1uk SP1380 in THY broth bulk RNA-seq 1


title: HJ7JJBGXH_1#146379_CATGGC

value: Cross breed horse

value: Male


title: HJ7JJBGXH_1#146370_ACTGAT

value: chondrocytes


title: Patient100_Sample4

description: COUNTS_TABLE_RAW13: P100_S4


title: HJ7JJBGXH_1#146378_CAGGCG

value: Cob cross

value: Moderate-severe OA


title: MCF10A_STAG1_Control3_ChIP-seq

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

library_source: genomic

data_processing:
Alignment of reads to the reference human genome (hg19) was performed using ‘Bowtie2′ (version 2.4.2) under default settings
Duplicates were removed using GATK4 (version 4.1.9.0)
peak calling was carried out using MACS2 (version 2.2.7.1) after setting the q value (FDR) to 0.05 and using the ‘–extsize’ argument with the values obtained in the ‘macs2 predictd’ step
Assembly: hg19
Supplementary files format and content: bigwig

source_name: breast

growth_protocol: MCF10A cells are grown AT 37ºC at 5% CO2 in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol:
Cells were fixed for 15 min in 1% formaldehyde and after quenchig and lysis, sonication with performed in Covaris instrument. Around 50 micrograms of antibody was added to immunoprecipitate chromatin from 10 million cells. 5% mouse ES cell chromatin was added for calibration.
At least 5 ng of DNA were processed through subsequent enzymatic treatments with "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" from New England BioLabs (ref. E7805). Briefly, a short fragmentation of 10 min was followed by end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8-12 cycles). Resulting average fragment size is 300 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on Illumina NextSeq 500 (with v2.5 reagent kits) following manufacturer's recommendations.

treatment_protocol: MCF10A cells were transfected with 50 nM siRNAs using DharmaFECT reagent 1 and Gibco Opti-MEM I Reduced Serum Media and harvested 72h later.

value: breast

value: epithelial

tag: chip antibody

value: STAG1, custom made

value: mock transfection


title: HJ7JJBGXH_1#146368_ATGTCA

value: Synovial fluid

value: Irish Draught


title: HJ7JJBGXH_1#146374_CAACTA

value: Welsh pony

value: Female


title: HJ7JJBGXH_1#146375_CACCGG

value: Icelandic pony

value: 7y 8m


title: MCF10A_Input_CTCF-KD2_ChIP-seq

value: CTCF siRNA


title: Tg(mitfa:dgat1a) Rep3

city: Manchester

first: Adam

last: Hurlstone

address: Michael Smith Building

institute: University of Manchester

data_processing:
Adapters were trimmed from raw sequencing reads using Trimmomatics v0.32
Trimmed reads were aligned to the zebrafish genome (Ensembl, GRCz11) using STAR v2.5.3
Reads that mapped to chromosomes 1-25 were retained
Gene counts were determined using featureCounts v1.6.2 and differential expression analysis was performed using DESeq2 v1.14.1, using a adjusted p-value cut off of <0.05
DESeq2 was used to generate log2 normalised variance stabilising transformed (VST) counts
Genome_build: Ensembl, GRCz11
Supplementary_files_format_and_content: fpm_DGAT1_RNAseq_GEO
Supplementary_files_format_and_content: GFP_DGAT1_allresults_GEO
Supplementary_files_format_and_content: VST_DGAT1_RNAseq_GEO

organism: Danio rerio

source_name: Tumour

growth_protocol: Age matched tumours were harvested at 10-12 weeks

extract_protocol:
Tumours were removed and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: tp53m214K/m214k; mitfa-/-; nras G12D

value: Melanoma


title: Tg(mitfa:dgat1a) Rep5

tag: tissue


title: Patient100_Sample1

description: COUNTS_TABLE_RAW13: P100_S1

value: nasopharyngeal samples


title: M1uk SP1384 in THY broth bulk RNA-seq 2

value: Bacterial culture

value: Bulk

tag: growth phase

value: Late logarithmic


title: Tg(mitfa:dgat1a) Rep2


title: HJ7JJBGXH_1#146377_CACTCA

value: Thoroughbred

value: Moderate-severe OA

value: chondrocytes