title: MADM wildtype; small clones; mouse #5 [19153_SmallClones]

description: Nextera XT DNA Library Preparation


title: Patient 11 ROI 03 DSP11_03_Stroma

status: Public on Aug 06 2022

type: RNA

city: Lausanne

first: François

last: Kuonen

address: Av. de Beaumont 29

country: Switzerland

institute: CHUV

hyb_protocol: Immunoflourecent tissue profiling was performed using PanCK (488) cytokeratin, and Syto13 for DNA staining to enable selection of 48 regions of interest (ROIs), divided into 48 tumor (panCK-positive) and 47 stromal (panCK-negative) areas of interest (AOIs) for targeted spatial transcriptomics using the commercial Nanostring GeoMx.

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing: Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences. Unique i5 and i7 sample indexes were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol. Pooled libraries were paired-sequenced at 2 × 27 base pairs and with unique dual indexes workflow on an Illumina HiSeq 4000 instrument. HiSeq-derived FASTQ files for each sample were compiled for each compartment using the bcl2fastq program of Illumina, and then demultiplexed and converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline. DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.2.0.111 (Nanostring). A minimum of 10,000 reads were required for each sample. Probes were checked for outlier status by implementing a global Grubb’s outlier test with alpha set to 0.01. The counts for all remaining probes for a given target were then collapsed into a single metric by taking the geometric mean of probe counts. For each sample, an RNA-probe-pool-specific negative probe normalization factor was generated on the basis of the geometric mean of negative probes in each pool. To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.

label: NanoString

molecule: total RNA

organism: Homo sapiens

source_name: Basal cell carcinoma

label_protocol: The spatial transcriptomic panel included 1812 genes targeted cancer transcriptome atlas panel to encompass a comprehensive detection of tumor-host interactions.

growth_protocol: FFPE blocks

extract_protocol: For GeoMx DSP sample collections, entire slides were imaged at 20X magnification and morphologic markers were used to select ROI using organic shapes. Automatic segmentation of ROI based on panCKpos markers were used to define AOIs, allowing to separate tumor cells (panCKpos) from adjacent stromal cells (panCKneg). A total of 95 AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 μl of DEPC-treated water.

treatment_protocol: For slide preparation, we followed the GeoMx DSP slide preparation user manual (MAN-10087-04). In brief, FFPE tissue section of 5-µm were mounted on positively charged histology slides by grouping 3 patients per slide. Sections were incubated at 65 °C for 1 hour. Slides were deparaffinized in 3 xylene baths of 5 min, then rehydrated in ethanol gradient: 2 baths of 5 min in 100% EtOH, followed by 5 min in 95% EtOH. Slides were then washed with PBS 1X. Antigen retrieval was performed in Tris-EDTA pH 9.0 at 100°C for 15 min at low pressure. Slides were first dived into hot water for 10 seconds, and then into Tris-EDTA buffer. Cooker vent stayed open during the procedure to ensure low pressure. Slides were then washed in PBS 1X, incubated in proteinase K in PBS (1ug/ml) for 15 min at 37°C and washed again with PBS 1X. Tissues were post-fixed in 10% neutral-buffered formalin (NBF) for 5 min, washed twice for 5 min in NBF stop buffer (0.1M Tris Base, 0.1M Glycine) and finally once in PBS 1X. The RNA probe mix (CTA (https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-cancer-transcriptome-atlas/), a pool of in situ hybridization probes with UV photocleavable oligonucleotide barcodes) was placed on each section and covered with HybriSlip Hybridization Covers. Slides were then incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced Cell Diagnostics). The day after, HybriSlip covers were gently removed and 25-min stringent washes were performed twice in 50% formamide and 2X Saline Sodium Citrate (SSC) at 37 °C. Tissues were washed for 5 min in 2X SSC, then blocked in Buffer W (Nanostring Technologies) for 30 min at room temperature in a humidity chamber. Next, tissues were stained with panCK-532 (clone AE1+AE3) (Novus, NBP2-33200) at 1:20 and SYTO 13 at 1:10 (Thermo Scientific S7575) in Buffer W for 1 h at room temperature. Slides were washed twice in fresh 2X SSC then loaded on the GeoMx Digital Spatial Profiler (DSP).

tag: tumor type

value: Basal cell carcinoma

tag: histology

value: Infiltrative

tag: compartment

value: Stroma


title: Patient 10 ROI 01 DSP10_01_Stroma


title: Patient 10 ROI 02 DSP10_02_Stroma


title: Patient 10 ROI 02 DSP10_02_CK

value: Tumor


title: MADM wildtype; large clones; mouse #5 [19153_LargeClones]

type: SRA

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

country: USA

institute: University of Virginia

description: Nextera XT DNA Library Preparation

library_source: transcriptomic

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the mouse (GRCm38.95) transcriptome using RSEM. RSEM options  --bowtie2 --single-cell-prior (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Assembly: GRCm38.95
Supplementary files format and content: .csv file contains the RSEM estimated abundances for each gene per sample

molecule: polyA RNA

organism: Mus musculus

source_name: Fallopian tube

extract_protocol:
Laser-guided microdissection followed by proteinase K digestion and poly(A) amplification
Nextera XT DNA Library Preparation Kit

tag: tissue

value: Fallopian tube

tag: cell type

value: Distal region

tag: genotype

value: MADM RG;GR alleles, mixed background

tag: treatment


title: ntCZC,Nalcn-het, rep2

city: Cambridge

first: Amir

last: Jassim

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw RNA reads were processed with cellranger using mm10 from 10X as the reference genome to create filtered gene expression matrices. Cell barcodes detected by cellranger were used as input to CITESeq for hashtagged sequence data (solid organs) generating a counts matrix with cell barcodes and hashtag oligo sequences per cell.
The HTODemux function from Seurat was then used to identify clusters and classify cells according to their barcodes including negative and doublet cells.
Quality control metrics were generated using Scater followed by single cell object conversion to Seurat objects, merging of objects and then analyses run using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ZSG+ sorted peripheral blood

extract_protocol:
Single-cell RNA-seq libraries were prepared using Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Chip B Kit and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev A; 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells.
RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications (for most of the samples 12 cycles was used for cDNA amplification, 16 for samples with very low cell concentration).

value: non-tumour circulating zsgreen+ cells

value: ZSG+ sorted peripheral blood

tag: strain

tag: age

value: 551 days

tag: Sex

value: male


title: MADM wildtype; small clones; mouse #4 [19152_SmallClones]

description: Nextera XT DNA Library Preparation


title: Patient 11 ROI 04 DSP11_04_Stroma


title: Spinal cord injury, 3 days, replicate 1

city: Nanchang

first: Jian

last: Cao

state: Jiangxi

address: 1 Minde Road, East Laker District, Nanchang, Jiangxi, China

department: orthopaedics

country: China

institute: The Second Affiliated Hospital of Nanchang University

description: Gene expression after treatment with a modified Allen’s weight-drop apparatus spinal cord tissue

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0   pmol Cy3/μg cRNA) was fragmented at 60°C for 30   minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking   agent following the manufacturers' instructions. On   completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the   fragmentation mixture and hybridized to Agilent   Human Gene Expression（8*60K）for 17 hours at 65°C   in a rotating Agilent hybridization oven. After   hybridization, microarrays were washed 1 minute at   room temperature with GE Wash Buffer 1 (Agilent)   and 1 minute with 37°C GE Wash buffer 2 (Agilent),   then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on   the Agilent DNA Microarray Scanner (G2505C) using   one color scan setting for 4x180k array slides (Scan   Area 61x21.6 mm, Scan resolution 3um, Dye channel   is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature   Extraction Software 10.7.1.1 (Agilent) using default   parameters to obtain background subtracted and   spatially detrended Processed Signal intensities as   the raw data. Raw data were normalized in quantile   algorithm with Genespring 13.0(Agilent). Probe that   at least 1 out of 2 samples flagged as Detected were   maintained.

organism: Rattus norvegicus

source_name: Spinal cord tissue, treated with a modified Allen’s weight-drop apparatus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Studies were conducted using adult SPF male Sprague-Dawley rats (male, 200-240g) that had been housed under standard conditions (23-25°C, 12 h light/dark cycle) for at least one week before experimental use with free access to food and water.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561 ) following the manufacturer's instructions.

treatment_protocol: Rats were intraperitoneally (i.p.) injected with 10% chloral hydrate and randomized into sham and SCI groups (n=3/group). Following anesthetization, a T10 level laminectomy was conducted to facilitate spinal cord exposure without disrupting the dura mater. SCI modeling at the T10 level was then conducted with a modified Allen’s weight-drop apparatus (10 g × 80 mm; MEYUE, Changsha, China). Sham rats underwent the same laminectomy procedure without subsequent damage to the spinal cord. Manual voiding of the bladder was conducted thrice daily for all rats until spontaneous voiding activity had recovered. On the third day after spinal cord injury, spinal cord tissue removed from the rat was immediately stored in liquid nitrogen for microarray analysis.

value: Spinal cord tissue

tag: gender

value: Sprague-Dawley

tag: stress

value: SCI


title: Patient 10 ROI 01 DSP10_01_CK


title: Patient 12 ROI 11 DSP12_11_Stroma


title: Control, replicate 2

description: Gene expression after treatment with laminectomy procedure spinal cord tissue

source_name: Spinal cord tissue, treated with laminectomy procedure

value: control


title: Spinal cord injury, 3 days, replicate 3


title: ntCZC,Nalcn-het, rep1

description: 10x Genomics

value: 610 days


title: MADM wildtype; large clones; mouse #4 [19152_LargeClones]

description: Nextera XT DNA Library Preparation


title: Control, replicate 1


title: diaphragm metastatsis,Nalcn-het, rep1

description: 10x Genomics

source_name: diaphragm metastasis of intestinal adenocarcinoma

value: sorted ZSG+ tumour cells

value: 278 days


title: ntCZC,Nalcn-het, rep4

description: 10x Genomics


title: Patient 12 ROI 12 DSP12_12_CK

value: Basal cell carcinoma

value: Infiltrative


title: Control, replicate 3


title: Spinal cord injury, 3 days, replicate 2


title: Patient 12 ROI 11 DSP12_11_CK

value: Tumor


title: MADM wildtype; small clones; mouse #3 [19151_SmallClones]

description: Nextera XT DNA Library Preparation

value: Fallopian tube


title: ein2-1-3

city: Daejeon

first: Hyo-Jun

last: Lee

address: Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Seedlings were submerged for 1 hour and then leaf explants were incubated on CIM
Small RNA

data_processing:
Sequencing adapters were removed using the Cutadapt and low quality bases were trimmed using the DynamicTrim.
High quality reads were filtered to obtain miRNA reads, whose length was within 15-30 bases.
miR-PREFeR software was used for mapping and prediction of secondary structure of the miRNA-genome alignment.
CAP-miRSeq was used for differential expression of miRNAs.
psRNATarget was used for prediction of miRNA target genes.
Assembly: TAIR10
Supplementary files format and content: An excel file containing read counts, differentially expressed miRNAs, and their putative target genes.

organism: Arabidopsis thaliana

source_name: Uppler half of the leaf explants

growth_protocol: Seedlings were grown on MS-agar plates for 14 days under long-day conditions at light intensity of 100 mmol m-2 s-1

extract_protocol:
Total RNA including small RNA was extracted using miRNeasy kits (Qiagen, Cat.No. 217084)
Library construction was performed according to the protocol of Seeders, an RNA-sequencing company in South Korea

treatment_protocol: Seedlings were submerged for 1 hour and then leaf explants were incubated on CIM for 7 days.

value: Uppler half of the leaf explants

tag: developmental stage

value: 14-day-old seedlings.


title: small intestine tumour, Nalcn-het,rep3

description: 10x Genomics

source_name: small intestine tumour

value: small intestine tumour


title: MADM wildtype; large clones; mouse #3 [19151_LargeClones]

description: Nextera XT DNA Library Preparation

value: Distal region

value: MADM RG;GR alleles, mixed background


title: ein2-1-2


title: gastric tumour, Nalcn-wt, rep 1

description: 10x Genomics

source_name: gastric tumour

value: gastric tumour

value: 582 days

value: female


title: hashtagged tissue samples, Nalcn-het,rep 1

description: 10x Genomics

source_name: epididymis, kidney, liver, lung, stomach

value: mixed cell types

value: 551 days

value: male


title: ein2-1-1


title: small intestine tumour, Nalcn-wt, rep1

description: 10x Genomics

value: sorted ZSG+ tumour cells

value: 641 days


title: Patient 12 ROI 10 DSP12_10_Stroma

value: Basal cell carcinoma

value: Stroma


title: Patient 12 ROI 10 DSP12_10_CK

value: Infiltrative

value: Tumor


title: MADM wildtype; small clones; mouse #2 [18999_SmallClones]

description: Nextera XT DNA Library Preparation

value: Fallopian tube


title: Col-0-3

value: Uppler half of the leaf explants

value: 14-day-old seedlings.


title: MADM wildtype; large clones; mouse #2 [18999_LargeClones]

description: Nextera XT DNA Library Preparation

value: Distal region


title: Patient 12 ROI 09 DSP12_09_CK


title: Patient 12 ROI 09 DSP12_09_Stroma


title: Col-0-2


title: hashtagged tissue samples, Nalcn-wt, rep 2

description: 10x Genomics

value: epididymis, kidney, liver, lung, stomach

value: 571 days


title: Col-0-1


title: hashtagged tissue samples, Nalcn-wt, rep 1

description: 10x Genomics


title: MADM wildtype; large clones; mouse #1 [18996_LargeClones]

description: Nextera XT DNA Library Preparation

value: MADM RG;GR alleles, mixed background


title: Patient 12 ROI 08 DSP12_08_Stroma


title: ntCZC,Nalcn-wt, rep1

description: 10x Genomics

value: non-tumour circulating zsgreen+ cells

value: ZSG+ sorted peripheral blood


title: Patient 12 ROI 08 DSP12_08_CK


title: PDX1 10x Genomics Visium

status: Public on Aug 05 2022

city: New York

first: Dalia

last: Barkley

state: NY

address: 435 E 30th st

department: Institute for Computational Medicine

institute: NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop scRNA-Seq method were processed using a custom-built pipeline, available online (https:__github.com_flo-compbio_singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the 10x Genomics Visium method were processed using the SpaceRanger pipeline.
Raw sequencing data obtained from the 10x Gene Expression method were processed using the CellRanger pipeline.
Assembly: hg38, mm10
Supplementary files format and content: for inDrop single-cell RNA-Seq data: genes as rows and cells as columns. For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.

organism:
Homo sapiens
Mus musculus

source_name: Spatial transcriptomics of melanoma patient-derived xenograft

growth_protocol: For mouse pancreatic adenocarcinoma, Rag1-_- and WT C57BL_6 mice were obtained from Jackson Laboratories (Bar Harbor, ME). The KrasG12D;Tp53R172H;Pdx1Cre (KPC) derived cell line FC1242 was utilized for orthotopic injection of 100,000 cells into the tail of pancreata of 8-12 week old C57BL_6 or Rag mice. To model liver and peritoneal metastases, mice received FC1242 via splenic (1,000,000 cells) and intraperitoneal (100,000 cells) injection, respectively. Tumors were harvested 2-3 weeks after injection.

extract_protocol:
For inDrop single-cell RNA-Seq of patient tumor samples, cell suspension was generated from minced tumor tissue using human tumor dissociation kit (Miltenyi) prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For 10x Genomics spatial transcriptomics of patient tumor samples, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation for 12 minutes. For 10x Genomics single-cell RNA-Seq of mouse tumors, cell suspension was generated from minced tumor tissue using the mouse tumor dissociation kit (Miltenyi) enzymes D and R prior to droplet encapsulation and individual barcoding of cells using the 10x Genomics platform.
For inDrop single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England BiolaBS). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For 10x Genomics spatial transcriptomic and single-cell RNA-Seq library construction, we followed the manufacturer's instructions.

tag: cancer type

value: Melanoma

tag: organ

value: Xenograft

tag: method

value: 10x Genomics Visium


title: PDX 10x scRNA-seq

source_name: Single-cell RNA-Seq of melanoma patient-derived xenograft

value: 10x scRNA


title: FA11-1

city: New York City

first: Timothy

middle: A

last: Blenkinsop

address: 1 Gustave L Levy Place

department: Ophthalmology Cell Development and Regenerative Biology, Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

description: countmatrix.txt:  e5e0d003-6c2a-4988-8f56-4cf868b9662a

data_processing:
Raw data from the RNA-seq experiment were processed with a pipeline based on the ENCODE “Long RNA-seq” pipeline. Filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR  version 2.5.2b) allowing for soft clipping of adapter sequences. Quantification of transcript levels was performed using RSEM (RSEM version 1.3.0) and featureCount (featureCount version 1.5.1), with annotation from Ensembl95. Quality controls were implemented using FastQC (FastQC version 0.11.5), picardmetrics (picardmetrics version 0.2.4), and dupRadar (dupRadar version 1.0.0) at the respective steps.
Assembly: hg38/GRCh38
Supplementary files format and content: tab-delimited text file contains counts for all samples

source_name: iPSC-RPE

extract_protocol:
Human RPE cells were lysed in 350uL of RLT+ buffer containing 1% ß-Mercaptoethanol. Total RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA Universal Kit (80224)
Total RNA input of 200ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. The index PCR was performed with 12 cycles, while the final library was eluted in 30µL. mRNA libraries were then quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek).

tag: cell line

value: iPSC-RPE

value: Female

tag: donor id_mf

tag: death to_enucleation_minutes

value: #N/A

tag: rpe teer

tag: rpe morphology_grade

tag: replicate

value: GC

value: GG

value: CC

value: CT

value: TT

value: GT


title: RPE89

description: countmatrix.txt:  25fb871a-210f-405f-bbc4-40767e605c9d

source_name: ahRPE

tag: cell type

value: ahRPE

value: AG


title: ARPE-19-3

description: countmatrix.txt:  ad84f428-8a9f-44a5-8861-87324e8fa9b3

value: immortalized RPE

value: Male

value: CG


title: ARPE-19-2

description: countmatrix.txt:  5687676f-9852-4dd0-a3ae-6664603f3d11


title: FA10-3

description: countmatrix.txt:  9e991d09-ab3f-46a2-af36-9e2822659c61


title: ARPE-19-1

description: countmatrix.txt:  dab1a758-aaea-4afa-bc27-f39b5a522a22


title: FA11-2

description: countmatrix.txt:  9dac004b-0942-456d-901e-7e93692f6093


title: FA11-3

description: countmatrix.txt:  651e7e46-79d3-43f0-a799-b61fbb01c393


title: RPE87

description: countmatrix.txt:  6be7a86c-a05a-44ba-84bb-9012bfd38dfe


title: RPE85

description: countmatrix.txt:  afed789b-4ada-4256-ad3b-5e772502bd8d


title: FA10-2

description: countmatrix.txt:  ae1cab41-651d-4bba-bbff-2e4210540a7e


title: MADM wildtype; small clones; mouse #1 [18996_SmallClones]

description: Nextera XT DNA Library Preparation

tag: tissue

value: Fallopian tube

value: Distal region

tag: genotype

value: MADM RG;GR alleles, mixed background

tag: treatment


title: RPE81

description: countmatrix.txt:  8b34869d-8698-41d9-8c30-feba262afea7

tag: age


title: RPE80

description: countmatrix.txt:  4da4cc14-7dbe-429e-9a44-060748972d93

tag: gender

value: AA


title: FA10-1

description: countmatrix.txt:  0c1d479e-f721-4a47-a131-a57557f3ab92

value: iPSC-RPE


title: RPE77

description: countmatrix.txt:  dafaba5a-c9e8-46cc-bc33-f2d112adb6f9


title: RPE72

description: countmatrix.txt:  6acde992-68ce-4fea-8539-e6af826f4614

value: Female


title: RPE38

description: countmatrix.txt:  680e39d4-f8b6-4d6e-aaf5-6e67bbf03139


title: RPE41

description: countmatrix.txt:  83d2a7d8-f908-49e2-9ef6-d3002ac6a093


title: PDX2 10x Genomics Visium

value: Melanoma

value: Xenograft

value: 10x Genomics Visium


title: RPE37

description: countmatrix.txt:  9b4d403d-e86d-4ed2-81ce-3ea84dbcef5d

value: GC

value: GG

value: CC

value: CT


title: RPE9

description: countmatrix.txt:  a4ddd3e9-4312-41f1-b8f3-2218419aaf31

value: ahRPE

value: AG

value: TT


title: RPE8

description: countmatrix.txt:  f017b496-da49-4120-bcee-7334ab944a2f

value: Male

value: GT


title: RPE24

description: countmatrix.txt:  25cfcd2d-79b3-444c-aa95-b094ad88012b


title: RPE28

description: countmatrix.txt:  8c660c8e-96f1-4a51-8606-0d1ecbd50b27

value: #N/A


title: RPE5

description: countmatrix.txt:  afca03c8-ef32-4a1d-b3df-a82472a53250

value: CG


title: RPE3

description: countmatrix.txt:  82280b02-a049-4362-819d-4bb8f1e336e6


title: RPE2

description: countmatrix.txt:  f49572e7-5f23-4b8b-9040-7b65f01e336d


title: RPE1

description: countmatrix.txt:  9031ffe4-d26a-4042-9074-1fd854221be8

value: AA


title: human_MDM_HiC_TET2ASO_HiC3

city: La Jolla

first: Isidoro

last: Cobo

state: CA

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

library_source: genomic

data_processing:
FASTQ sequencing files were mapped to the mm10 or hg38 reference genomes for mouse samples or human samples, respectively using STAR with default parameters. Biological and technical replicates were used in all experiments. Quantification of transcripts was performed analyzeRepeats.pl (HOMER) with parameters -condenseGenes -count exons - noadj. Principal Component Analysis (PCA) was obtained based on the Transcripts Per kilobase Million (TPM) on all genes of all samples. Expression value for each transcript was calculated using the analyzeRepeats.pl tool of HOMER with the following parameters - condenseGenes -count exons -tpm. Differential expression analysis was calculated using getDiffExpression.pl tool of HOMER using default parameters (FDR <0.05 and log2fold change > 1 or < -1)). For the experiment shown in Figure 5A, Log2 fold change was calculated for CM DNMT3A ASO or CM TET2 ASO as compared to CM Scramble ASO for each individual and the average for the 4 samples was calculated. Pathway analyses were performed using the Molecular Signature Database of GSEA (Subramanian et al., 2005),(Mootha et al., 2003).
ChIP-Seq analysis as described somewhere else (Seidman et al., 2020). Briefly, peaks for replicates with corresponding input experiments were obtained using HOMER with the parameters –L 0 –C 0 –fdr 0.9 –minDist 200 –size 200. Only peaks with IDR < 0.05 were used for Downstream analysis (Li et al., 2011). The pooled tag directories from all replicates were used for visualization. HOMER mergePeaks to identify overlapping peaks and peaks were marked as DNMT3A unique, DNMT3A and TET2 co-binding, and TET2 unique groups. HOMER annotatePeaks.pl tool was used to count the number of DNMT3A or TET2 tags in DNMT3ATET2 co-bound peaks.
In silico promoter analysis of differentially expressed genes was performed using the findMotifs.pl tool of Homer searching for motifs of length 8 and 10 and from -2000 to +500 bp relative to the TSS, using 4 threads.

molecule: genomic DNA

source_name: Monocyte-derived macrophages

growth_protocol: Monocytes were incubated with RPMI 1640 (Sigma Aldrich, # 10-040) medium containing 10% de-complemented FBS (OmegaScientific, #FB-02), 1mM Sodium Pyruvate (Gibco  Thermofisher), Penicillin-Streptomycin (15140122, 1000U/ml) and 25ng/ml-50ng/ml of recombinant human M-CSF (StemCell #78057-2) for six days at 37oC and 5% CO2. Fresh media was added 48h and four days after seeding.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB) and treated with DNase I on column. 500 ng-1 μg of RNA solution was enriched in poly-A tailed RNA by incubation with Oligo d(T) Magnetic Beads (NEB, #S1419S).
Single cell RNA-Seq:For normal mDM, mDM from three healthy donors were washed twice with PBS, pelleted, and resuspended in PBS containing 0.04% BSA. Single cells were linked to beads using the 10X Chromium system (10X Genomics). Single-cell sequencing libraries were prepared following manufacturer ́s instructions using v3 chemistry. The demultiplexed fastq files produced by cellranger mkfastq were processed by cellranger count (10X genomics) using the human genome reference ‘refdata-cellranger-GRCh38-3.0.0’. For each sample, the filtered_feature_bc_matrix output from cellranger count was analyzed by the Seurat R package (Stuart et al, 2019), by adapting the code from the Guided Clustering Tutorial (https://satijalab.org/seurat/archive/v3.1/pbmc3k_tutorial.html). Single cell RNA-Seq data from atherosclerotic macrophages was provided by KHMP and is available in (Depuydt et al., 2020). The single cell expression data were filtered to include only the genes of interest: DNMT3A, TET2 and genes identified in the REACTOME Interferon alpha and beta signalling gene set. As surrogate of reduced DNMT3A or TET2, we compared cells in the top and bottom quartile of DNMT3A or TET2 levels for mDM or top two quartiles versus bottom two quartiles for macrophages isolated from the atherosclerotic plaque, for the expression of genes in the Reactome Interferon alpha and beta signalling gene set.
RNA-Seq library preparation: It was performed as described elsewhere (Gosselin et al., 2017); (Seidman et al., 2020)]. Briefly, mDM were lysed in TRIzol (ThermoFisher, #15596026). RNA and DNase treatment was carried out using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB). 500ng-1 μg total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94oC in 2X Superscript III first- strand buffer containing 10mM DTT (Invitrogen, #P2325). The 10 μl of fragmented RNA was added to 0.5 μl of Random primers (Invitrogen, #48190011), 0.5 μl of Oligo d(T) primer (Invitrogen, #18418020), 0.5 μl of SUPERase inhibitor (Ambion, #AM2696), 1 μl of 10mM dNTPs and incubated at 50oC for three minutes. Then, 5.8 μl of water, 1 μl of 10mM DTT, 0.1 μl of 2 μg/μl Actinomycin D (Sigma, #A1410), 0.2 μl of 1% Tween-20 (Sigma) and 0.5 μl of SuperScript III (Invitrogen, #ThermoFisher 18080044) was added to the mix. Reverse- transcription (RT) reaction was performed at 25oC for 10 min followed by 50oC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and eluted in 10 μl in 0.01% Tween-20. The RNA-cDNA complex was then added to 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5U/μl RNAseH (Enzymatics, #Y9220L), 1 μl of 10U/μl DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween-20 and 1.05 μl of nuclease free water; and incubated at 16oC for 2.5h or overnight. The resulting dsDNA product was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Healthcare, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration, washed twice with 80% etOH, air dry and eluted in 40 μl of 0.05% Tween-20. The purified 40 μl of dsDNA was end-repaired by blunting followed by A-tailing and adapter ligation as described elsewhere (Heinz et al., 2010) using BIOO Barcodes (BIOO Scientific, #514104), IDT TruSeq Unique Dual Indexes or Kapa Unique Dual-Indexed Adapters using 15 μl Rapid Ligation Buffer (Enzymatics, #L603-LC-L), 0.33 μl 1% Tween-20 and 0.5 μl T4 DNA ligase HC (Enzymatics, #L6030-HC- L). Libraries were amplified by PCR for 11-15 cycles using Solexa IGA and Solexa IGB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate in 15.2 μl of 20%PEG8000:2.5M NaCl, washed with 80% etOH and eluted in 0.05% Tween-20. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on a NextSeq 500 or Hi-Seq 4000 (Illumina, San Diego, California).
ChIP-Seq library preparation: For DNMT3A and TET2 ChIP was performed as described previously (Eichenfield et al., 2016; Troutman et al., 2020). Briefly, mDM were fixed with 3mM Disuccinimidyl-glutarate, DSG, (Proteochem, #C1104) in PBS for 30 min at room temperature followed by 10 min incubation with 1% formaldehyde (ThermoFisher, #28906) at room temperature. Next, 2.625 M Glycine was added to a final concentration of 125 mM to quench fixation. Cells were washed with 0.01%Triton-X-100:PBS, scraped and centrifuged for 10 min at 3,000 rpm at 4oC. Cells were washed once again with 0.01%Triton-X-100 in PBS, pelleted, snap frozen and stored at -80oC. For ChIP experiments, cells were thawed and permeabilised in 1 ml of ice-cold buffer containing 10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630 (Sigma Aldrich, #I8896), 1X protease inhibitor cocktail (Sigma, #11836145001) and 1 mM PMSF for 10 min on ice. Cells were then spun down and lysed in 130 μl of lysis buffer containing 20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Sodium Deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail and 1 mM PMSF and chromatin was sheared by sonication. In all buffers, DTT, protease inhibitor and PMSF were added freshly. Cell lysates were sonicated in a 96 microTUBE Rack (Covaris, #500282) using a Covaris E220 for 25 cycles with the following settings: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0. Sonicated lysates were recovered and spun at 10,000 rpm for 10 min at 4oC to remove cell debris. One percent of sonicated lysate was kept as ChIP input for analysis. Immunoprecipitation mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and DNMT3A antibody cocktail (2 μg of DNMT3A, #ab2850 plus 2 μg of DNMT3A, #C15410085), 5 μl of TET2 antibody (kindly provided by Ali Shilatifard, (Wang et al., 2018), 1.5 μl of ZNF143 (H00007702-M01) or 2 μl of RBPJ (#ab25949) was added to sonicated chromatin solution and incubated overnight on rotator at 4oC. Next day, immunocomplexes were placed on a magnet and bead complexes were washed for one minute with 150 μl of cold buffers as indicated: 3 times lysis buffer, 6 times with wash buffer containing 10 mM Tris/HCl pH7.5, 250mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate and 1% NP-40 alternative; 3 times with TET buffer containing 10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween-20; and 1 time with IDTE buffer containing 10 mM Tris/HCl pH 8.0 and 0.1 mM EDTA. Bead complexes were resuspended in 25 μl of TT buffer containing 10 mM Tris/HCl pH 8.0, 0.05% Tween-20. All wash buffer contained 1X Protease Inhibitor cocktail. ChIP libraries for sequencing were prepared while remained on beads using NEBNext Ultra II Library kit (NEB, #E7645L) by reducing 50% the reaction volume as previously described (Heinz et al., 2018; Troutman et al., 2020). Crosslinks were revered by adding 33.5 μl of mix containing 18.4 μl nuclease free water, 4 μl 10% SDS, 3 μl 0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10mg/ml Proteinase K (Biolabs, #P8107S), 1 μl 10mg/ml RNase A, 4.5 μl 5M NaCl by incubating at 55oC for 1h followed by 75oC for 30 min. Dynabeads were removed and libraries were cleaned by adding 2 μl of SpeadBeads in 124 μl of 20% PEG 8000/1.5M NaCl, washed by adding 150 μl 80% etOH, air dry and eluted in 12.5 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was PCR- amplified for 14 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. Libraries were size selected 200-500 bp by running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using using either a HiSeq 4000 or a NextSeq 500.

value: macrophages

tag: sample type

value: Pool of three donors


title: RPE7

description: countmatrix.txt:  0b2c4c67-c73b-4a1e-be5b-8a87e5afe441


title: ZNF143ChIPrep1


title: scRNAseq_1


title: TET2ChIPrep4


title: scRNAseq_3


title: human_MDM_HiC_ScrambleASO_HiC1


title: scRNAseq_2


title: inputrep2forRBPJorZNF143ChIP

value: Input


title: TET2ChIPrep2


title: inputrep3forDNMT3AorTET2ChIP


title: TET2ChIPrep3


title: RBPJChIPrep2


title: inputrep4forDNMT3AorTET2ChIP


title: TET2ChIPrep1


title: human_MDM_HiC_DNMT3AASO2_HiC2


title: ZNF143ChIPrep2


title: RBPJChIPrep1


title: inputrep1forDNMT3AorTET2ChIP


title: RPE4

description: countmatrix.txt:  d18e3db6-9922-4e15-99f5-6497147d953a

value: Female


title: inputrep1forRBPJorZNF143ChIP


title: inputrep2forDNMT3AorTET2ChIP


title: DNMT3AChIPrep4


title: DNMT3AChIPrep1


title: DNMT3AChIPrep3


title: DNMT3AChIPrep2


title: Vehiclerep2


title: Vehiclerep1


title: Vehicleforagonistsrep3

value: Vehicleforagonists


title: Vehiclerep3


title: Vehicleforagonistsrep2


title: Vehicleforagonistsrep1


title: TET2ASO2rep2


title: TET2ASO2rep3


title: siControlrep2

value: siControl


title: TET2ASO1rep1


title: ScrambleASOforTET2ASOsrep2


title: TET2ASO1rep3


title: ScrambleASOforTET2ASOsrep3


title: TET2ASO1rep2


title: ScrambleASOforDNMT3AASOsrep2


title: ScrambleASOforDNMT3AASOsrep3


title: siTFAM2rep1


title: siTFAM2rep3


title: siTFAM2rep2


title: ScrambleASOforTET2ASOsrep1


title: siControlrep3


title: siTFAM1rep3


title: TET2ASO2rep1


title: ScrambleASOforDNMT3AASOsrep1


title: RecombinantDNArep2

value: RecombinantDNA


title: RecombinantDNArep3


title: siTFAM1rep2


title: siTFAM1rep1


title: RecombinantDNArep1


title: R8486hrep2


title: R8486hrep3


title: R8486hrep1


title: R8482hrep2


title: R8482hrep1


title: Mockrep2

value: Mock


title: R8482hrep3


title: IFNA5hrep3


title: IFNA5hrep2


title: siControlrep1

value: siControlr


title: Mockrep3


title: KLA6hrep3


title: IFNA2hrep1


title: IFNA5hrep1


title: Mockrep1


title: KLA6hrep2


title: IFNA2hrep3


title: KLA2hrep3


title: KLA2hrep2


title: IFNA2hrep2


title: KLA2hrep1


title: KLA6hrep1


title: IFNA1hrep1


title: IFNA1hrep3


title: IFNA1hrep2


title: DNMT3AASO2rep2


title: DNMT3AASO2rep3


title: DNMT3AASO1rep1


title: DNMT3AASO1rep3


title: DNMT3AASO2rep1


title: CMScrambleASOrep3


title: CMTET2ASO2rep4


title: CMScrambleASOrep2


title: CMScrambleASOrep4


title: CMDNMT3AASO1rep2


title: CMScrambleASOrep1


title: CMDNMT3AASO1rep4


title: CMTET2ASO2rep1


title: CMDNMT3AASO1rep3


title: CMDNMT3AASO1rep1


title: NKI-4941-SARC-TR3084

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

value: Thrombocytes

tag: classification group

value: nonMalignant

tag: patient group

value: Former Sarcoma


title: NKI-6232-SARC-TR3101


title: NKI-5148-SARC-TR3129


title: NKI-4591-SARC-TR3075


title: NKI-4707-SARC-TR3079


title: NKI-6348-SARC-TR3134


title: NKI-5196-SARC-TR3131


title: CMTET2ASO2rep3


title: CMTET2ASO2rep2


title: DNMT3AASO1rep2


title: NKI-4854-SARC-TR3080


title: NKI-4589-SARC-TR3128


title: TR4755-URO-RAD

value: Malignant

value: Urothelial Carcinoma


title: NKI-4879-SARC-TR3081


title: TR4699-URO-RAD


title: TR4696-URO-RAD


title: TR4697-URO-RAD


title: TR4694-URO-RAD


title: NKI-6345-SARC-TR3133


title: TR4693-URO-RAD


title: TR4721-URO-RAD


title: TR4610-URO-RAD


title: TR4611-URO-RAD


title: TR4606-URO-RAD


title: TR4607-URO-RAD


title: NKI-4904-SARC-TR3083


title: NKI-5275-SARC-TR3099


title: TR4062-URO-RAD


title: TR3961-URO-RAD


title: TR4065-URO-RAD


title: TR3960-URO-RAD


title: TR3830-URO-RAD


title: TR3652-Uro-RAD


title: TR3765-URO-RAD


title: TR4618-SARC-NKI

value: Sarcoma


title: TR4621-SARC-NKI


title: TR4626-SARC-NKI


title: TR4617-SARC-NKI


title: TR4735-SARC-NKI


title: TR4623-SARC-NKI


title: TR4625-SARC-NKI


title: TR4619-SARC-NKI


title: TR4720-URO-RAD


title: TR4130-URO-RAD


title: TR4624-SARC-NKI


title: TR4622-SARC-NKI


title: TR3657-Uro-RAD


title: TR4549-SARC-NKI


title: TR4616-SARC-NKI


title: TR3827-URO-RAD


title: TR4543-SARC-NKI


title: TR4614-SARC-NKI


title: TR4542-SARC-NKI


title: TR4553-SARC-NKI


title: TR4547-SARC-NKI


title: TR4550-SARC-NKI


title: TR4544-SARC-NKI


title: TR4551-SARC-NKI


title: TR4545-SARC-NKI


title: TR4546-SARC-NKI


title: TR4552-SARC-NKI


title: TR4615-SARC-NKI


title: MGH-R-41-RENAL-TR3210

value: Renal Cell Carcinoma


title: TR4554-SARC-NKI


title: MGH-R-36-RENAL-TR3208


title: MGH-R-35-RENAL-TR3207


title: MGH-R-31-RENAL-TR3204


title: MGH-R-33-RENAL-TR3205


title: TR3203-RC-MGH


title: TR4620-SARC-NKI


title: TR4063-URO-RAD

value: Prostate Cancer


title: TR4685-URO-RAD


title: TR4058-URO-RAD


title: TR4548-SARC-NKI


title: MGH-R-43-RENAL-TR3211


title: TR4609-URO-RAD


title: TR3861-NKI-NKI


title: TR3206-RC-MGH


title: TR3962-URO-RAD


title: TR3650-Uro-RAD


title: TR3653-Uro-RAD


title: VUMC-141-2017432-PANC-TR3421

value: Pancreatic Cancer


title: TR3656-Uro-RAD


title: TR4066-URO-RAD


title: TR4064-URO-RAD


title: TR3651-Uro-RAD


title: VUMC-120-20171359-PANC-TR3420


title: MGH-R-40-RENAL-TR3209


title: VU-136-201713693-PANC-TR3409


title: VUMC-95-2017649-PANC-TR3381


title: VU-107-201713474-PANC-TR3408


title: VUMC-135-2017137-PANC-TR3419


title: VUMC-103-2017134-PANC-TR3384


title: VUMC-87-20171317-PANC-TR3378


title: VUMC-45-20171271-PANC-TR3368


title: VUMC-44-2017127-PANC-TR3305


title: VUMC-72-2017434-PANC-TR3484


title: VUMC-50-201712744-PANC-TR3307


title: VUMC-14-20171227-PANC-TR3362


title: VUMC-68-2017129-PANC-TR3374


title: VUMC-73-2017103-PANC-TR3485


title: VUMC-49-201712716-PANC-TR3306


title: VUMC-79-2017471-PANC-TR3487


title: VUMC-96-2017133-PANC-TR3382


title: VUMC-61-201712817-PANC-TR3308


title: VUMC-90-2017623-PANC-TR3380


title: VUMC-76-2017057-PANC-TR3486


title: VUMC-55-20171281-PANC-TR3463


title: TR3967-NKI-NKI

value: Ovarian Cancer


title: TR3970-NKI-NKI


title: TR3856-NKI-NKI


title: VUMC-43-2017126951-PANC-TR3367


title: VUMC-53-20171277-PANC-TR3372


title: TR3858-NKI-NKI


title: VUMC-42-201712695-PANC-TR3366


title: VUMC-33-20171254-PANC-TR3304


title: VUMC-4-2017119-PANC-TR3504


title: TR3972-NKI-NKI


title: TR3859-NKI-NKI


title: TR4310-OVA-LUMC

source_name: Blood_Platelets_LUMC-GYN 53


title: TR3964-NKI-NKI


title: VUMC-38-2017126-PANC-TR3365


title: TR4309-OVA-LUMC


title: TR4342-OVA-LUMC


title: TR4341-OVA-LUMC


title: TR4315-OVA-LUMC

source_name: Blood_Platelets_LUMC-GYN 59


title: TR4335-OVA-LUMC


title: TR4263-OVA-LUMC


title: TR3519-OVA-LUMC


title: VUMC-11-20171223-PANC-TR3506


title: TR3401-OVA-LUMC


title: TR4336-OVA-LUMC


title: TR4337-OVA-LUMC


title: TR3517-OVA-LUMC


title: TR3971-NKI-NKI


title: TR4379-OVA-GDANSK

source_name: Blood_Platelets_OC 139


title: TR4378-OVA-GDANSK

source_name: Blood_Platelets_OC 138


title: TR3400-OVA-LUMC


title: TR3398-OVA-LUMC


title: TR4353-OVA-GDANSK

source_name: Blood_Platelets_OC 132


title: TR4377-OVA-GDANSK

source_name: Blood_Platelets_OC 137


title: TR4376-OVA-GDANSK

source_name: Blood_Platelets_OC 136


title: TR4313-OVA-LUMC

source_name: Blood_Platelets_LUMC-GYN 57


title: TR4352-OVA-GDANSK

source_name: Blood_Platelets_OC 131


title: TR4326-OVA-GDANSK

source_name: Blood_Platelets_119 TEPs


title: TR4351-OVA-GDANSK

source_name: Blood_Platelets_OC 130


title: TR4146-OVA-GDANSK


title: TR4210-OVA-Supernat

source_name: Blood_Platelets_EC 057 TEPS


title: VUMC-77-20176287-PANC-TR3501


title: TR4325-OVA-GDANSK

source_name: Blood_Platelets_118 TEPs


title: TR4043-OVA-GDANSK


title: TR4187-OVA-GDANSK


title: TR4026-OVA-Supernat


title: TR4191-OVA-GDANSK


title: TR4320-OVA-GDANSK

source_name: Blood_Platelets_OC 113


title: TR4214-OVA-Supernat

source_name: Blood_Platelets_OC 061 TEPS


title: TR4023-OVA-Supernat


title: TR4017-OVA-GDANSK


title: TR4340-OVA-LUMC


title: TR4087-OVA-Supernat


title: TR4097-OVA-Supernat


title: TR4019-OVA-Supernat


title: TR4718-OVA-CATH

source_name: Blood_Platelets_CZE 119


title: TR4238-OVA-CATH

source_name: Blood_Platelets_CZE 108


title: TR4012-OVA-GDANSK


title: TR4237-OVA-CATH

source_name: Blood_Platelets_CZE 107


title: TR4235-OVA-CATH

source_name: Blood_Platelets_CZE 104


title: TR4232-OVA-CATH

source_name: Blood_Platelets_CZE 101


title: TR4010-OVA-GDANSK


title: TR4229-OVA-CATH

source_name: Blood_Platelets_CZE 097


title: TR4300-OVA-CATH

source_name: Blood_Platelets_CZE 092


title: TR4303-OVA-CATH

source_name: Blood_Platelets_CZE 095


title: TR4086-OVA-GDANSK


title: TR4294-OVA-CATH

source_name: Blood_Platelets_CZE 086


title: TR3664-OVA-CATH


title: TR3530-OVA-CATH


title: TR3531-OVA-CATH


title: TR3660-OVA-CATH


title: TR3637-OVA-CATH


title: TR3658-OVA-CATH


title: TR4915-NSCLC-MAAS

value: Non-Small-Cell Lung Cancer


title: TR3528-OVA-CATH


title: TR4913-NSCLC-MAAS


title: TR4911-NSCLC-MAAS


title: TR4906-NSCLC-MAAS


title: TR4902-NSCLC-MAAS


title: TR4898-NSCLC-MAAS


title: TR4900-NSCLC-MAAS


title: TR4908-NSCLC-MAAS


title: TR4909-NSCLC-MAAS


title: TR4231-OVA-CATH

source_name: Blood_Platelets_CZE 099


title: TR4302-OVA-CATH

source_name: Blood_Platelets_CZE 094


title: TR4890-NSCLC-MAAS


title: TR4892-NSCLC-MAAS


title: TR4896-NSCLC-MAAS


title: TR4888-NSCLC-MAAS


title: TR4884-NSCLC-MAAS


title: TR4886-NSCLC-MAAS


title: TR3948-OVA-CATH

source_name: Blood_Platelets_CZE 080


title: TR4816-NSCLC-MAAS


title: TR4682-NSCLC-NKI


title: TR4818-NSCLC-MAAS


title: TR4296-OVA-CATH

source_name: Blood_Platelets_CZE 088


title: TR4644-NSCLC-NKI


title: TR4645-NSCLC-NKI


title: TR4680-NSCLC-NKI


title: TR4670-NSCLC-NKI


title: TR4671-NSCLC-NKI


title: TR4673-NSCLC-NKI


title: TR4633-NSCLC-NKI


title: TR4663-NSCLC-NKI


title: TR4683-NSCLC-NKI


title: TR4666-NSCLC-NKI


title: TR4659-NSCLC-NKI


title: TR4657-NSCLC-NKI


title: TR4634-NSCLC-NKI


title: TR4654-NSCLC-NKI


title: TR4676-NSCLC-NKI


title: TR4669-NSCLC-NKI


title: TR4668-NSCLC-NKI


title: TR4658-NSCLC-NKI


title: TR4656-NSCLC-NKI


title: VUMC-Vumc-1941-NSCLC-TR3167


title: VUMC-Vumc-1588-NSCLC-TR3163


title: VUMC-Vumc-1160-NSCLC-TR3171


title: VUMC-Vumc-1863-NSCLC-TR3166


title: VUMC-Vumc-1702-NSCLC-TR3174


title: VUMC-Vumc-1617-NSCLC-TR3165


title: VUMC-Vumc-1601-NSCLC-TR3164


title: VUMC-Vumc-1250-NSCLC-TR3172


title: VUMC-Vumc-1773-NSCLC-TR3062


title: VUMC-Vumc-1867-NSCLC-TR3063


title: VUMC-Vumc-1740-NSCLC-TR3061


title: GRON-Gron-1118-NSCLC-TR3023


title: VUMC-VUmc-1576-NSCLC-TR3056


title: VUMC-vumc-1529-NSCLC-TR3054


title: VUMC-Vumc-1556-NSCLC-TR3055


title: VUMC-Vumc-1457-NSCLC-TR3051


title: VUMC-Vumc-1086-NSCLC-TR3170


title: VUMC-Vumc-1638-NSCLC-TR3173


title: VUMC-Vumc-913-NSCLC-TR3169


title: TR3923-MS-MGH

value: Multiple Sclerosis


title: TR3852-MS-MGH


title: TR3924-MS-MGH


title: TR3846-MS-MGH


title: TR3849-MS-MGH


title: TR3925-MS-MGH


title: TR3854-MS-MGH


title: TR3850-MS-MGH


title: TR3848-MS-MGH


title: TR3921-MS-MGH


title: TR3926-MS-MGH


title: TR4033-MS-MGH


title: TR3847-MS-MGH


title: TR3989-MS-MGH


title: TR3922-MS-MGH


title: TR3853-MS-MGH


title: TR3851-MS-MGH


title: TR3990-MS-MGH


title: TR3920-MS-MGH


title: TR4769-MELA-RAD

value: Melanoma


title: TR4765-MELA-RAD


title: TR4756-URO-RAD


title: TR4754-URO-RAD


title: TR4702-URO-RAD


title: TR4686-URO-RAD


title: TR4703-URO-RAD


title: TR4751-URO-RAD


title: TR4764-URO-RAD


title: TR4698-URO-RAD


title: TR4714-URO-RAD


title: TR4603-URO-RAD


title: TR4602-URO-RAD


title: MGH-M-193-MELA-TR3190


title: TR4608-URO-RAD


title: TR3266-MELA-MGH


title: MGH-M-177-MELA-TR3184


title: TR4695-URO-RAD


title: TR4604-URO-RAD


title: MGH-M-198-MELA-TR3229


title: TR4763-URO-RAD


title: TR4605-URO-RAD


title: MGH-M-197-MELA-TR3228


title: MGH-M-182-MELA-TR3186


title: MGH-M-183-MELA-TR3187


title: MGH-M-187-MELA-TR3146


title: MGH-M-174-MELA-TR3183


title: TR4687-URO-RAD


title: MGH-M-194-MELA-TR3227


title: MGH-M-184-MELA-TR3188


title: MGH-M-185-MELA-TR3161


title: TR3359-HL-MGH

value: Hodgkin Lymphoma


title: MGH-M-173-MELA-TR3160


title: MGH-M-172-MELA-TR3159


title: MGH-M-168-MELA-TR3158


title: TR3361-HL-MGH


title: TR3357-HL-MGH


title: MGH-HL-2-HL-TR3140


title: TR4760-URO-RAD

value: Hematuria


title: TR3766-URO-RAD


title: TR3764-URO-RAD


title: TR3360-HL-MGH


title: TR3358-HL-MGH


title: TR4592-HN-VUMC

source_name: Blood_Platelets_210091 t=0

value: Head and Neck Cancer


title: TR4758-URO-RAD


title: TR4701-URO-RAD


title: TR4537-HN-VUMC

source_name: Blood_Platelets_210165 M0


title: TR4080-HN-VUMC-BB

source_name: Blood_Platelets_HN 110099


title: TR4252-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210226 T=0


title: MGH-M-181-MELA-TR3185


title: TR4240-HN-VUMC-BB

source_name: Blood_Platelets_310177 T=0


title: TR4700-URO-RAD


title: TR4597-VUMC-HN

source_name: Blood_Platelets_210157 t=0


title: TR4684-URO-RAD


title: TR4595-VUMC-HN

source_name: Blood_Platelets_210080 t=0


title: TR4593-VUMC-HN

source_name: Blood_Platelets_210150 t=0


title: TR4596-HN-VUMC

source_name: Blood_Platelets_210098 t=0


title: TR4250-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210211 T=0


title: TR4255-HN-VUMC-BB

source_name: Blood_Platelets_310201 T=0


title: TR4242-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210008 T=0


title: TR4246-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 220188 T=0


title: TR4251-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210213 T=0


title: TR4228-HN-VUMC-BB

source_name: Blood_Platelets_210128 M0


title: TR4247-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210193 T=0


title: TR4256-HN-VUMC-BB

source_name: Blood_Platelets_310116 T=0


title: TR4253-HN-VUMC-BB

source_name: Blood_Platelets_310056 T=0


title: TR4260-HN-VUMC-BB

source_name: Blood_Platelets_310148 T=0


title: TR4241-HN-VUMC-BB

source_name: Blood_Platelets_310189 T=0


title: TR4249-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210199 T=0


title: TR4138-HN-VU

source_name: Blood_Platelets_HN 110225


title: TR4245-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210117 T=0


title: TR4243-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210124 T=0


title: TR4136-HN-VU

source_name: Blood_Platelets_HN 110127


title: TR4167-HN-VU

source_name: Blood_Platelets_HN 115012 M0


title: TR4254-HN-VUMC-BB

source_name: Blood_Platelets_310080 T=0


title: TR4227-HN-VUMC-BB

source_name: Blood_Platelets_210118 M0


title: TR4244-HN-VUMC-BB

source_name: Blood_Platelets_RESP nr. 210170 T=0


title: TR4078-HN-VU

source_name: Blood_Platelets_HN 110084


title: TR4074-HN-VU

source_name: Blood_Platelets_HN 110049 M0


title: TR4076-HN-VU

source_name: Blood_Platelets_HN 110059 M0


title: TR4128-HN-VU

source_name: Blood_Platelets_HN 115026 M0


title: TR4257-HN-VUMC-BB

source_name: Blood_Platelets_310118 T=0


title: TR4072-HN-VU

source_name: Blood_Platelets_HN 110017 M0


title: TR4261-HN-VUMC-BB

source_name: Blood_Platelets_310165 T=0


title: TR4127-HN-VU

source_name: Blood_Platelets_HN 115018 M0


title: TR4258-HN-VUMC-BB

source_name: Blood_Platelets_310140 T=0


title: TR4069-HN-VU

source_name: Blood_Platelets_HN 110006 M0


title: TR4071-HN-VU

source_name: Blood_Platelets_HN 110016 M0


title: TR4091-HN-VU

source_name: Blood_Platelets_HN 110160


title: TR4131-HN-VU

source_name: Blood_Platelets_HN 110038


title: TR4089-HN-VU

source_name: Blood_Platelets_HN 110121


title: TR4134-HN-VU

source_name: Blood_Platelets_HN 110205


title: TR4094-HN-VU

source_name: Blood_Platelets_HN 110187


title: TR4168-HN-VU

source_name: Blood_Platelets_HN 115017 M0


title: TR4125-HN-VU

source_name: Blood_Platelets_HN 110162 M0


title: TR4135-HN-VU

source_name: Blood_Platelets_HN 110213


title: TR4092-HN-VU

source_name: Blood_Platelets_HN 110171


title: TR4077-HN-VU

source_name: Blood_Platelets_HN 110073


title: TR4073-HN-VU

source_name: Blood_Platelets_HN 110033 M0


title: TR4070-HN-VU

source_name: Blood_Platelets_HN 110007 M0


title: TR4068-HN-VU

source_name: Blood_Platelets_HN 110004 M0


title: TR4075-HN-VU

source_name: Blood_Platelets_HN 110053 M0


title: TR4137-HN-VU

source_name: Blood_Platelets_HN 110217


title: TR4090-HN-VU

source_name: Blood_Platelets_ HN 110125


title: TR4088-HN-VU

source_name: Blood_Platelets_HN 110119


title: TR4813-NSCLC-MAAS

value: Asymptomatic Controls


title: TR4815-NSCLC-MAAS

value: Thrombocytes


title: TR4809-NSCLC-MAAS


title: TR4807-NSCLC-MAAS


title: TR4803-NSCLC-MAAS


title: TR4801-NSCLC-MAAS


title: TR4800-NSCLC-MAAS


title: TR4805-NSCLC-MAAS


title: TR4806-NSCLC-MAAS


title: TR4804-NSCLC-MAAS


title: TR4799-NSCLC-MAAS


title: TR4798-NSCLC-MAAS


title: TR4814-NSCLC-MAAS


title: TR4797-NSCLC-MAAS


title: TR4811-NSCLC-MAAS


title: TR4796-NSCLC-MAAS


title: TR3677-GBM-VUMC

source_name: Blood_Platelets_VU624 T0

value: Glioma


title: TR3815-GBM-VUMC

source_name: Blood_Platelets_VU584 T0


title: TR3726-GBM-VUMC

source_name: Blood_Platelets_VU782 T0


title: TR4812-NSCLC-MAAS


title: TR4808-NSCLC-MAAS


title: TR3681-GBM-VUMC

source_name: Blood_Platelets_VU635 T0


title: TR3770-GBM-VUMC

source_name: Blood_Platelets_VU671 T0


title: TR3712-GBM-VUMC

source_name: Blood_Platelets_VU604 T0


title: TR3690-GBM-VUMC

source_name: Blood_Platelets_VU666 T0


title: TR3687-GBM-VUMC

source_name: Blood_Platelets_VU648 T0


title: TR4810-NSCLC-MAAS


title: TR3684-GBM-VUMC

source_name: Blood_Platelets_VU639 T0


title: TR3707-GBM-VUMC

source_name: Blood_Platelets_VU595 T0


title: TR3696-GBM-VUMC

source_name: Blood_Platelets_VU703 T0


title: TR3723-GBM-VUMC

source_name: Blood_Platelets_VU729 T0


title: TR4802-NSCLC-MAAS


title: TR3703-GBM-VUMC

source_name: Blood_Platelets_VU594 T0


title: TR3819-GBM-VUMC

source_name: Blood_Platelets_VU590 T0


title: TR3675-GBM-VUMC

source_name: Blood_Platelets_VU620 T0


title: TR3717-GBM-VUMC

source_name: Blood_Platelets_VU609 T0 GBM mogelijk apart variant


title: TR4795-NSCLC-MAAS


title: TR3809-GBM-VUMC

source_name: Blood_Platelets_VU578 T0


title: MGH-E1-ESO-TR3230

value: Esophageal Cancer


title: VUMC-EPI-039-EPI-TR2846

value: nonMalignant

value: Epilepsy


title: GRON-P105-t0-ESO-TR3121

value: Malignant


title: MGH-E3-ESO-TR3191


title: GRON-P104-t0-ESO-TR3120


title: VUMC-EPI-037-EPI-TR2844


title: TR4383-OVA-GDANSK

source_name: Blood_Platelets_EC 143

value: Endometrial Cancer


title: TR4194-OVA-Supernat


title: TR4354-OVA-GDANSK

source_name: Blood_Platelets_EC 133


title: TR4382-OVA-GDANSK

source_name: Blood_Platelets_EC 142


title: TR4324-OVA-GDANSK

source_name: Blood_Platelets_117 TEPs


title: TR4321-OVA-GDANSK

source_name: Blood_Platelets_EC 114


title: TR4327-OVA-GDANSK

source_name: Blood_Platelets_120 TEPs


title: TR4328-OVA-GDANSK

source_name: Blood_Platelets_EC 121


title: TR4350-OVA-GDANSK

source_name: Blood_Platelets_EC 129


title: TR4346-OVA-GDANSK

source_name: Blood_Platelets_EC 125


title: TR4323-OVA-GDANSK

source_name: Blood_Platelets_EC 116


title: TR4349-OVA-GDANSK

source_name: Blood_Platelets_EC 128


title: TR4347-OVA-GDANSK

source_name: Blood_Platelets_EC 126


title: TR4381-OVA-GDANSK

source_name: Blood_Platelets_EC 141


title: TR4322-OVA-GDANSK

source_name: Blood_Platelets_EC 115


title: TR4330-OVA-GDANSK

source_name: Blood_Platelets_EC 123


title: TR4348-OVA-GDANSK

source_name: Blood_Platelets_EC 127


title: TR4333-OVA-GDANSK

source_name: Blood_Platelets_EC 109


title: TR4319-OVA-GDANSK

source_name: Blood_Platelets_EC 112


title: TR4334-OVA-GDANSK

source_name: Blood_Platelets_EC 111


title: TR4217-OVA-Supernat

source_name: Blood_Platelets_EC 065 TEPS


title: TR4278-OVA-GDANSK

source_name: Blood_Platelets_EC 103


title: TR4216-OVA-Supernat

source_name: Blood_Platelets_EC 063 TEPS


title: TR4150-OVA-Supernat

source_name: Blood_Platelets_EC 056 TEPS


title: TR4052-OVA-Supernat


title: TR4104-OVA-Supernat


title: TR4095-OVA-Supernat


title: TR4055-OVA-Supernat


title: TR4051-OVA-Supernat


title: TR4045-OVA-Supernat


title: TR4027-OVA-Supernat


title: TR4025-OVA-Supernat


title: TR3949-OVA-CATH

source_name: Blood_Platelets_CZE 081


title: TR4014-OVA-Supernat


title: TR4016-OVA-GDANSK


title: TR3490-PANC-VUMC


title: TR3515-PANC-VUMC


title: TR3489-PANC-VUMC


title: TR4013-OVA-GDANSK


title: TR3491-PANC-VUMC


title: TR4331-OVA-GDANSK

source_name: Blood_Platelets_EC 106


title: TR3488-PANC-VUMC


title: TR4021-OVA-Supernat


title: TR3516-PANC-VUMC


title: TR4047-OVA-Supernat


title: VUMC-83-2017265-PANC-TR3312

value: Pancreatic Disease


title: TR3493-PANC-VUMC


title: TR3514-PANC-VUMC


title: TR3512-PANC-VUMC


title: TR3243-CRC-MGH

value: Colorectal Cancer


title: TR3840-CRC-MGH


title: TR3495-PANC-VUMC


title: TR3496-PANC-VUMC


title: TR3492-PANC-VUMC


title: TR3513-PANC-VUMC


title: TR3842-CRC-MGH


title: TR3494-PANC-VUMC


title: TR3836-CRC-MGH


title: VUMC-19-20171232-PANC-TR3414


title: TR3841-CRC-MGH


title: MGH-C-48-CRC-TR3231


title: TR3843-CRC-MGH


title: VUMC-35-2015994-PANC-TR3115


title: MGH-C-73-CRC-TR3201


title: TR3834-CRC-MGH


title: TR3833-CRC-MGH


title: TR3835-CRC-MGH


title: TR3838-CRC-MGH


title: TR3845-CRC-MGH


title: TR3242-CRC-MGH


title: MGH-C-69-CRC-TR3246


title: MGH-C-64-CRC-TR3241


title: MGH-C-40-CRC-TR3192


title: MGH-C-49-CRC-TR3232


title: MGH-C-74-CRC-TR3202


title: MGH-C-72-CRC-TR3200


title: VUMC-254-CHIR-AMC-PANC-TR3422


title: TR3837-CRC-MGH


title: VUMC-88-2017767-PANC-TR3379


title: MGH-C-71-CRC-TR3199


title: MGH-C-58-CRC-TR3237


title: MGH-BD-22-CHOL-TR3148

value: Cholangiocarcinoma


title: MGH-C-42-CRC-TR3193


title: TR3261-HCC-MGH


title: MGH-C-51-CRC-TR3234


title: VIENNA-Vien-7-CRC-TR2954


title: VUMC-108-2017135-PANC-TR3418


title: VUMC-27-20171251-PANC-TR3302


title: MGH-BD-24-CHOL-TR3150


title: MGH-BD-21-CHOL-TR3147


title: MGH-BD-23-CHOL-TR3149


title: MGH-BD-30-CHOL-TR3156


title: MGH-BD-28-CHOL-TR3154


title: MGH-BD-18-CHOL-TR3145


title: MGH-BD-31-CHOL-TR3157


title: VUMC-109-20171334-PANC-TR3502


title: MGH-BD-26-CHOL-TR3152


title: MGH-BD-27-CHOL-TR3153


title: MGH-BD-25-CHOL-TR3151


title: VUMC-77-20155964-PANC-TR3019


title: VUMC-82-20161136-PANC-TR3020


title: MGH-BD-17-CHOL-TR3144


title: VUMC-92-2016610-PANC-TR3010


title: VUMC-46-20171274-PANC-TR3415


title: TR3223-BREAST-MGH

value: Breast Cancer


title: MGH-H-198-Breast-TR3226


title: MGH-H-147-Breast-TR3182


title: MGH-H-104-Breast-TR3176


title: MGH-H-188-Breast-TR3225


title: MGH-H-216-Breast-TR3143


title: MGH-H-131-Breast-TR3177


title: MGH-H-103-Breast-TR3175


title: MGH-BD-29-CHOL-TR3155


title: MGH-H-136-Breast-TR3179


title: MGH-H-186-Breast-TR3224


title: MGH-H-138-Breast-TR3180


title: MGH-H-133-Breast-TR3178


title: MGH-H-201-Breast-TR3142


title: MGH-H-196-Breast-TR3162


title: VUMC-144-20171340-PANC-TR3466


title: MGH-H-146-Breast-TR3181


title: MGH-H-199-Breast-TR3141


title: VUMC-118-20171351-PANC-TR3509


title: VUMC-127-2017497-PANC-TR3510


title: VUMC-67-2017628-PANC-TR3310


title: VUMC-138-2017198-PANC-TR3483


title: VUMC-21-20171239-PANC-TR3462


title: VUMC-71-2017197-PANC-TR3508


title: VUMC-146-2017440-PANC-TR3467


title: VUMC-70-2017853-PANC-TR3464


title: VUMC-24-2015294-PANC-TR3103


title: VUMC-10-2015790-PANC-TR3111


title: VUMC-1-2017940-PANC-TR3503


title: VUMC-2-2016681-PANC-TR3114


title: VUMC-40-2015495-PANC-TR3116


title: VUMC-42-2015675-PANC-TR3104


title: VUMC-97-2015497-PANC-TR3118


title: VUMC-16-2016649-PANC-TR3113


title: VUMC-122-2015298-PANC-TR3112


title: MGH-Hc-2-Liver-TR3212

value: Hepatocellular Carcinoma


title: TR3221-HCC-


title: TR3214-HCC-MGH


title: TR3220-HCC-


title: TR3219-HCC-


title: TR3217-HCC-


title: TR3213-HCC-MGH


title: TR3216-HCC-MGH


title: VUMC-98-2015AMC005-PANC-TR3127


title: TR3264-HCC-MGH


title: TR3352-HCC-MGH


title: TR3356-HCC-MGH


title: TR3354-HCC-MGH


title: TR3353-HCC-MGH


title: TR3262-HCC-MGH


title: TR3265-HCC-MGH


title: TR3259-HCC-MGH


title: TR3263-HCC-MGH


title: TR3222-HCC-MGH

source_name: Blood_Platelets_Hc 14


title: TR3350-HCC-MGH

source_name: Blood_Platelets_Hc 15


title: TR3355-HCC-MGH


title: VUMC-82-2015796-PANC-TR3117


title: TR3351-HCC-MGH


title: VUMC-90-2015896-PANC-TR3022


title: VUMC-45-2016102-PANC-TR3015


title: VUMC-20-2015794-PANC-TR3014


title: TR3218-HCC-


title: TR3219-HCC-MGH


title: VUMC-119-20171355-PANC-TR3469


title: VUMC-51-20171275-PANC-TR3370


title: VUMC-104-2017068-PANC-TR3385


title: VU-101-201713277-PANC-TR3383


title: TR3774-MM-VUMC

value: Multiple Myeloma


title: TR3768-MM-VUMC


title: TR3772-MM-VUMC


title: TR3769-MM-VUMC


title: TR3844-CRC-MGH


title: MGH-C-63-CRC-TR3240


title: TR3965-NKI-NKI


title: TR3245-CRC-MGH


title: MGH-C-61-CRC-TR3238


title: TR3244-CRC-MGH


title: TR3773-MM-VUMC


title: MGH-C-62-CRC-TR3239


title: TR3775-MM-VUMC


title: TR3776-MM-VUMC


title: MGH-C-41-CRC-TR3194


title: TR4042-OVA-GDANSK

value: Ovarian Cancer


title: TR3860-NKI-NKI


title: TR4147-OVA-Supernat


title: TR3839-CRC-MGH


title: MGH-C-56-CRC-TR3236


title: MGH-C-50-CRC-TR3233


title: MGH-C-47-CRC-TR3198


title: MGH-C-54-CRC-TR3235


title: TR4056-OVA-Supernat


title: TR4218-OVA-Supernat

source_name: Blood_Platelets_EC 066 TEPS


title: MGH-C-46-CRC-TR3197


title: TR4280-OVA-GDANSK

source_name: Blood_Platelets_OC 105


title: MGH-C-45-CRC-TR3196


title: TR4298-OVA-CATH

source_name: Blood_Platelets_CZE 090


title: TR3520-OVA-LUMC


title: TR4306-OVA-LUMC


title: TR4212-OVA-Supernat

source_name: Blood_Platelets_EC 059 TEPS


title: TR4048-OVA-Supernat


title: TR4020-OVA-Supernat


title: TR3947-OVA-CATH


title: TR3548-OVA-LUMC


title: TR3523-OVA-LUMC


title: TR3638-OVA-CATH


title: TR3552-OVA-CATH


title: TR3407-OVA-LUMC


title: TR3662-OVA-CATH


title: VUMC-64-20171286-PANC-TR3309

value: Pancreatic Cancer


title: VUMC-125-20171363-PANC-TR3468


title: VUMC-31-2017853-PANC-TR3303


title: VUMC-82-20171313-PANC-TR3311


title: VUMC-86-20171318-PANC-TR3377


title: VUMC-23-2017124-PANC-TR3363


title: TR4024-OVA-Supernat


title: VUMC-9-2017121-PANC-TR3505


title: VUMC-26-20171125-PANC-TR3507


title: TR3699-GBM-VUMC

source_name: Blood_Platelets_VU591 T0


title: TR4039-HD-NKI


title: VUMC-47-201712743-PANC-TR3369


title: TR3477-HD-NKI


title: TR3295-HD-NKI


title: TR3431-HD-NKI


title: TR3570-OVA-CATH


title: TR3544-OVA-LUMC


title: VUMC-HC440-HD-TR3446


title: TR3428-HD-NKI


title: VUMC-HC423-HD-TR3444


title: VUMC-HC441-HD-TR3445


title: VUMC-HC428-HD-TR3325


title: VUMC-HC434-HD-TR3320


title: VUMC-HC426-HD-TR3324


title: VUMC-HC442-HD-TR3323


title: VUMC-59-2017987-PANC-TR3373


title: NKI-107-005497-HD-TR3287


title: NKI-107-005484-HD-TR3285


title: NKI-107-005500-HD-TR3288


title: NKI-107-005472-HD-TR3284


title: NKI-107-005462-HD-TR3283


title: NKI-107-005456-HD-TR3479


title: NKI-107-005455-HD-TR3478


title: TR3299-HD-NKI


title: NKI-107-005440-HD-TR3289


title: NKI-107-005450-HD-TR3476


title: NKI-107-005437-HD-TR3475


title: NKI-107-005433-HD-TR3301


title: NKI-107-005417-HD-TR3293


title: NKI-107-005414-HD-TR3433


title: NKI-107-005402-HD-TR3425


title: NKI-107-005404-HD-TR3427


title: VUMC-HC425-HD-TR3322


title: NKI-107-005400-HD-TR3424


title: VUMC-HC438-HD-TR3321


title: VUMC-HC439-HD-TR3319


title: NKI-107-005385-HD-TR3458


title: NKI-107-005384-HD-TR3457


title: NKI-107-005386-HD-TR3497


title: NKI-107-005379-HD-TR3455


title: NKI-107-005371-HD-TR3451


title: NKI-107-005370-HD-TR3396


title: NKI-107-005314-HD-TR3349


title: NKI-107-005315-HD-TR3386


title: NKI-107-005313-HD-TR3348


title: NKI-107-005461-HD-TR3482


title: NKI-107-005304-HD-TR3344


title: VUMC-HC0175-DOT-HD-48h-TR3108


title: NKI-107-005289-HD-TR3341


title: VUMC-HC0094-DOT-HD-48h-TR3095


title: VUMC-HC0083-DOT-HD-48h-TR3093


title: VUMC-HC0161-DOT-HD-48h-TR3137


title: VUMC-HC0049-DOT-HD-48h-TR3086


title: NKI-107-005310-HD-TR3346


title: VUMC-HC0097-DOT-HD-48h-TR3098


title: NKI-107-005389-HD-TR3460


title: VUMC-HC0131-DOT-HD-48h-TR3069


title: VUMC-HC0095-DOT-HD-48h-TR3096


title: VUMC-HC0143-DOT-HD-48h-TR3072


title: VUMC-HC0129-DOT-HD-48h-TR3068


title: VUMC-HC0118-DOT-HD-48h-TR3066


title: VUMC-HC0053-DOT-HD-48h-TR3087


title: VUMC-HC0166-DOT-HD-48h-TR3105


title: VUMC-HC0054-DOT-HD-48h-TR3088


title: VUMC-HC0172-DOT-HD-48h-TR3107


title: VUMC-HC0069-DOT-HD-48h-TR3094


title: VUMC-HC0125-DOT-HD-48h-TR3067


title: VUMC-HC0146-DOT-HD-48h-TR3074


title: VUMC-HC0096-DOT-HD-48h-TR3097


title: VUMC-HC0082-DOT-HD-48h-TR3092


title: VUMC-HC0103-DOT-HD-48h-TR3065


title: VUMC-HC0151-DOT-HD-48h-TR3136


title: VUMC-HC0068-DOT-HD-48h-TR3090


title: Vumc-P-PH-001-034-TR1512

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico with the counts from Vumc-P-PH-001-034-TR1512-seq2_GGCTAC_L008_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.

value: Pulmonary Hypertension


title: P-PH-001-013-TR1400


title: Vumc-P-PH-001-010-TR1505

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico with the counts from Vumc-P-PH-001-010-TR1505-seq2_TGACCA_L006_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.


title: NKI-SARC-7330-TR3050

value: Former Sarcoma


title: NKI-NSCLC-107-270-TR725

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.

value: Thrombocytes

value: Non-Small-Cell Lung Cancer


title: Patient 2 Fallopian Tube Epithelium

city: Grand Rapids

first: Benjamin

middle: K

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Base calling was done by Illumina NextSeq or NovaSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v1.9.0.
Subsampling was performed using seqtk (v1.3-r107-dirty) on the trimmed fastqs to the various read depths.
Demultiplexed fastqs were then trimmed using TrimGalore (v0.6.0) and cutadapt (v2.10) with the following parameters: --illumina, --trim-n, --length 36, --paired, --clip_R2 3, --fastqc. Pre- and post-trimming quality control was assessed using FastQC (v0.11.9).
Trimmed fastqs were processed using salmon quant (v1.3.0) to either a reference genome (K-562) or a spliced and unscpliced reference transcriptome (FTE; generated with eisaR v1.3.0) with the following parameters: -l ISR, --seqBias, --gcBias, --posBias, --softclip, --numBootstraps 100.
SummarizedExperiment objects were generated using tximeta (v1.6.3) in R (4.0.0). Gene counts were summarized using the tximeta function summarizeToGene with the argument countsFromAbundance = "lengthScaledTPM".
Genome_build: GRCh38 release 101
Supplementary_files_format_and_content: Tab-delimited TPM matrices

source_name: Fallopian Tube Epithelium

growth_protocol: The K562 cell line was purchased from the American Type Culture Collection (ATCC; CCL-243). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/Streptomycin (Gibco). Cells were maintained at 37oC in 5% CO2 and sub-cultured at 1:5 ratio every 3-4 days.

extract_protocol:
BULK TOTAL RNA: Total RNA from 5 million K562 cells were isolated using TRIzol (Invitrogen). STORM-seq: total RNA extraction is integrated into the library preparation protocol with Takara Bio's lysis buffer that comes in the SMART-seq Stranded kit (Takara Bio, USA)
BULK TOTAL RNA: Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Illumina UDIs. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA). SMART-seq STRANDED: Single-cell K562 libraries were prepared using the SSS Kit, following the manufacturer instructions with modifications. Following sorting into PBS, Takara Shearing Master Mix was added to all samples to a final concentration recommended by the kit. The samples underwent 6 minute fragmentation time at 85 °C. Section B step 4 in the protocol was modified to account for the incorporation of UDIs (Takara SMARTer RNA Unique Dual Index Kit-96A, Takara Bio, USA). A total of 2 uL of each UDI was used instead of the recommended 1 uL each of the 5’ and 3’ PCR primers. For PCR1, 10 cycles of amplification were performed, followed by pooling according to Appendix A. The remainder of the protocol was performed according to manufacturer recommendations. STORM-seq: Single cells were prepared using the SMART-Seq Stranded Kit (Takara USA) on the SPT Labtech Mosquito (HV) at 1:6, then 1:4 dilutions relative to the recommended volumes for subsequent steps in the protocol. In contrast to the manually prepared K562 libraries, for the miniaturized protocol, cells were sorted into a 384-well plate (Eppendorf twin-tec) containing a combination of Shearing Master Mix plus PBS and immediately transferred to a thermocycler and fragmented for 3 minutes at 85 °C. Following 1st Strand Synthesis, PCR1 (10 cycles of amplification) was performed with the addition of SMARTer RNA Unique Dual Index Set A (Takara SMARTer RNA Unique Dual Index Kit-96A) instead of Takara 5’ and 3’ PCR Primers. Samples were pooled across rows into groups of 12 cells according to Appendix A: Pooling Strategy for Single-Cell Applications and depletion of ribosomal cDNA was performed as indicated. 13 cycles of amplification were performed for PCR2 and the final library was eluted in 13ul 10mM Tris-HCl pH 8.0.

treatment_protocol: None.

tag: disease state

value: Healthy

tag: tissue source

value: Fallopian Tube Epithelium

value: Female

tag: experiment type

value: STORM-seq


title: VUMC-HC0140-DOT-HD-48h-TR3071

value: nonMalignant

value: Asymptomatic Controls


title: NKI-SARC-6475-TR3047


title: NKI-SARC-6222-TR3042


title: NKI-SARC-6373-TR3044


title: NKI-SARC-6474-TR3046


title: NKI-SARC-6430-TR3045


title: VUMC-HC0171-DOT-HD-48h-TR3106


title: NKI-SARC-6179-TR3040


title: NKI-SARC-6344-TR3043


title: NKI-SARC-6181-TR3041

value: Prostate Cancer


title: VUMC-HC0102-DOT-HD-48h-TR3064


title: Vumc-P-PH-001-024-TR1414


title: Vumc-P-PH-001-016-TR1404


title: VUMC-HC0144-DOT-HD-48h-TR3073


title: Vumc-P-PH-001-013-TR1400


title: Vumc-NSCLC-216-TR874

value: Malignant


title: NKI-SARC-5525-TR3038


title: MGH-NSCLC-L121-TR907


title: NKI-SARC-4727-TR3036


title: NKI-SARC-5153-TR3037


title: G7-106N


title: Vumc-EPI-012-TR1466

value: Epilepsy


title: Vumc-ChronPan-1-2016584-TR1946

value: Pancreatic Disease


title: Vumc-P-PH-001-054-TR1424


title: Pisa-ChronPan-2015VIT-TR972


title: NKI-SARC-7316-TR3048


title: NKI-SARC-5576-TR3039


title: E1-5N


title: B7-19N


title: G6-105N


title: UMCU-HC-1-0208-TR822


title: G4-103N


title: G5-104N


title: UMCU-HC-1-0206-TR815


title: G2-101N


title: G3-102N


title: UMCU-HC-1-0204-TR813


title: C3-12N


title: UMCU-HC-1-0212-TR818


title: UMCU-HC-1-0203-TR814


title: UMCU-HC-1-0201-TR821


title: UMCU-HC-1-0198-TR820


title: UMCU-HC-1-0210-TR819


title: UMCU-HC-1-0211-TR826


title: E12-24N


title: Vumc-GBM-follow-up-VU554t0-TR1658

value: Glioma


title: Vumc-GBM-follow-up-VU548t0-TR1652


title: Vumc-GBM-follow-up-VU535t0-TR1660


title: UMCU-HC-1-0209-TR823


title: UMCU-HC-1-0205-TR811


title: UMCU-HC-1-0207-TR817


title: UMCU-HC-1-0202-TR812


title: UMCU-HC-1-0199-TR825


title: UMCU-HC-1-0200-TR816


title: Vumc-GBM-follow-up-VU502t0-TR1661


title: UMCU-HC-1-0197-TR824


title: RAD-ProsBlad-56297-TR2823

value: Urothelial Carcinoma


title: Vumc-GBM-follow-up-VU559t0-TR1659


title: Vumc-GBM-follow-up-VU527t0-TR1651


title: RAD-ProsBlad-55450-TR2860


title: Vumc-GBM-477t0


title: Vumc-GBM-follow-up-VU523t0-TR1650


title: RAD-ProsBlad-55178-TR2753


title: Vumc-GBM-follow-up-VU501t0


title: UMCU-unstAP-2-0586-TR2085

value: Angina Pectoris


title: Vumc-GBM-follow-up-VU474t0-TR1569


title: RAD-ProsBlad-54898-TR2752


title: UMCU-unstAP-2-0622-TR2086


title: Vumc-GBM-493t0


title: Vumc-GBM-follow-up-VU472t0-TR1556


title: RAD-ProsBlad-55613-TR2755


title: UMCU-unstAP-3-1120-TR2056


title: Vumc-GBM-follow-up-VU551t0-TR1653


title: Vumc-GBM-follow-up-VU423t0-TR1547


title: UMCU-unstAP-2-0594-TR2088


title: RAD-ProsBlad-56114-TR2822


title: UMCU-unstAP-3-1135-TR2057


title: UMCU-unstAP-3-1076-TR2055


title: UMCU-unstAP-1-0091-TR2087


title: UMCU-unstAP-3-1034-TR2053


title: Vumc-GBM-491t0


title: UMCU-2-0585-AP-unstable-TR949


title: UMCU-unstAP-2-0649-TR2051


title: UMCU-2-0570-AP-unstable-TR948


title: UMCU-unstAP-3-1058-TR2054


title: UMCU-stableAP-1-0071-TR2050


title: UMCU-2-0536-AP-unstable-TR945


title: UMCU-stableAP-1-0032-TR2046


title: UMCU-2-0566-AP-unstable-TR947


title: UMCU-2-0540-AP-unstable-TR946


title: UMCU-2-0533-AP-unstable-TR944


title: UMCU-stableAP-1-0031-TR2058


title: UMCU-1-0024-AP-stable-TR943


title: UMCU-stableAP-1-0033-TR2049


title: NKI-GIST-1694-TR2291

value: Sarcoma


title: NKI-GIST-2050-TR2290


title: MGH-Renal-R24-TR2839

value: Renal Cell Carcinoma


title: UMCU-1-0056-AP-stable-TR936

value: Thrombocytes


title: UMCU-1-0002-AP-stable-TR937


title: UMCU-1-0018-AP-stable-TR942


title: UMCU-unstAP-2-0652-TR2052


title: MGH-Renal-R9-TR2866


title: UMCU-1-0006-AP-stable-TR938


title: MGH-Renal-R15-TR2868


title: MGH-Renal-R8-TR2865


title: MGH-Renal-R7-TR2864


title: MGH-Renal-R5-TR2863


title: NKI-GIST-3345-TR2530


title: MGH-Renal-R4-TR2862


title: MGH-Renal-R26-TR2841


title: MGH-Renal-R25-TR2840


title: MGH-Renal-R3-TR2861


title: MGH-Renal-R23-TR2838


title: MGH-Renal-R21-TR2836


title: MGH-Renal-R13-TR2830


title: MGH-Renal-R10-TR2827


title: MGH-Renal-R18-TR2833


title: Cath-Ova-CZE-012-TR2280

source_name: Blood_Platelets_CZE 012


title: MGH-Renal-R1-TR2825


title: MGH-Renal-R11-TR2828


title: MGH-OVARY-O21-TR676


title: Vumc-BRMETA-18-TR2163


title: MGH-Renal-R2-TR2826


title: Vumc-P-PH-001-095-TR2581

value: Pulmonary Hypertension


title: Vumc-P-PH-001-102-TR2564


title: Vumc-P-PH-001-091-TR2664


title: Vumc-P-PH-001-101-TR2563


title: Vumc-P-PH-001-100-TR2562


title: Vumc-P-PH-001-099-TR2561


title: Vumc-P-PH-001-088-TR2576


title: Vumc-P-PH-001-097-TR2583


title: Vumc-P-PH-001-096-TR2582


title: Vumc-P-PH-001-080-TR2572


title: Vumc-P-PH-001-094-TR2580


title: Vumc-P-PH-001-098-TR2584


title: Vumc-P-PH-001-092-TR2579


title: Vumc-P-PH-001-077-TR2570


title: Vumc-P-PH-001-089-TR2577


title: Vumc-P-PH-001-070-TR2558


title: Vumc-P-PH-001-103-TR2565


title: Vumc-P-PH-001-072-TR2559


title: Vumc-P-PH-001-074-TR2560


title: Vumc-P-PH-001-062-TR2551


title: Vumc-P-PH-001-078-TR2571


title: Vumc-P-PH-001-081-TR2573


title: Vumc-P-PH-001-087-TR2663


title: Vumc-P-PH-001-076-TR2569


title: Vumc-P-PH-001-067-TR2556


title: Vumc-P-PH-001-066-TR2555


title: Vumc-P-PH-001-065-TR2554


title: Vumc-P-PH-001-058-TR2548


title: Vumc-P-PH-001-090-TR2578


title: Vumc-P-PH-001-064-TR2553


title: Vumc-P-PH-001-055-TR2546


title: Vumc-P-PH-001-053-TR1461


title: Vumc-P-PH-001-060-TR2550


title: Vumc-P-PH-001-082-TR2574


title: Vumc-P-PH-001-042-TR1423


title: Vumc-P-PH-001-050-TR1460


title: Vumc-P-PH-001-059-TR2549


title: Vumc-P-PH-001-057-TR2547


title: Vumc-P-PH-001-041-TR1422


title: Vumc-P-PH-001-034-TR1512-seq2


title: Vumc-P-PH-001-029-TR1434


title: Vumc-P-PH-001-026-TR1408


title: Vumc-P-PH-001-035-TR1418


title: Vumc-P-PH-001-023-TR1407


title: Vumc-P-PH-001-028-TR1410


title: Vumc-P-PH-001-037-TR1420


title: Vumc-P-PH-001-033-TR1417


title: Vumc-P-PH-001-022-TR1511


title: Vumc-P-PH-001-027-TR1409


title: Vumc-P-PH-001-014-TR1459


title: Vumc-P-PH-001-020-TR1509


title: Vumc-P-PH-001-012-TR1506


title: Vumc-P-PH-001-017-TR1507


title: Vumc-P-PH-001-010-TR1505-seq2


title: Vumc-P-PH-001-011-TR1458


title: Vumc-P-PH-001-039-TR1421


title: Vumc-P-PH-001-002-TR1391


title: Vumc-P-PH-001-009-TR1397


title: Vumc-P-PH-001-006-TR1457


title: Vumc-P-PH-001-008-TR1504


title: Vumc-P-PH-001-001-TR1502


title: Vumc-P-PH-001-005-TR1503


title: Vumc-P-PH-001-003-TR1392


title: Umea-Pca-912-32-TR575


title: Umea-Pca-169-36-TR571


title: Umea-Pca-169-33-TR570


title: Umea-Pca-1034-36-TR574


title: Umea-Pca-1034-33-TR572


title: Umea-Pca-1034-35-TR573


title: Vumc-P-PH-001-018-TR1413


title: Umea-Pca-91235-TR540


title: Umea-Pca-96331-TR543


title: Umea-Pca-96334-TR544


title: Umea-Pca-93431-TR542


title: Umea-Pca-96335-TR545


title: Umea-Pca-67833-TR535


title: Umea-Pca-16934-TR539


title: Vumc-P-PH-001-007-TR1395


title: Umea-Pca-16935-TR538


title: Umea-Pca-91232-TR541


title: Umea-Pca-67834-TR536


title: Umea-Pca-16931-TR537


title: Umea-Pca-116231-TR546


title: RAD-ProsBlad-56704-TR2824


title: RAD-ProsBlad-55813-TR2756


title: RAD-ProsBlad-55511-TR2754


title: Vumc-xIPMN111-20161026-TR2631

value: Pancreatic Cancer


title: Vumc-IPMN-2015094-TR330


title: RAD-ProsBlad-54854-TR2751


title: Vumc-PDAC-96-20161160-TR2681


title: Vumc-PDAC-86-2016787-TR2677


title: Vumc-PDAC-88-2016116-TR2679


title: Vumc-PDAC-76-20162283-TR2622


title: Vumc-PDAC-72-20161131-TR2673


title: Vumc-PDAC-74-201611300-TR2621


title: Vumc-PDAC-71-20161132-TR2620


title: Vumc-PDAC-6-2016397-TR2662


title: Vumc-PDAC-70-2016112-TR2672


title: Vumc-PDAC-57-2016398-TR2670


title: Vumc-PDAC-56-2016723-TR2619


title: Vumc-PDAC-115-2015098-TR2661


title: Vumc-PDAC-64-20166377-TR2671


title: Vumc-PDAC-103-2015470-TR2657


title: Vumc-PDAC-109-20151978-TR2660


title: Vumc-PDAC29-2016236-TR2063


title: Umea-Pca-67831-TR534


title: Vumc-PDAC-105-2015197-TR2659


title: Vumc-PDAC91-2015801-TR2060


title: Vumc-PDAC8-20160983-TR2059


title: Vumc-PDAC-102-2015897-TR2656


title: Vumc-PAAD-95-2015297-TR1922


title: Vumc-PDAC-100-20161166-TR2624


title: Vumc-PAAD22-20166996-TR1924

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico  with the counts from Vumc-HD-41-201669969-TR2669_S36_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.


title: Vumc-PAAD-15-2016698-TR1925


title: Vumc-exIPMN-84-2015196-TR1926


title: Gron-PDAC-P31t30-TR1228


title: Gron-PDAC-P24t0-TR1223


title: Vumc-PDAC-113-2016487-TR2650


title: Vumc-PDAC-79-TR1024


title: Gron-PDAC-P29t0-TR1225


title: Vumc-PAAD-18-2016599-TR1923


title: Gron-PDAC-P29t30-TR1226


title: Vumc-PDAC-71-TR1014


title: Vumc-PDAC-64-TR992


title: Vumc-PDAC-74-TR1015


title: Vumc-PDAC-54-TR1025


title: Vumc-PDAC-53-TR990


title: Vumc-PDAC-60-TR991


title: Vumc-PDAC-50-TR989


title: Vumc-PDAC-49-TR967


title: Vumc-PDAC-41-TR1030


title: Vumc-PDAC94-2015610-TR2061


title: Vumc-PDAC-37-TR994


title: Vumc-PDAC-33-TR1018


title: Vumc-PDAC-27-TR963


title: Vumc-PDAC-26-TR1013


title: Vumc-PDAC-30-TR988


title: Vumc-PDAC-25-TR987


title: Vumc-PDAC-21-TR1011


title: Gron-PDAC-P31t0-TR1227


title: Gron-PDAC-P24t30-TR1224


title: Pisa-PDAC-2015PUC-TR1038


title: Pisa-PDAC-2015GAB-TR964


title: Pisa-exIPMN-2015TAG-TR971


title: Pisa-PDAC-2015FRA-TR1017


title: Pisa-exIPMN-2015CEC-TR969


title: MGH-OVARY-38-TR1367

value: Ovarian Cancer


title: MGH-OVARY-43-TR1263


title: Vumc-PDAC-44-TR995


title: Vumc-PDAC-17-TR985


title: Pisa-PDAC-2015LOA-TR965


title: MGH-OVARY-35-TR1256


title: MGH-OVARY-34-TR1265


title: Vumc-PDAC-22-TR1012


title: MGH-OVARY-O7-TR858


title: MGH-OVARY-P5-TR859


title: MGH-Ovary-O3-TR839


title: MGH-Ovary-O4-TR840


title: MGH-OVARY-O6-TR857


title: UMCG-esoph-P94t0-TR2684

value: Esophageal Cancer


title: Vumc-exIPMN-56-TR1043


title: Vumc-Brain-metastasis-VU570-TR1603


title: VUMC-EPI-036-TR2843


title: VUMC-EPI-038-TR2845


title: VUMC-EPI-035-TR2842


title: MGH-OVARY-40-TR1260


title: Vumc-EPI-041-TR2869


title: Vumc-EPI-034-TR2133


title: Vumc-EPI-027-TR2126


title: MGH-OVARY-37-TR1266


title: Vumc-EPI-043-TR2871


title: Vumc-EPI-025-TR2124


title: Vumc-EPI-029-TR2128


title: Vumc-EPI-026-TR2125


title: MGH-Ovary-O5-TR841


title: Pisa-PDAC-2015PRO-TR966


title: Vumc-EPI-024-TR2123


title: Pisa-exIPMN-2015CUF-TR1044


title: Vumc-EPI-VU627t0-TR2134


title: Vumc-EPI-VU667t0-TR2135


title: Vumc-EPI-032-TR2131


title: Vumc-EPI-042-TR2870


title: Vumc-EPI-017-TR1584


title: Vumc-EPI-030-TR2129


title: Vumc-GBM-626-TR1452


title: Vumc-EPI-020-TR1526


title: Vumc-EPI-018-TR1524


title: Vumc-EPI-010-TR1426


title: Vumc-EPI-019-TR1525


title: Vumc-EPI-016-TR1436


title: Vumc-EPI-028-TR2127


title: Vumc-EPI-022-TR1438


title: Vumc-EPI-023-TR2122


title: Vumc-EPI-011-TR1465


title: Vumc-EPI-014-TR1427


title: Vumc-EPI-007-TR1463


title: Vumc-EPI-002-TR1462


title: Vumc-EPI-033-TR2132


title: Vumc-EPI-016-TR1437


title: Vumc-EPI003-TR797


title: Vumc-EPI004-TR798


title: Vienna-CRC-Vien-13-TR2991

value: Bowel Disease


title: Vienna-CRC-Vien-18-TR2996

value: nonMalignant


title: Vumc-HD-41-201669969-TR2669


title: Vumc-HD-42-2016395-TR2690


title: Vienna-CRC-Vien-5-TR2952


title: Vumc-IPMN-80-20161534-TR2675


title: Vumc-IPMN-55-2016574-TR2634


title: Vumc-EPI-009-TR1464


title: Vumc-IPMN-47-20161073-TR2632


title: Vumc-IPMN-54-2016450-TR2633


title: Vumc-IPMN-49-2016907-TR2651


title: Vumc-IPMN-89-2015996-TR1928


title: Vumc-IPMN-57-TR1039


title: Vumc-IPMN-6215176-TR331


title: Vumc-EPI-001-TR1425


title: Vumc-EPI-015-TR1435


title: Vumc-ORC-01-038-TR2373

value: Colorectal Cancer


title: Vienna-CRC-Vien-8-TR2955


title: Vumc-EPI006-TR800


title: Vumc-EPI005-TR799


title: Vumc-ORC-01-033-TR2370


title: Vumc-ORC-01-018-TR2357


title: Vumc-EPI008-TR802


title: Vumc-ORC-01-043-TR2376


title: Vumc-ORC-01-039-TR2374


title: Vumc-ORC-01-011-TR2331


title: Vumc-ORC-01-017-TR2356


title: Vumc-ORC-01-005-TR2327


title: VUMC-EPI-040-TR2847


title: Vumc-ORC-01-030-TR2367


title: Vumc-ORC-01-042-TR2375


title: Vumc-ORC-01-032-TR2369


title: Vumc-ORC-01-009-TR2329


title: Vumc-ORC-01-010-TR2330


title: Vumc-ORC-01-025-TR2363


title: Vumc-ORC-01-047-TR2379


title: Vumc-ORC-01-027-TR2365


title: Vumc-ORC-01-024-TR2362


title: Vumc-ORC-01-035-TR2371


title: Vumc-ORC-01-022-TR2360


title: Vumc-ORC-01-023-TR2361


title: Vumc-ORC-01-003-TR2326


title: Vumc-ORC-01-029-TR2366


title: Vumc-ORC-01-012-TR2332


title: Vumc-ORC-01-001-TR2324


title: Vumc-ORC-01-021-TR2359


title: Vum-chPan-44-2016109-TR2636


title: Vumc-ORC-01-014-TR2334


title: Vumc-BRMETA-15-TR2160


title: Vumc-chPan-38-2016720-TR2689


title: Vumc-ORC-01-013-TR2333


title: Vumc-ORC-01-002-TR2325


title: Vumc-chPan-117-2015563-TR1945


title: Vumc-chPan-84-2016313-TR2652


title: Vumc-ChronPan-61-TR1047


title: Vumc-chPan-37-20161051-TR2688


title: Vumc-chPan93-201611735-TR2653


title: Vumc-ChronPan-59-TR1046


title: Vumc-ChronPan-29-TR1045


title: Vumc-ORC-01-031-TR2368


title: Vumc-ChronPan-21-2016119-TR1947


title: VUMC-CHOL-51-20161059-TR2977

value: Cholangiocarcinoma


title: Vumc-PDAC-99-20161180-TR2623

value: Malignant


title: VUMC-CHOL-89-2016719-TR2979


title: VUMC-CHOL-78-2016114-TR2978


title: Vumc-ORC-01-020-TR2358


title: VUMC-CHOL-43-2016734-TR2933


title: VUMC-CHOL-81-2015952-TR2899


title: VUMC-CHOL-2-20171209-TR2928


title: VUMC-CHOL-48-2015037-TR2898


title: VUMC-Chol-86-20155964-TR3021


title: VUMC-Chol-9-2015892-TR3017


title: VUMC-Chol-52-2015162-TR3002


title: VUMC-Chol-5-2017263-TR3016


title: VUMC-Chol-108-2015039-TR2997


title: MGH-Chol-Bd-11-TR2109


title: VUMC-CHOL-79--20161140-TR3013


title: VUMC-Chol-17-20171234-TR3000


title: VUMC-Chol-24-2017120-TR3001


title: MGH-Chol-Bd-16-TR2111


title: MGH-Chol-Bd-4-TR2078


title: MGH-Chol-Bd-2-TR2077


title: MGH-Chol-Bd-7-TR2081


title: MGH-Chol-Bd-1-TR2076


title: AMC-Chol-017-TR2100


title: AMC-Chol-025-TR2107


title: AMC-Chol-013-TR2096


title: AMC-Chol-022-TR2104


title: VUMC-CHOL-33-2016716-TR2931


title: AMC-Chol-024-TR2106


title: Vumc-Chol-2015793


title: AMC-Chol-007-TR2090


title: MGH-BrCa-86-TR1197

value: Breast Cancer


title: AMC-Chol-006-TR2089


title: MGH-CRC-BRAF4-TR547


title: AMC-Chol-004-TR2074


title: AMC-Chol-010-TR2093


title: MGH-BrCa-97-TR1198


title: AMC-Chol-008-TR2091


title: MGH-BrCa-82-TR1199


title: MGH-BrCa-590-TR1193


title: MGH-BrCa-55-TR1189


title: MGH-BrCa-85-TR1196


title: MGH-BrCa-6-TR1200


title: MGH-BrCa-50-TR1179


title: MGH-BrCa-61-TR1195


title: MGH-BrCa-564-TR1191


title: MGH-BrCa-33-TR1186


title: MGH-BrCa-21-TR1177


title: MGH-BrCa-59-TR1192


title: MGH-BrCa-42-TR1187


title: AMC-Chol-023-TR2105


title: MGH-BrCa-16-TR1176


title: MGH-BrCa-454-TR1188


title: MGH-BrCa-48-TR1178


title: MGH-BrCa-10-TR1184


title: MGH-BrCA-100-TR1185


title: MGH-BrCa-15-TR1175


title: MGH-BrCa-08-TR1174


title: MGH-BrCa-03-TR1173


title: MGH-BrCa-60-TR1194


title: MGH-BrCa-P9-TR700


title: MGH-BrCa-H110-TR851


title: MGH-BrCa-P13-TR704


title: MGH-BrCa-H115-TR662


title: MGH-BrCa-P12-TR703


title: MGH-BrCa-P10-TR701


title: MGH-BrCa-P11-TR702


title: MGH-BrCa-H125-TR698


title: MGH-BrCa-H124-TR697


title: MGH-BrCa-H121-TR681


title: MGH-BrCa-H120-TR680


title: MGH-BrCa-H118-TR665


title: MGH-BrCa-P45-TR627


title: MGH-BrCa-P39-TR623


title: MGH-BrCa-P38-TR622


title: MGH-BrCa-P32-TR618


title: MGH-BrCa-P43-TR626


title: MGH-BrCa-P42-TR625


title: MGH-BrCa-P37-TR621


title: MGH-BrCa-P17-TR569


title: MGH-BrCa-P3-TR568


title: MGH-BrCa-P21-TR614


title: MGH-BrCa-P16-TR613


title: MGH-BrCa-K16-TR553


title: MGH-BrCa-P33-TR619


title: MGH-BrCa-H64-TR607


title: MGH-BrCa-H57-TR410


title: MGH-BrCa-H56-TR603


title: MGH-BrCa-P27-TR498


title: MGH-BrCa-P25-TR497


title: MGH-BrCa-H128-TR635


title: MGH-BrCa-H63-TR-491


title: MGH-BrCa-H114-TR630


title: MGH-BrCa-H119-TR679


title: MGH-BrCa-H38-TR467


title: MGH-BrCa-H-75


title: MGH-BrCa-H-80


title: MGH-BrCa-H-68


title: MGH-BrCa-H-74


title: MGH-BrCa-H35-TR490


title: MGH-BrCa-H-67


title: MGH-BrCa-H-59


title: MGH-BrCa-H-66


title: MGH-BrCa-H-11


title: Vumc-BRMETA-VU692-TR2166


title: Vumc-BRMETA-16-TR2161


title: Vumc-Brain-metastasis-BRMETA3t0-TR1543


title: Vumc-BRMETA-VU654-TR2158


title: Vumc-HD-95-2016532-TR2680

value: Pancreatic Disease


title: Vumc-HD-73-2016736-TR2628


title: Vumc-BRMETA-13-TR1451


title: VUMC-CHOL-5-2016898-TR2934


title: VUMC-CHOL-35-2016897-TR2932


title: VUMC-CHOL-123-2015798-TR2927


title: MGH-BrCa-K22-TR473


title: VUMC-Chol-65-2015352-TR3018


title: VUMC-Chol-59-2016241-TR3003


title: VUMC-Chol-114-2015198-TR2998


title: AMC-Chol-011-TR2094


title: MGH-Chol-Bd-9-TR2108


title: MGH-Chol-Bd-6-TR2080


title: MGH-Chol-Bd-14-TR2110


title: MGH-Chol-Bd-5-TR2079


title: AMC-Chol-020-TR2102


title: AMC-Chol-016-TR2099


title: AMC-Chol-012-TR2095


title: AMC-Chol-015-TR2098


title: AMC-Chol-021-TR2103


title: Vumc-BRMETA-12-TR1450


title: AMC-Chol-005-TR2075


title: AMC-Chol-003-TR2073


title: AMC-Chol-002-TR2072


title: Vumc-Chol-2015092


title: Radb-GBM-N13-18-TR2139

value: Glioma


title: Maas-GBM-M00011-TR2119


title: MGH-HGG-B107-TR1683


title: Vumc-LGG-VU658-TR2153


title: VUMC-CHOL-30-2016288-TR2930


title: Vumc-LGG-VU605-TR1663


title: Vumc-LGG-VU603-TR1664


title: Vumc-LGG-VU683-TR2156


title: MGH-LGG-B103-TR1682


title: Vumc-GBM-467-TR1453


title: Vumc-LGG-VU509-1-TR617


title: Vumc-LGG-VU528-TR612


title: Vumc-LGG-VU427-T03-TR582


title: Vumc-LGG-498-1-TR556


title: Vumc-LGG-503-1-TR557


title: Vumc-LGG-VU473-TR510


title: NKI-Sarc-2914-TR2528


title: AMC-Chol-009-TR2092


title: NKI-Sarc-2913-TR2527


title: NKI-GIST-1986-TR2293


title: NKI-Sarc-2576-TR2445


title: NKI-Sarc-1773-TR2440


title: NKI-Sarc-2503-TR2447


title: NKI-Sarc-1807-TR2438


title: NKI-GIST-4533-TR2302


title: NKI-GIST-4480-TR2301


title: NKI-GIST-3558-TR2299


title: NKI-Sarc-1699-TR2439


title: NKI-GIST-2703-TR2297


title: NKI-GIST-2601-TR2296


title: NKI-GIST-2505-TR2295


title: NKI-GIST-3911-TR2289


title: NKI-GIST-2891-TR2298


title: NKI-GIST-1687-TR2286


title: Vumc-MM-SMM5-TR2470

value: Multiple Myeloma


title: Vumc-MM-SMM4-TR2469


title: Vumc-MM-SMM2-TR2467


title: Vumc-MM-SMM1-TR2466


title: Vumc-MM-SMM3-TR2468


title: Vumc-MM-MM8-TR2428


title: Vumc-MM-MM5-TR2425


title: NKI-Sarc-2607-TR2526


title: Vumc-MM-MM3-TR2423


title: Vumc-MM-MM4-TR2424


title: Vumc-MM-MM20-TR2464


title: Vumc-MM-MM21-TR2465


title: Vumc-MM-MM18-TR2462


title: NKI-GIST-3942-TR2300


title: Vumc-MM-MM16-TR2460


title: Vumc-MM-MM17-TR2461


title: Vumc-MM-MM15-TR2459


title: Vumc-MM-MM14-TR2458


title: Vumc-MM-MM1-TR2421


title: NKI-GIST-2061-TR2287


title: Vumc-MM-MM10-TR2454


title: Vumc-MM-MM12-TR2456


title: Vumc-MM-MM13-TR2457


title: Vienna-CRC-Vien-12-TR2976


title: Vienna-CRC-Vien-6-TR2953


title: Vienna-CRC-Vien-16-TR2994


title: Vumc-ORC-01-015-TR2355


title: Vumc-MM-MM7-TR2427


title: Vienna-CRC-Vien-7-TR2954


title: Vienna-CRC-Vien-9-TR3009


title: Vienna-CRC-Vien-3-TR2950


title: Vumc-MM-MM19-TR2463


title: MGH-CRC-BRAF6-TR465


title: MGH-CRC-BRAF5-TR548


title: Cath-Ova-CZE-032-TR2717

source_name: Blood_Platelets_CZE 032


title: Cath-Ova-CZE-038-TR2721

source_name: Blood_Platelets_CZE 038


title: Vumc-ORC-01-006-TR2328


title: Cath-Ova-CZE-031-TR2716

source_name: Blood_Platelets_CZE 031


title: MGH-CRC-368


title: Cath-Ova-CZE-017-TR2285

source_name: Blood_Platelets_CZE 017


title: Cath-Ova-CZE-014-TR2282

source_name: Blood_Platelets_CZE 014


title: MGH-MELA-M97-TR598

value: Melanoma


title: MGH-MELA-M96-TR597


title: Cath-Ova-CZE-022-TR2770

source_name: Blood_Platelets_CZE 022


title: MGH-MELA-M93-TR599


title: MGH-MELA-M95-TR596


title: MGH-MELA-M84-TR567


title: MGH-MELA-M94-TR595


title: MGH-MELA-M92-TR608


title: MGH-MELA-M83-TR594


title: Vumc-ORC-01-044-TR2377


title: MGH-MELA-M78-TR591


title: MGH-MELA-M75-TR4566


title: MGH-MELA-M76-TR589


title: Cath-Ova-CZE-037-TR2720

source_name: Blood_Platelets_CZE 037


title: MGH-MELA-M11-TR602


title: MGH-MELA-M73-TR588


title: MGH-NSCLC-M16-TR528


title: MGH-MELA-M91-TR475


title: MGH-MELA-M53-TR494


title: MGH-MELA-M74-TR565


title: Cath-Ova-CZE-001-TR2270

source_name: Blood_Platelets_CZE 001


title: MGH-MELA-M70-TR495


title: MGH-MELA-M-89


title: MGH-MELA-M18-TR493


title: MGH-MELA-M-63


title: MGH-MELA-M-88


title: Vumc-HNSCC-HN-637-TR1942

value: Head and Neck Cancer


title: MGH-MELA-M-48


title: MGH-MELA-M81-TR593


title: Vumc-HNSCC-HN-636-TR1941


title: Vumc-HNSCC-HN-628-TR1980


title: Vumc-HNSCC-HN-633-TR1940


title: Vumc-HNSCC-HN-627-TR1979


title: MGH-MELA-M77-TR590


title: Vumc-HNSCC-HN-625-TR1919


title: Vumc-HNSCC-HN-626-TR1920


title: Vumc-HNSCC-HN-623-TR1978


title: Vumc-HNSCC-HN-622-TR1977


title: Vumc-HNSCC-HN-621-TR1918


title: Vumc-headNeck-615-TR1078


title: Vumc-headNeck-612-TR1076


title: Vumc-HNSCC-HN-618-TR1975


title: Vumc-headNeck-606-TR1091


title: MGH-MELA-M-37


title: Vumc-headNeck-603-TR1071


title: Vumc-headNeck-596-TR1067


title: Vumc-HNSCC-HN-640-TR1943


title: Vumc-headNeck-601-TR1070


title: Vumc-HNSCC-HN-635-TR1921


title: Vumc-headNeck-592-TR1055


title: Vumc-headNeck-595-TR1057


title: Vumc-headNeck-599-TR1069


title: Vumc-headNeck-591-TR1054


title: Vumc-headNeck-586-TR1049


title: Vumc-headNeck-588-TR1051


title: MGH-BrCa-P35-TR620


title: Vumc-headNeck-582-TR1090


title: Vumc-PDAC-87-20161119-TR2678


title: Vumc-exIPMN-58-2016494-TR2629


title: MGH-BrCa-H76-TR469


title: Vumc-headNeck-613-TR1077


title: Vumc-PDAC-83-20161151-TR2676


title: Vumc-PDAC-77-20160632-TR2674


title: Vumc-PDAC-46-2016106-TR2618


title: Vumc-headNeck-607-TR1073


title: Vumc-PDAC-40-2016107-TR2617


title: Vumc-PDAC-28-2016105-TR2668


title: Vumc-headNeck-598-TR1068


title: Vumc-PDAC-19-2016973-TR2616


title: Vumc-PDAC-116-2015476-TR2691


title: Vumc-PDAC-108-20161187-TR2687


title: Vumc-PDAC-104-2016118-TR2626


title: Vumc-PDAC-106-2016132-TR2682


title: Vumc-PDAC-112-20161199-TR2655


title: Vumc-PDAC-103-2016634-TR2625


title: Vumc-PDAC-66-TR1037


title: Vumc-PDAC-104-2015046-TR2658


title: Vumc-headNeck-590-TR1053


title: MGH-BrCa-P28-TR499


title: Vumc-PDAC-18-TR986


title: Vumc-PDAC-36-TR993


title: MGH-NSCLC-L217-TR2499

value: Non-Small-Cell Lung Cancer


title: Vumc-NSCLC-577-TR2483

value: Thrombocytes


title: Vumc-exIPMN-3-TR1042


title: Vumc-NSCLC-859-TR2503


title: Vumc-NSCLC-724-TR2186


title: NKI-NSCLC-2571-TR2225


title: NKI-NSCLC-2149-TR1848


title: Vumc-NSCLC-533-TR2182


title: NKI-NSCLC-1574-TR1836


title: NKI-NSCLC-281-TR1834


title: NKI-NSCLC-1114-TR1838


title: Vumc-NSCLC-130-TR952


title: Vumc-NSCLC-211-TR903


title: MGH-NSCLC-L158-TR913


title: MGH-NSCLC-L173-TR915


title: MGH-NSCLC-L180-TR919


title: MGH-NSCLC-L10-TR606


title: MGH-NSCLC-L145-TR912


title: Vumc-NSCLC-244-TR1003


title: MGH-NSCLC-L59-TR522


title: MGH-NSCLC-L65-TR523


title: Vumc-PDAC-32-TR1009


title: NKI-NSCLC-107-508-TR734


title: Vumc-NSCLC-092


title: Vumc-NSCLC-081


title: MGH-NSCLC-L01-TR458