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• CBD-RAW-REPERTOIRE-T: T cell bulk repertoire sequence files

  fastq and filtered fasta files for T-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007961

• COVID-19 scRNA-seq, TCR-seq and BCR-seq

  COVID-19 scRNA-seq, TCR-seq and BCR-seq for 291 samples collected from 109 patients. Among 291 samples, 249 of them have two libraries (sequencing runs) for each assay, while 42 have only one library.

  Dataset EGAD00001007995

• HCC cfMeDIP-seq

  This dataset comprises 406 raw fastq files derived from 203 plasma cfDNA samples from 90 patients diagnosed with hepatocellular carcinoma (HCC). The samples include 90 baseline HCC (b-HCC) samples, collected during liver transplant or resection surgeries, and 113 postoperative follow-up (f-HCC) samples. For each sample, 10ng of cfDNA was used for library preparation utilizing cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on Illumina NovaSeq 6000 or HiSeq 2500 platform with paired-end 150-bp (NovaSeq) or 125-bp (HiSeq) model for ~100 million reads per sample.

  Dataset EGAD50000000651

• Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer

  The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. We aim to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations.

  Study EGAS00001005981

• Long-read sequencing for cell-free DNA analysis (mouse)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced with the two platforms.

  Study EGAS00001006329

• Cancer sequencing for somatic variant calling

  This dataset includes WES and RNAseq for 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy tissues, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems.

  Study EGAS00001007101

• Sequencing data for oesophageal and related samples - Ogden et al (WGS, RNA)

  Data supporting: "Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling" Ogden et al. WGS for tumour and normal samples. RNAseq for tumour samples.

  Dataset EGAD00001007496

• LUMC Department Biomedical Data Sciences, Osteoarthritis group

  Committee to control single nucleus multiomics data generated within the project Single Cell Microgel embedded iPS-cells to map molecular variability of cell differentiation using a systems biology approach (SCI-MAP) at the LUMC.

  Dac EGAC50000000644

• WGBS of stepwise-edited melanoma model

  This dataset contains WGBS of a stepwise-edited, human melanoma model including in vitro samples and corresponding xenografts.

  Dataset EGAD50000001317

• Whole Genome Sequencing of 2 expanded clones from rhabdoid tumor case 3

  Whole Genome Sequencing of 2 expanded clones from a cell line derived from the rhabdoid tumor case 3 (2 WGS 20X)

  Dataset EGAD50000000240

• Nanopore sequencing of brain tumor tissue obtained by cavitating ultrasonic aspiration

  This dataset contains 21 pediatric brain tumor cases which where obtained during surgery using a cavitating ultrasonic aspiration and submitted to nanopore whole genome sequencing.

  Dataset EGAD50000000269

• Methylation profiling of CDS and ES tumor samples

  Methylation profiling of 9 CDS and ES tumor samples, using the approach described in "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dataset EGAD00010002760

• Assessing mitochondrial bioenergetics in coronary artery disease: A translational left ventricular tissue study in humans (The AMBITION study).

  Single nuclei transcriptomic data from the AMBITION study.

  Dataset EGAD00001011078

• Spatial Maps of Prostate Cancer Transcriptomes

  A total of 14 samples that has been analyzed with the Spatial Transcriptomics method. H&E stain can be sent if requested.

  Dataset EGAD00001004121

• Plasma-Seq follow-up CSPC4

  We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy.

  Dataset EGAD00001000396

• Case Report of a Leukemic Patient with Invasive Mucormycosis

  Whole exome sequencing of germline DNA was performed and subsequent polymorphisms in genes known and putatively involved in the innate immune response to fungi were identified

  Dataset EGAD00001001692

• RNAseq following stent placement and removal in a porcine model 

  This dataset includes 2*76bp RNA-seq reads from 9 pigs sequenced using Illumina NextSeq500.

  Dataset EGAD00001009783

• TDB-mediated activation of NK cells

  transcriptome analysis of NK cells sorted from PBMCs at baseline and after addition of a CD20 (B cell)-targeted T cell dependent bispecific antibody (TDB)

  Dataset EGAD00001010895

• Enhanced detection of circulating tumor DNA by fragment size analysis

  Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on sensitivity for detecting genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for non-invasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 cancer patients using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90–150 bp, and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90–150 bp improved detection of tumor DNA, with more than 2-fold median enrichment in >95% of cases, and more than 4-fold enrichment in > 10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with AUC> 0.99 compared to AUC < 0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91, compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection. This could reduce the required depth of cfDNA sequencing for clinical applications, earlier diagnosis and study of tumor biology.

  Study EGAS00001003258

• DAC for "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis"

  DAC for the data of "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis" with: • Holger Sültmann • h.sueltmann@dkfz.de • German Cancer Research Center (DKFZ) • Ann-Kathrin Daum • a.daum@dkfz.de • German Cancer Research Center (DKFZ)

  Dac EGAC50000000076

• Genetic Analysis of Tuberous Sclerosis Complex (TSC) Hypomelanotic Macules

  In this study we searched for mutations in the TSC1 and TSC2 genes in cultured melanocytes from individuals with the genetic disease Tuberous Sclerosis Complex.

  Study phs001236

• Progressive multifocal leukoencephalopathy (PML)

  We generated RNAseq, ATACseq, Multiomics and CITEseq for patients with Progressive multifocal leukoencephalopathy (PML) to profile the chromatin accessibility, transcriptional profiles and surface proteins at single-cell level.

  Study EGAS50000000139

• Circulating immune cell landscape in colorectal cancer patients

  To understand the circulating immune cells in colorectal cancer patients, we performed single-cell RNA sequencing for 14 PBMC samples from 14 colorectal cancer patients.

  Study EGAS50000000590

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 1), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000917

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 2), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000921