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• Single-Nuclei RNA-seq of healthy (post-mortem) and temporal lobe epilepsy (biopsy) subjects.

  To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects.

  Dataset EGAD00001006575

• Whole Exome sequencing data from Shwachman-Diamond syndrome bone marrow samples

  This dataset includes paired WES from bone marrow samples of patients with SDS and paired bone marrow-derived fibroblasts as a germline reference. Some patients have multiple samples collected serially over time. There are 74 BAM files included in this dataset.

  Dataset EGAD00001006815

• AfricanNeo WGS aDNA Dataset

  This dataset includes WGS data of 12 ancient individuals (97–688 years BP) from Zambia and South Africa, presented in Fortes-Lima et al. Nature 2023. Further details like C14-dates and archaeological descriptions were reported elsewhere (Meyer et al. Azania 2021; Steyn et al. African Archaeological Review 2022).

  Dataset EGAD00001011320

• Sequencing Data of Leukemic Samples

  Sequencing data of leukemic samples included in study. Including WES, WGS and targeted sequencing files from patients at diagnosis, remission and at relapse. The dataset includes samples from 52 pediatric patients, totaling 311 samples.

  Dataset EGAD00001015662

• Lindsey E. Jones et al. Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma. Neuro-Oncology Advances, 2020. We established robust, versatile, and well-characterized Patient Derived Cells (PDC) of an IDH1-mutant astrocytoma and an IDH1-mutant oligodendroglioma that represents defined evolutionary stages of chemotherapy-induced hypermutation. The PDCs retain tumor subtype defining features over time as well as classic hallmarks of cancer, including anchorage independent growth and cell immortality. The integrated phylogenies composed of PDCs,single-cell-derived PDCs, patient-derived xenografts, and corresponding spatiotemporal tumor tissue samples also provide new insight into the clonality, evolutionary pattern, and immense mutational load of hypermutated IDH mutant gliomas.

  IDH-mutant lower-grade gliomas can undergo malignant progression via temozolomide-driven hypermutation. Patient-derived cells (PDC) that model the genetically distinct hypermutated (HM) tumor subgroup are generally lacking, and few if any human brain tumor cell models are from defined evolutionary time points. Here, we characterize multiple PDC derived from independent surgical specimens of IDH1-mutant recurrences, including an ATRX and TP53-mutant astrocytoma and a 1p/19q co-deleted and TERT promoter-mutant oligodendroglioma. We determined the evolutionary time points represented by each PDC using exome sequencing and phylogenetic reconstruction, comparing the PDC and single cell clones of the PDC (scPDC) to multiple spatiotemporal tumor tissue samples, PDC-derived xenografts (PDX) and patient-matched blood. The tumor samples exhibited TMZ-induced mutagenesis and a branching pattern of evolution. We found clear evidence of two fully independent founder HM clones in the tumor tissue that are faithfully represented by independent PDC. The PDC, scPDC and PDX also shared the mutagenesis signature and represent the mid and later evolutionary time points of their corresponding tumors. The PDC maintained the tumor subtype-defining features over many passages, including heterozygosity of the IDH1 R132H mutation, production of 2-hydroxyglutarate (2-HG), and subtype-specific telomere maintenance mechanisms. The PDC from both tumors exhibited anchorage-independent growth in soft agar. The oligodendroglioma PDC formed infiltrative intracranial tumors with characteristic oligodendroglioma histology, initially with a long period to tumor formation. We conclude that the PDC, scPDC and PDX faithfully model the heterogeneous clonal origins of the corresponding tumor tissue. The multilevel analysis also provides new insight into the intratumoral heterogeneity and vast mutational load of HM glioma. The PDC from multiple evolutionary time points presented in the context of full clinical timelines may be useful to model evolution and intratumoral heterogeneity, important sources of therapeutic failure.

  Study EGAS00001003992

• Single cell RNA-seq and ATAC-seq of CD4+ T cells from blood and tumor of NSCLC patients

  This dataset contains fastq files for paired blood-tumor scRNA-seq samples from 5 NSCLC patients and paired blood-tumor scATAC-seq samples from 2 NSCLC patients, both sequenced with NovaSeq or Illumina HiSeq - Rapid Run.

  Dataset EGAD50000000424

• mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines

  mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines before and after siRNA-mediated knockdown of ADAM8 (n=5 cell lines), ADAM9 (n=7 cell lines) and ADAM15 (n=5 cell lines). Paired-end sequencing was performed on a NovaSeq (Illumina). Fastq and bam files are provided for each sample.

  Dataset EGAD50000000575

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

  This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001098

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Total RNAseq data from 8 patients with muscle invasive bladder cancer

  For this dataset we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The data consists of 8 sets of paired fastq files with accompanying UMI fastq files. Sequenced on the Illumina NoveSeq6000 platform using S2 flow cells (v1.5,2x150 cycles), with a mean yield of 313 million reads.

  Dataset EGAD50000001380

• snRNA-seq

  This dataset contains raw sequencing and processed data of single nuclei transcriptomes. The data were generated with 10x Chromium probe-based single-nucleus assay on FFPE tissues of 63 ST-EPN tumour resections. Raw data contain BAM (and BAM.BAI) files of the sequencing. Processed data contain aligned .h5 counts matrices as generated by 10x CellRanger for raw and filtered running options.

  Dataset EGAD50000001875

• ALS-FTD brain motor cortex single-nucleus RNA-seq of NeuN+ nuclei sorted for TDP-43 low vs. high

  A dataset of single-nucleus RNA-seq data of nuclei from the post-mortem human primary motor cortex from patients with ALS-FTD. The nuclei were sorted by flow cytomotetry into NeuN+ (neuronal) TDP-43 low vs. TDP-43 high fractions.

  Dataset EGAD50000002243

• ERDERA WES reanalysis - DPF1 Batch 2

  This dataset comprises processed genomic data from 733 samples, corresponding to 733 whole-exome sequencing experiments. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002331

• ERDERA WES reanalysis - DPF1 Batch 3

  This dataset comprises processed genomic data from 1243 samples, corresponding to 1243 whole-exome sequencing experiments. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002332

• ERDERA WES reanalysis - DPF1 Batch 4

  This dataset comprises processed genomic data from 1063 samples, corresponding to 1063 whole-exome sequencing experiments. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002389

• Single-cell DNA sequencing dataset of aplastic anemia and RCC (31 samples)

  This dataset contains raw single-cell DNA sequencing data generated from 31 patients with aplastic anemia using the Mission Bio Tapestri platform. Libraries were prepared with a targeted DNA amplicon panel and sequenced on an Illumina platform. These raw data capture single-cell variant profiles and clonal architecture and serve as the basis for downstream analysis of somatic mutations and clonal hematopoiesis.

  Dataset EGAD50000002189

• Whole genome DNA sequencing for two long-lived humans.

  Two long-lived human samples were sequenced to a mean 20x coverage genome wide. Sequencing was done using the Illumina hi-seq platform, alignment to GRCh37/hg19 reference genome was done using the BWA alignment tool.

  Study EGAS00001000877

• RData

  The file data.RData contains data objects needed to run the .rmd template that generates the manuscript's figures. These include ExpressionSets for the training and test sets, module content and annotations, PCA results, the lasso58 signature with coefficients, and Foundation Medicine CDKN2A copy-number alteration data.

  Dataset EGAD00001007585

• Genomic data of acute myeloid leukemia cases for integration with metabolomic analyses

  Whole exome sequencing (WES) data of paired (germline and leukemic) samples of 100 adult patients affected by acute myeloid leukemia. Targeted sequencing data of myeloid-related genes of 21 leukemia (not paired) samples from adult patients affected by acute myeloid leukemia.

  Dataset EGAD00001007941

• Epigenome of sorted human muscle stem cell

  This dataset contain RNA-seq, ChIP-seq, WGBS and ATAC-seq of 1 human muscle stem cell sample. NCAM+ITGB1+ CD31−CD45−CD34− were used as the sorting strategy for the sample. H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K36me3 and H3K9me3 are the targets of ChIP-seq.

  Dataset EGAD00001008686

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS BOs/normals)

  Dataset EGAD00001011255

• Dataset_for_linked_WES_and_WGS_data_from_EGAS00001004813 which belong also to EGAS00001005537 for germline controls of rare cancers

  WES/WGS sequencing data of 37 germline runs, which were uploaded to umbrella studies. The sequencing was always paired. The WGS sequencing was on HiSeq X Ten using the Illumina TruSeq DNA Nano Kit. The WES Sequencing was on HiSeq4000 with Agilent Sureselect V5+UTR.

  Dataset EGAD00001010046

• Genome Denmark Phase II - alignments

  Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).

  Dataset EGAD00001003157

• Genomic Profiling of Advanced Pancreatic Cancer to inform therapy - RNA-Seq unmapped reads

  Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer - Early Results from the COMPASS Trial - RNA-Seq unmapped reads

  Dataset EGAD00001003582