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• Single-cell CITE-seq and TCR-seq data from AIM⁺ HIV-1-specific T cells

  Single-cell sequencing data from 2 HIV-1 post-intervention controllers and 2 non-controllers reported in Fisher, Garcia, Frattari, Naasz, et al. Longitudinal samples were collected before antiretroviral therapy inititation, during suppressive therapy, and after analytical treatment interruption.

  Dataset EGAD50000002247

• RNA-seq transcriptome of bronchial brush samples from COPD and control

  Human subjects (COPD patients or apparently healthy controls) where investigated by bronchoscopy and a 5 mm brush was used to sample the subsegment airways of the right lung. The material obtained mainly consist of bronchial epithelial cells plus some contamination with leukocytes. For further details see Ziegler-Heitbrock et al, European Respiratory Journal, 40:823-829, 2012.

  Dataset EGAD00001002003

• Sequencing data for oesophageal / related samples - Kazachenka et al (DNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples

  Dataset EGAD00001011095

• BulkTCR-sequencing data from different human intestinal CD8 T cell subsets.

  5000 cells of each subset of CD8 T cells (CD103-KLRG1+, CD103-KLRG1- and CD103+ from LP and CD103+ IELs) were sorted into tubes. A modified SMART protocol was used in first-strand cDNA synthesis, and TCRalpha / TCRbeta genes were amplified in two rounds of semi-nested PCR reaction, following the method described in detail in Risnes et al., 2018.

  Dataset EGAD00001005049

• Genotype data

  This dataset contains the imputed genotypes for 197 individuals. All individuals were genotyped with the Illumina HumanCoreExome-24 array. The individuals were phased with SHAPEIT and imputed to the 1000 Genomes Project Phase III using IMPUTE2. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005038

• RNA sequencing on colonic biopsies from inflammatory bowel disease patients treated with vehicle control, MEK inhibitor, or infliximab

  This dataset consists of RNA sequencing data (FASTQs) from intestinal mucosal biopsies from 9 IBD patients. All patients endoscopically active disease and were not receiving immunosuppressive or biologic therapies. All biopsies (6 per donor) were collected from a single inflamed site. Biopsies were cultured for 18 hours at an air-liquid interface in media containing either DMSO (vehicle control), PD-0325901 (0.5uM) or infliximab (10ug/ml; MSD) - two biopsies per condition. Sequencing was performed on a NovaSeq 6000 (100bp, PE reads). After 18 hours, biopsies were harvested and snap frozen. After lysis, RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NovaSeq 6000 (100bp, PE reads).

  Dataset EGAD00001011333

• Genomic Profiling of Peripheral T-cell Lymphoma

  Peripheral T-cell lymphomas (PTCLs) are malignant and highly aggressive hematologic tumors arising from mature post-thymic T cells. The diagnosis of PTCL includes diverse lymphoma subgroups, altogether accounting for about 15% of all non-Hodgkin lymphomas. Despite recent advances in uncovering the mutational landscape of PTCLs, the prognoses of most PTCLs remain poor. To overcome the limits of exome sequencing and identify new genomic abnormalities in PTCL, we performed RNAseq and whole genome sequencing. From our analyses, we identified a recurrent in-frame deletion (VAV1 Δ778-786) generated by a focal deletion-driven alternative splicing mechanism as well as novel VAV1 gene fusions (VAV1-THAP4, VAV1-MYO1F, and VAV1-S100A7). These genetic lesions result in increased activation of VAV1 catalytic-dependent (MAPK, JNK) and non-catalytic-dependent (nuclear factor of activated T cells, NFAT) VAV1 effector pathways. These results support an oncogenic role for VAV1 signaling in the pathogenesis of PTCL (Abate et al., 2017). Recently, we have also identified a novel chimeric oncogene, FYN-TRAF3IP2, in the RNA-seq and whole genome sequencing analyses. FYN-TRAF3IP2 leads to aberrant NF-κβ activity downstream of T-cell receptor signaling and induces NF-κβ-driven T-cell transformation when expressed in hematopoietic progenitors in mice. This novel gene fusion supports the oncogenic driver role of NF-κβ signaling in the pathogenesis of PTCL (Kim et al., in review).

  Study phs001962

• Single cell targeted DNA-sequencing (and antibody sequencing) of high hyperdiploid B-ALL

  This dataset contains all sequencing data of the publication "Single-cell DNA and Surface Protein Characterization of High Hyperdiploid Acute Lymphoblastic Leukemia at Diagnosis and During Treatment". We provide both the raw fastq-files as well as the processed data in the form of .h5 files. There are 13 patients: XJ176, XH135, XJ180, XI145, XI148, XI167, XI150, XJ175, XJ178, XI162, XF98, XG111 and XG115. Of 9 patients, also follow-up samples during/after treatment were sequenced: XJ180, XI145, XI148, XI167, XI150, XJ175, XJ178, XI162 and XG111. To identify the cell types and distinguish between normal and leukemic cells, cell surface proteins were also captured for 6 samples: XF98, XG111 (at diagnosis and during treatment), XG115, XI162 (after treatment) and XJ175 (after treatment). All samples were processed on the MissionBio platform with a custom amplicon panel, and DaB-seq for the combined targeted DNA and protein sequencing.

  Dataset EGAD50000000829

• fragmentomic features of individuals with different cfDNA concentrations

  The uploaded data includes sequencing data of 862 individuals from the nasopharyngeal carcinoma (NPC) screening study. Samples from this cohort were sequenced using targeted sequencing methods for the Epstein Barr Virus (EBV) and selected autosomal DNA, but only ‘off-target’ reads were used for fragmentomic analyses. We have also performed genome-wide (non-targeted sequencing) for 1) Individuals with the highest and lowest cell-free DNA concentration (40 individuals); 2) A subsequent collection of the subjects with the highest and lowest DNA concentrations after six years (26 individuals); 3) 30 cases of pregnancy and 4) 20 patients with hepatocellular carcinoma. All sequencing data are of extracted plasma cfDNA from human subjects. The targeted sequencing samples from 862 individuals were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19). The alignments were provided in bam format. The original fastq files of the remaining non-target sequencing samples were provided.

  Dataset EGAD50000000970

• Metabolic reprogramming towards OXPHOS identifies a novel therapeutic target for mantle cell lymphoma

  Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways to overcome resistance, an urgent clinical need in all relapsed/refractory cancers, remains difficult. Through genomics analysis of clinical specimens, we show that metabolic reprogramming towards oxidative phosphorylation (OXPHOS) and glutaminolysis is associated with therapeutic resistance to the Bruton’s tyrosine kinase inhibitor ibrutinib in mantle cell lymphoma (MCL), an incurable B-cell lymphoma with poor clinical outcomes. Inhibition of OXPHOS with a novel, clinically applicable small molecule, IACS-010759, which targets complex I of the mitochondrial electron transport chain, results in significant growth inhibition in vitro and in vivo in ibrutinib-resistant patient-derived cancer models. This work suggests that targeting metabolic pathways to subvert therapeutic resistance is a clinically viable approach to treat highly refractory malignancies.

  Dataset EGAD00001004577