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• An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases

  At 5' ends of RNAs, there is a unique "cap signature" derived from a 7-methylguanosine cap. By leveraging this signature, we developed ReapTEC (read-level pre-filtering and transcribed enhancer call), a method for simultaneously profiling gene expression and enhancer activities using 5'-end single-cell RNA sequencing (5' scRNA-seq). We applied ReapTEC and single-nucleus ATAC-seq to a total of ~1 million single human CD4+ T cells.

  Study JGAS000689

• Combinatorial Indexed 10x Genomics Single-Cell ATAC-seq on Human Cerebral Cortex

  Single-cell chromatin accessibility profiling (scATAC) using droplet fluidics (10x Genomics) is inherently limited in throughput due to the number of available indexed droplets. This study leverages single-cell combinatorial indexing workflows with modified adapter designs to enable indexed tagmentation and superloading of pre-indexed nuclei into the 10x Genomics scATAC workflow, enabling a substantial increase in the number of cell profiles that can be obtained per channel. This workflow, 10x single-cell combinatorial indexed ATAC-seq (txsciATAC), is demonstrated on human brain tissue (middle frontal gyrus), along with mouse brain tissue to enable doublet and crosstalk assessment. This study includes all human data and includes a single preparation taken through nuclei isolation and indexed tagmentation using 96 indexes then split to produce two datasets, one targeting 20k cells and one targeting 70k, each using a single channel of the 10x Chromium controller.

  Study phs003497

• Tissue-specificity and co-expression analyses identify human long non-coding RNAs related to inherited retinal disease genes

  The role of long non-coding RNAs (lncRNAs) in biological and pathological processes is still poorly understood. In this study, we aimed to identify lncRNAs that potentially contribute to retinal biology and Inherited Retinal Disease (IRD) by using two complementary strategies, tissue-specificity and location in topologically associating domains (TADs) containing IRD genes on one hand, and co-expression analyses on the other, applied to human retinal omics datasets. This combined approach resulted in the selection of 11 Retina Enriched IRD-gene Related (REIR) lncRNAs, one of which is novel. In-depth in silico and experimental characterization of REIRs identified novel REIR isoforms and confirmed retina-predominant (often photoreceptor-specific) expression as well as predicted functional association with visual function. Long-read direct cDNA sequencing (ONT) of three post-mortem human retina samples was used to delineate the novel REIR isoforms.

  Study EGAS50000000963

• The effect of blood tube and time delay on the genome-wide methylation pattern of cfDNA

  In this study, we evaluated the effect of preservation agens on the effect of the methylation pattern of cell-free DNA. The methylation pattern was assessed with cell-free reduced representation sequencing (cf-RRBS). All 45 samples were sequenced on a NovaSeq6000, and samples are provided as raw fastq files.

  Dataset EGAD00001006007

• Hyperfibrinolysis

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such pedigree, hyperfibrinolysis is associated with increased fibrinolytic activity, resulting in increased bleeding. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000104

• Bleeding

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who exhibit severe bleeding with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000106

• Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL), a group of malignancies derived from skin-homing malignant T cells. We subjected tumor biopsies from MF patients to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001002860

• Various_Platelet_Disorders

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who have a platelet disorder with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000107

• Exome sequencing of pseudomyxoma peritonei

  Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma mainly restricted to the peritoneal cavity and most commonly originating from the appendix. In this study, we sequenced whole coding genome of nine PMP tumors and paired normal tissues in order to identify commonly mutated genes and signaling pathways affected in PMP.

  Study EGAS00001002418

• Multi-omics of Richter syndrome

  Richter syndrome (RS) is the aggressive transformation of Chronic Lymphocytic Leukemia, mostly with Diffuse Large B-Cell Lymphoma histology. While histologically similar, RS and de novo DLBCLs present with different clinical courses. We characterized the RS epigenome by combining genome-wide DNA methylation with transcriptome-sequencing on a large RS cohort.

  Study EGAS00001005495