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• exploration of biomarkers in colorectal cancer

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

  Study JGAS000489

• Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors

  We performed whole genome and whole exome sequencing analyses of pancreatic tumors, duodenal tumors and biliary tumors and investigated the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling.

  Study JGAS000359

• WGS_skin_punches

  We wish to understand the degree of copy number alterations in normal human sun exposed skin. We have collected small punches of epithelia and using a bait set design have shown the these span a clone. WGS will provide copy number information on these.

  Study EGAS00001004465

• Low-coverage whole-sequencing of metastasised colorectal cancer samples treated with bevazicumab

  Low-coverage whole-genome sequencing (LC-WGS) was performed on tumor tissue, normal tissue and plasma samples collected from mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444) and the University Medical Center Mannheim (UMM).

  Study EGAS50000000131

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell RNA-sequencing (CITE-seq) and single-nucleus RNA-sequencing data were generated from neuroblastoma patient tumors to uncover transcriptional heterogeneity at a single-cell resolution. In addition, we used the data to validate our findings of the NBAtlas.

  Study EGAS50000000223

• Batch-corrected read-count matrix of the RNAseq Datasets of CLUSTER JIA pre-MTX cohort

  Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq.

  Dataset EGAD50000002169

• RNA-Sequencing data of Fusobacterium nucleatum treated CAFs and HT-29 tumor spheroid exposed to Fusobacterium nucleatum treated CAFs conditioned medium.

  RNA-Sequencing data of CAFs (patient derived CAF180 and CAF181 as well as the CT5.3 CAF cell line) and HT-29 tumor spheroid samples performed in the context of the study of the interaction of Fusobacterium nucleatum with CRC CAFs. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to enhance colorectal cancer progression

  Dataset EGAD50000001614

• Single-cell RNA-sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We undertook single-cell RNA sequencing to establish gene expression and lymphocyte receptor sequences of CSF and peripheral blood leukocytes derived from patients with a variety of inflammatory, infectious and non-inflammatory neurological disorders. The aim of the study was the investigation of functional changes of the cells involved in neuroinflammatory responses.

  Dataset EGAD50000001173

• A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

  PacBio HiFi Revio WGS data from 16 individuals sequenced in the Genomic Medicine Sweden (GMS) Long read project. Each individual was sequenced on one PacBio Revio SMRT cell. The DNA was extracted from blood. The HiFi data was aligned to GRCh38 using minimap2 or the SMRT-link software.

  Dataset EGAD50000000676