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• Organoid Derivation Project: TGS (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011089

• Organoid Derivation Pilot: RNAseq (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011091

• Organoid Derivation Project - GRCh38 - TGS (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011094

• MGUS/SMM to MM WES

  This dataset contains raw sequencing reads for matched MGUS/SMM to MM patient samples, including normal germline controls. FASTQ files were generated on Illumina NextSeq 500 and HiSeq 4000 machines following exome capture using the Agilent Clinical Research Exome kit. DNA was extracted from CD138+CD38++ cells (representing MGUS/SMM/MM cells) and CD138-CD38- (representing normal cells) isolated from bone marrow. 10 patients are included with 3 samples each representing normal, MGUS/SMM, MM stages.

  Dataset EGAD00001004190

• Epigenetic analyses of methylation and nucleosome occupancy in cell-free DNA (cfNOMe)

  Cell-free DNA (cfDNA) has become essential in cancer diagnostics and prenatal testing. We investigate enzymatic cytosine conversion for epigenetic analyses of cfDNA and find that it reliably measures cytosine methylation and nucleosome occupancy. Whereas previously, separate experiments had to be performed to study either epigenetic marking, this approach delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic profiling of cfDNA.

  Study EGAS00001004370

• Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than to kidney function

  Despite recent progress, microbial markers in Chronic Kidney Disease (CKD) remain inconclusive. We combined quantitative faecal metagenomics (N=130 CKD cohort) and cross-study biomarker comparisons (Ntotal=4420) to study microbiome associations with glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Transit time (TT) and medications primarily explained microbiome variation, trumping eGFR-related effects. Metagenome analysis showed increased p-cresol and indole synthesis potential and decreased plant-to-animal CAZyme ratios with lower eGFR, coupled to a Bact1 to Rum enterotype shift, suggesting saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down TT. Peritoneal dialysis patients showed increased (dysbiotic) Bact2 prevalence and linked intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were confounder-independent markers for eGFR, but these nor previous markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Together, poor evidence for microbiome biomarkers but substantial eGFR-independent effects were found, suggesting potential for nutritional and TT interventions in CKD.

  Study EGAS50000000646

• ONT and PacBio data of 22q11 patient-parent duos/trios

  ONT and PacBio FASTQ files generated for de novo assembly and resulting de novo assemblies

  Study EGAS50000001647

• Integrative multi-omic analyses of malignant pleural mesothelioma

  Multi-omic data (whole-genome sequencing, RNA-seq, EPIC 850K methylation arrays) for 123 samples from the MESOMICS project, the French project of molecular characterization of malignant pleural mesothelioma

  Study EGAS00001004812

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (WG)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutaiton burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010111

• RNA-Seq data for manuscript titled: A sporadic Alzheimers blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies

  RNA-Seq data for manuscript titled: A sporadic Alzheimers blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies

  Dataset EGAD00001008670