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• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007854

• Human CCO+ liver mtDNA sequencing

  BAM files containing paired-end mtDNA sequencing data from morphologically normal human liver. CCO-proficient hepatocytes acquired from human livers in which clonal CCO-deficient hepatocyte patches had been previously identified. Individual BAM files are named according to their patch, line and sample location, where PT denotes tissue near to the portal triad (PT), central hepatic vein (CV) and midway between these two structures (Mid). "Stroma" control samples were used for identifying germ-line variants. Sequenced on NextSeq 500 platform.

  Dataset EGAD00001010016

• 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

• RNA sequencing data for primary and recurrent ovarian granulosa cell tumors

  RNA sequencing dataset for primary and recurrent ovarian granulosa cell tumors consists of 24 .bam files with aligned reads, including 8 primary and 16 recurrent tumors. Total RNA was extracted from cryopreserved tissue of adult-type granulosa cell tumor samples. Libraries were prepared from cDNA using the NuGEN Ovation Ultralow Library System V2 (San Carlos, CA). Paired-end bulk RNA sequencing was performed on the Illumina HiSeq 2000 platform. RNA sequencing reads were aligned to the hg19/GRCh37 reference human genome using the STAR software (version 2.6.0b) with default parameters. Samples description: GCT001 Adult-type Granulosa Cell Tumor: recurrent tumor GCT002 Adult-type Granulosa Cell Tumor: primary tumor GCT003 Adult-type Granulosa Cell Tumor: recurrent tumor GCT004 Adult-type Granulosa Cell Tumor: primary tumor GCT005 Adult-type Granulosa Cell Tumor: recurrent tumor GCT006 Adult-type Granulosa Cell Tumor: recurrent tumor GCT007 Adult-type Granulosa Cell Tumor: primary tumor GCT008 Adult-type Granulosa Cell Tumor: recurrent tumor GCT009 Adult-type Granulosa Cell Tumor: recurrent tumor GCT010 Adult-type Granulosa Cell Tumor: recurrent tumor GCT011 Adult-type Granulosa Cell Tumor: primary tumor GCT012 Adult-type Granulosa Cell Tumor: recurrent tumor GCT013 Adult-type Granulosa Cell Tumor: recurrent tumor GCT014 Adult-type Granulosa Cell Tumor: recurrent tumor GCT015 Adult-type Granulosa Cell Tumor: recurrent tumor GCT016 Adult-type Granulosa Cell Tumor: recurrent tumor GCT017 Adult-type Granulosa Cell Tumor: recurrent tumor GCT018 Adult-type Granulosa Cell Tumor: primary tumor GCT019 Adult-type Granulosa Cell Tumor: recurrent tumor GCT020 Adult-type Granulosa Cell Tumor: primary tumor GCT021 Adult-type Granulosa Cell Tumor: primary tumor GCT022 Adult-type Granulosa Cell Tumor: recurrent tumor GCT023 Adult-type Granulosa Cell Tumor: recurrent tumor GCT024 Adult-type Granulosa Cell Tumor: primary tumor

  Dataset EGAD00001009108

• EUROBATS RNAseq BAM files for the Fat samples

  RNAseq BAM files for the Fat samples of the EUROBATS project

  Dataset EGAD00001001089

• EUROBATS RNAseq BAM files for LCLs

  These analysis are the BAM files for the LCLs samples of the EUROBATS samples.

  Dataset EGAD00001001086

• EUROBATS RNAseq BAM files for the Skin samples

  RNAseq BAM files for the Skin samples of the EUROBATS project.

  Dataset EGAD00001001087

• EUROBATS RNAseq BAM files for the Blood samples

  RNAseq BAM files for the blood samples of the EUROBATS project

  Dataset EGAD00001001088

• Colorectal Adenoma Gene Screen

  A pilot to establish the feasability of using a custom Agilent targeted pulldown of 110 genes implicated in colorectal tumourigensis to sequence for driver mutations in a set of 30 FFPE colorectal adenomas. If successful, we propose to sequence an additional 350 adenomas as part of a MRC research study in order to define the pattern of driver mutations across the spectrum of pathological subtypes including coventional adenomas, serrated adenomas and hyperplastic polyps

  Dataset EGAD00001001879

• MM samples for epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking

  Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called enhancer hijacking. To examine this phenomenon we used ChipSeq based on a combination of six histone modifications as follows: H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac and H3K36me3. Samples are patient-derived xenografts generated by passaging primary patient CD138+ selected cells through the SCID-rab myeloma mouse model.

  Study EGAS00001005684

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (WG)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to women who had breast cancer and those who are BRCA 1/2 carriers. This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010109

• NAR-GAB 2025 deposit data

  Human exome gVCFs: rare-disease cohort for the NAR-GAB 2025 study on splicing-SNV prioritization.

  Study EGAS50000001456

• HICHIP_TALL_t_14_16_translocation

  For patient P01, HiChIP experiment for was performed using the Arima-HiC+ kit (A510008, Arima genomics) according to the manufacturer’s protocols.

  Dataset EGAD50000002167

• Primary Neuroblastoma Circle-seq

  We generated Circle-seq data for primary neuroblastoma to describe the landscape of extrachromosomal circular DNA in neuroblastoma.

  Study EGAS00001004797

• January 2016 update of RNA-Seq data for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  January 2016 update of RNA-Seq data (bams, fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001885

• CCA RNA-seq data (60 CCA, 6 normal, 16 cell-line)

  Fastq files for RNA-seq for 60 CCAs, 6 normal bile duct tissues, 14 CCA cell-lines (including replicates), and 2 normal cholangiocyte cell-lines (including replicates). RNA was extracted using the Qiagen RNeasy Mini kit. Illumina Tru-Seq Stranded Total RNA kit (Illumina, San Diego, California, USA) was used to prepare RNA libraries from 1 µg of total RNA. Paired-end 150 bp sequencing was performed using Illumina HiSeq4000 sequencer with the paired-end 150 bp read option.

  Dataset EGAD00001011998

• Highly differentiated, fusion-negative rhabdomyosarcoma.

  Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 14 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples, and 8 non-matched normal skeletal muscle samples weer sequenced. BAM files are available for download.

  Dataset EGAD00001003746

• Myeloma Follow up Pilot

  Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.

  Dataset EGAD00001000998

• Single-nucleus BIN1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for BIN1 using custom designed primers.

  Dataset EGAD00001008288

• Single-nucleus SPP1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for SPP1 using custom designed primers.

  Dataset EGAD00001008285

• Single-nucleus APP Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for APP using custom designed primers.

  Dataset EGAD00001008284

• Dataset for MCPlus_WGS

  WES/WGS sequencing data of 44 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009277

• Dataset for central nervous system glioma samples

  This dataset contains VCF files for 124 central nervous system glioma samples for the study "Cerebrospinal fluid cfDNA sequencing for classification of central nervous system glioma"

  Dataset EGAD50000000085

• NIHR BioResource Common Disease Patients 2016

  NIHR BioResource Common Disease Patients 2016. The dataset includes 13489 samples from blood donors, they were not screened for any particular disease, and therefore they are representative of the general population. Genomic data includes 845487 snps collected using the UK BioBank V1 Affymetrix array. Phenotypic data includes gender, age, ethnicity and disease. According to our internal quality check there are 81 duplicates in this dataset.

  Dataset EGAD00010002059

• RNA-Seq of novel miR (nmiR-1 and nmiR-2) overexpression and knockdown in BL

  After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets.

  Dataset EGAD00001001612

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model – 2D versus 3D co-culture comparison

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions (each as biological triplicates): - wild-type cells from 2D or 3D co-cultures after 3 months of culturing (2D_WT, 3D_WT) - knock-in cells from 2D or 3D co-cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (2D_KI, 3D_KI) - 2D and 3D KI cultures treated with Bumetanide (KI_bum) or BACE IV (KI_bace) inhibitor

  Study EGAS50000001392

• Cholesterol homeostasis and lipid raft dynamics at the basis of tumor-induced immune dysfunction in chronic lymphocytic leukemia

  Autologous T-cell therapies show limited efficacy in chronic lymphocytic leukemia (CLL), where acquired immune dysfunction prevails. In CLL, disturbed mitochondrial metabolism has been linked to defective T-cell activation and proliferation. Recent research suggests that lipid metabolism regulates mitochondrial function and differentiation in T cells, yet its role in CLL remains unexplored. This comprehensive study compares T-cell lipid metabolism in CLL patients and healthy donors, revealing critical dependence on exogenous cholesterol for human T-cell expansion following TCR-mediated activation. Using multi-omics and functional assays, we found that T cells present in viably frozen samples of patients with CLL (CLL T cells) showed impaired adaptation to cholesterol deprivation and inadequate upregulation of key lipid metabolism transcription factors. CLL T cells exhibited altered lipid storage, with increased triacylglycerols and decreased cholesterol, and inefficient fatty acid oxidation (FAO). Functional consequences of reduced FAO in T cells were studied using samples from patients with inherent FAO disorders. Reduced FAO was associated with lower T-cell activation but did not affect proliferation. This implicates low cholesterol levels as a primary factor limiting T-cell proliferation in CLL. Consequently, CLL T cells displayed fewer and less clustered lipid rafts, potentially explaining the impaired immune synapse formation observed in these patients. Our findings highlight significant disruptions in lipid metabolism as drivers of functional deficiencies in CLL T cells, underscoring the pivotal role of cholesterol in T-cell proliferation. This study suggests that modulating cholesterol metabolism could enhance T-cell function in CLL, presenting novel immunotherapeutic approaches to improve outcome in this challenging disease.

  Study EGAS50000000933

• ChIP-seq fastq and alignment files

  ChIP-seq experiments: fastq files; both ChIP and Input for each sample. Illumina HiSeq 2500. ChIP-seq alignment files for trimmed, mapping q20 and nonredundant reads; both ChIP and Input for each sample. Software: Trim Galore v0.3.7; Bowtie 2 v2.1.0; samtools v1.7

  Dataset EGAD00001006279

• EASI-Genomics GM21886 Cell Line High Molecular Weight DNA Sequencing

  An interlaboratory study was performed with GM21886 cells to evaluate methods for high molecular weight (HMW) genomic DNA extraction and compare sample and sequencing QC metrics, and pipelines for structural variant (SV) calling. Four laboratories prepared HMW genomic DNA using four alternative extraction methods FireMonkey (Revolugen), Genomic Tip (QIAGEN), Nanobind (Circulomics), and Puregene (QIAGEN), followed by Short Read Elimination (Circulomics) and long-read sequencing with MinION and PromethION flowcells (Oxford Nanopore Technologies).

  Study phs003958

• Fastq data for ChIP-Seq (H3K9me3) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K9me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001408

• Fastq data for ChIP-Seq (Input) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (Input) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001409

• 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

• Single cell chromatin accessibility profiles from myelofibrosis patients

  To explore how JAK2V617F disrupts cell-fate and the regulatory chromatin landscape of HSCs, we applied GoT-ChA to CD34+ sorted progenitor cells from 21 human primary samples, comprising 18 patients with JAK2V617F-mutated MF (no additional mutations, except for Pt-08), who either had no treatment (n = 12; including three longitudinal samples from a PV patient who progressed to MF) or who were treated with ruxolitinib (n = 6), a JAK1/2 inhibitor. We included a JAK2V617F CH sample (Pt-19) to explore early epigenetic changes, before the onset of overt hematological abnormality.

  Dataset EGAD50000000234

• Garvan/St Vincent’s Prostate Cancer Tissue and Data

  The cohort (n=53) consists of prostate cancer patients from Australia. For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

  Dataset EGAD00001009066

• MutWP5: CRUK Mutographs of Cancer: Cancer Mastectomy (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 40 women who underwent mastecomies due to breast cancer. LCM and sequencing will be conducted on both normal, unaffected breast, and, where possible, tumour tissue. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue, and compare findings between the normal and associated cancer tissues. 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 women who had cosmetic breast reduction surgeries and those who are BRCA carriers. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010117

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - ExomeNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016058

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - TargetedNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016059

• Single Cell DNA Methylation Analysis for Forensic Epigenetics

  As part of the Epigenetic CHaracterization and Observation (ECHO) program, the Genomic Analysis Laboratory at the Salk Institute generated the DNA methylation profiles of certain PBMC cell types to determine the change in methylation levels before, during or after exposure to certain biological or chemical agents. Samples from individuals who either handled anthrax in controlled environments or who tested positive to MRSA, MSSA, HIV, COVID-19 or exposed to Flu virus or organophosphates, or control samples were used in single-nucleus methylation (snmC-seq) assays to quantify DNA methylation levels of cytosine residues of the DNA. Around 5-10% cytosine sites were sampled in the assay. Using computational analyses, regions in the genome differentially methylated in response to the exposure were identified. This information can be used to develop diagnostic tools to predict the type of infection or time since exposure.

  Study phs003204

• CONSERTING: integrating copy number analysis with structural variation detection

  We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection to achieve high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. This study contains all data for "CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data", which was previously split between EGAS00001001202 and EGAS00001001050.

  Study EGAS00001001202

• Mutation tracking in single cell RNA-Seq reveals consequences of subclonal evolution in acute myeloid leukemia

  Total bone marrow from AML patients was FACS index sorted with staining for Lineage markers (Lin), CD33, CD34, CD38, CD45RA, CD90, CD99, Tim3 and GPR56, and enrichment for Lin- and Lin-CD34+ cells. Single cells were subjected to a modified smart-seq2 protocol with targeting of mutant sites of interest ("MutaSeq”).

  Study EGAS00001003414

• Medulloblastoma WES

  WES for tumor and normal samples

  Study EGAS50000000261

• Single-cell RNA-sequencing of CD19 Chimeric Antigen Receptor (CAR) T-cells (CD19 CAR T-cells) from a Phase I clinical study in paediatric ALL: CARPALL

  Chimeric antigen receptor (CAR)-modified T-cells have become established as an effective treatment of haematological cancers. In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukaemia (B ALL), CD19 targeting CAR T-cells often induce durable remissions. Previously, we generated a novel low-affinity CAR incorporating a CD19-specific single-chain variable fragment (scFV) called CAT, displaying a faster off-rate of interaction than the FMC63 CD19 binder used in prior clinical studies. Here, we systematically analysed CD19 CAR T-cells of ten children with relapsed or refractory B ALL enrolled in the CARPALL trial (NCT02443831). To characterize persisting CD19 CAR T-cells, we performed high throughput single-cell gene expression and T-cell receptor (TCR) sequencing of infusion products and serial blood and bone marrow samples up to five years post-infusion. We isolated CAR T-cells from peripheral blood or bone marrow by flow cytometry for CD3 and CAR expression, prior to single cell sequencing (Chromium 10X) platform.

  Dataset EGAD00001010018

• WTCCC2 BO (Barretts oesophagus) samples

  A WTCCC2 project genome-wide case-control association study for Barretts oesophagus in individuals from the UK.

  Study EGAS00001000628

• DATA FILES FOR PCGP SJCBF RNASEQ

  Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed RNASeq data referenced in this paper.

  Dataset EGAD00001002530

• A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

  A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome - cell line data

  Dataset EGAD00001008963

• 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