12312 results for "cancer rna-seq"

in 22.93 milliseconds.

• Sequencing data for oesophageal / related samples - Foley, Shorthouse et al (RNA)

  Data supporting: "SMAD4 and KCNQ3 Alterations are Associated with Lymph Node Metastases in Oesophageal Adenocarcinoma" RNAseq (FASTQ files) 6 samples

  Dataset EGAD00001011065

• Single-cell RNA/ATAC multiome profiling of hepatoblastoma resection samples

  10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression data of hepatoblastoma tissue samples. BAM files containing sequencing data of resection material of PT13 and PT17.

  Dataset EGAD50000001750

• Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer

  Our understanding of genomic heterogeneity in lung cancer is largely based on the analysis of early-stage surgical specimens. Here we used endoscopic sampling of paired primary and intrathoracic metastatic tumors from 11 lung cancer patients to map genomic heterogeneity inoperable lung cancer with deep whole-genome sequencing. Intra-patient heterogeneity in driver or targetable mutations was predominantly in the form of copy number gain. Private mutation signatures, including patterns consistent with defects in homologous recombination, were highly variable both within and between patients. Irrespective of histotype, we observed a smaller than expected number of private mutations, suggesting that ancestral clones accumulated large mutation burdens immediately prior to metastasis. Single-region whole-genome sequencing of from 20 patients showed that tumors in ever-smokers with the strongest tobacco signatures were associated with germline variants in genes implicated in the repair of cigarette-induced DNA damage. Our results suggest that lung cancer precursors in ever-smokers accumulate large numbers of mutations prior to the formation of frank malignancy followed by rapid metastatic spread. In advanced lung cancer, germline variants in DNA repair genes may interact with the airway environment to influence the pattern of founder mutations, whereas similar interactions with the tumor microenvironment may play a role in the acquisition of mutations following metastasis.

  Study EGAS00001003830

• PD-L1 blockade immunotherapy rewires cancer-induced emergency myelopoiesis

  Introduction Immune checkpoint blockade (ICB) immunotherapy has revolutionized cancer treatment, demonstrating exceptional clinical responses in a wide range of cancers. Despite the success, a significant proportion of patients still fail to respond, highlighting the existence of unappreciated mechanisms of immunotherapy resistance. Delineating such mechanisms is paramount to minimize immunotherapy failures and optimize the clinical benefit. Methods In this study, we treated tumour-bearing mice with PD-L1 blockage antibody (aPD-L1) immunotherapy, to investigate its effects on cancer-induced emergency myelopoiesis, focusing on bone marrow HSPCs. We examined the impact of aPD-L1 treatment on HSPC quiescence, proliferation, transcriptomic profile, and functionality. Results Herein, we reveal that aPD-L1 in tumour-bearing mice targets the hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (ΒΜ), mediating their exit from quiescence and promoting their proliferation. Notably, disruption of the PDL1/PD1 axis induces transcriptomic reprogramming in HSPCs, observed in both individuals with Hodgkin lymphoma (HL) and tumour-bearing mice, shifting towards an inflammatory state. Furthermore, HSPCs from aPDL1-treated mice demonstrated resistance to cancer-induced emergency myelopoiesis, evidenced by a lower generation of MDSCs compared to control-treated mice. Discussion: Our findings shed light on unrecognized mechanisms of action of ICB immunotherapy in cancer, which involves targeting of BM-driven HSPCs and reprogramming of cancer-induced emergency myelopoiesis.

  Study EGAS00001007873

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of esophageal tumoroids derived from esophageal cancer patient. We performed whole exome sequencing to analyze genetic background of the tumoroids.

  Study JGAS000749

• Duplex sequencing of selected breast cancer patients

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primaty tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000769

• WES of breast cancer patients and controls

  Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primary tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.

  Dataset EGAD50000000770

• Breast_Cancer_Matched_Pair_Cell_Line_Whole_Genomes

  We propose to definitively characterise the somatic genetics of matched pair breast cancer cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000166

• Y_chromosome_mis_segregation_in_the_DLD_1_cell_line

  Study of the well-established DLD-1 colorectal cancer cell line, engineered with an inactivatable Y centromere that leads to mis-segregation. The goal is to gain insights into the mechanism of chromothripsis due to chromosome mis-segration.

  Study EGAS00001002551

• Triple_Negative_Breast_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000092

• Transcriptome_Sequencing_of_Cancer_Cell_Lines

  In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000261

• Whole-genome sequencing of paired tumor and blood samples from 65 bladder cancer patients

  65 paired tumor and normal whole-genome sequencing samples from urothelial bladder carcinomas (UBC, the most common type of bladder cancer) are used to uncover the whole-genome mutational landscape of UBC. Recurrent mutations in noncoding regions affecting gene regulatory elements and structural variations leading to gene disruptions are prevalent in this type of cancer.

  Dataset EGAD00001004545

• Colorectal cancer genomics with primary and metastatic samples

  We performed whole genome sequencing of metastatic colorectal cancer from 16 patients. Normal adjacent tissue, primary tissue, and metastatic tissue were analyzed to uncover metastatic progression and difference between primary and distant metastatic lesions.

  Study EGAS00001006465

• Colorectal cancer transcriptomics with primary and metastatic samples

  We performed RNAseq analysis of metastatic colorectal cancer from 16 patients. Normal adjacent tissue, primary tissue, and metastatic tissue were analyzed to uncover metastatic progression and difference between primary and distant metastatic lesions.

  Study EGAS00001006464

• Whole exome and targeted sequencing of non-muscle-invasive bladder cancer

  Tumor-blood paired whole-exome sequencing of 58 pairs of non-muscle-invasive bladder cancer samples (stageT1). Targeted sequencing of 112 non-muscle-invasive bladder cancer samples (34 stage T1; 78 stage Ta) Please note the following files have been removed: EGAR00003025153, EGAR00003025435, EGAR00003025294, EGAR00003025262, EGAR00003025224.

  Dataset EGAD00001008332

• RNASeq data from one small cell prostate cancer patient (4 samples from 3 time points)

  RNASeq data from one small cell prostate cancer patient - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points. mRNA was selected using the Magnetic mRNA Isolation Module (NEB) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011154

• Single-Cell Profiling of the Human Endometrium in Polycystic Ovary Syndrome: Uncovering Disease Signatures and Treatment Responses

  Single-nuclei map of human endometrial biopsies from women with and without PCOS to identify cell-type-specific disease signatures, compositional variations, and transcriptomic reversibility after a 16-week intervention with metformin or lifestyle. Single nuclei were extracted from 27 frozen endometrial biopsies for snRNA-seq using the 10X Genomics protocol.

  Dac EGAC50000000468

• BIOMIROX

  This dataset regroups RNAseq of paired primary colorectal cancers and liver metastases extracted from 113 patients In Paris and Besançon University Hospitals. 216 FASTQ files from single-end 3' PolyA (QuantSeq 3′mRNA-Seq Kit FWD for Illumina (Lexogen)) RNAseq samples were generated On NOVASEQ 6000 (ILLUMINA).

  Dataset EGAD50000000443

• Transcriptome atlas of brain organoid developent

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. We used scRNA-seq to profile transcriptome. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000223

• Human brain development single cell sequencing

  379 tissue samples from various parts of the developing human embryo brain were dissociated and single cells were collected and processed without bias for mRNA-seq using 10X chromium 3' protocol. Libraries were sequenced on Illumina NovaSeq and reads aligned against the human GRCh38 genome.

  Dataset EGAD00001006049

• Sequencing data

  WES: (7 samples, BAM files), scRNA-Seq (4 samples, BAM files), TruSight (56 samples, BAM or FASTQ files)

  Dataset EGAD00001007749

• Mixture of 4

  Mixture of 4 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008724

• Mixture of 3

  Mixture of 3 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008729

• KCL PRECSION Mutations targeted-seq

  105 Normal, DCIS and recurrences samples target-sequenced

  Dataset EGAD00001008376

• Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

  This dataset contains the open chromatin profiles of 8 patient H3-K27M mutant DMGs utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Dataset EGAD00001010170

• Dr. Fatima Mechta-Grigoriou, PhD, DR1 Head of Stress and Cancer Laboratory Deputy Director Genetic and Biology of Cancer Dpt Institut Curie - Inserm U830

  Dac EGAC00001000581

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Data access committe for the project: Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Dac EGAC50000000074

• Thoracic Patient-Derived Xenografts

  Targeted capture sequencing of 341 cancer associated genes in thoracic patient-derived xenografts.

  Study phs001192

• Whole exome sequencing of 103 pairs BLCA-CN

  We sequenced 50M exomes of 103 pairs bladder cancer of chinese

  Study EGAS00001000677

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumouroids

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008273

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008275

• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008276

• Somatic cancer gene mutation screening

  Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2

  Dataset EGAD00001001010

• Premalignant SOX2 in ovarian cancer patients

  Whole Genome Sequencing data set for the study "Premalignant SOX2 in ovarian cancer patients"

  Dataset EGAD00001002734

• Plasma methylome of metastatic prostate cancer

  The dataset contains plasma DNA methylation data derived from metastatic prostate cancer patients.

  Dataset EGAD00001005433

• Genomic and Genetic Characterization of Prostate Tumors Treated with Neoadjuvant Intense Androgen Deprivation Therapy

  The purpose of this study was to develop better ways of detecting prostate cancer before and after pre-operative treatment, and to test the feasibility of multi parametric magnetic resonance imaging (mpMRI) for the localization and detection of focal prostate cancer both before and after pre-operative treatment with ADT and enzalutamide. In this study, patients with intermediate and high risk prostate cancer received six months of neoadjuvant intense androgen deprivation therapy prior to radical prostatectomy. Biopsies were acquired prior to treatment. Tissue from biopsy and radical prostatectomy were subjected to sequencing and analysis for determination of features associated with response or resistance to treatment.

  Study phs001938

• Integrative Analysis of Lung Adenocarcinoma in EAGLE (Version 2)

  We performed a comprehensive analysis of intratumor heterogeneity of somatic mutations in cancer driver genes, copy number aberrations and DNA methylation in 292 tumor samples from 84 lung adenocarcinoma (LUAD) patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. SNVs of 37 established lung cancer driver genes were profiled by deep target sequencing in 180 tumor samples and 55 blood samples and 1 buccal sample from 56 subjects. Somatic copy number alterations were profiled using SNP arrays in 268 tumor samples from 80 subjects. DNA methylation levels were profiled with methylation arrays in 205 tumor samples and 74 normal tissue samples from 68 subjects.

  Study phs001169

• The EGA joins EUCAIM, the European project powering AI and imaging in cancer research

  EUCAIM (EUropean Federation for CAncer IMages) is the cornerstone of the European Cancer Imaging Initiative, one of the flagships of the Europe’s Beating Cancer Plan (EBCP). The European Genome-Phenome Archive (EGA), as member of the EUCAIM consortium, attended the kick-off meeting organized this week in Brussels for the launch of the Initiative. The EGA will contribute to the project with the experience gained in the deployment of our federated network, the Federated EGA (FEGA), and the experience gained as partners of EuCanImage (AI4HI initiative) contributing to the definition of common data models, ontologies and data standards. The ultimate goal of the project is to unlock the power of imaging and Artificial Intelligence for the benefit of cancer patients, clinicians and researchers. The consortium will deploy a pan-European digital federated infrastructure hosting cancer-related images, and associated pathology, molecular and laboratory data from Real-World. This endeavour will provide a comprehensive dashboard for imaging data discovery, federated search, metadata harvesting, annotation and distributed data processing. EUCAIM joins 76 partners, gathering the experience and previous effort made by the different repositories of the AI4HI initiative, European Research Infrastructures and national/regional repositories. Find out more information about the EUCAIM launch here

  Blog the-ega-joins-eucaim

• 2014_Lung_sq_WES

  Purpose Lung squamous cell carcinoma (SqCC) is the second most prevalent type of lung cancer. Currently, no targeted-therapeutics are approved for treatment of this cancer, largely due to lack of systematic understanding of the molecular parthenogenesis of the disease. To identify therapeutic targets and comparatively analyze them in lung SqCC, we probed somatic alterations of Korean lung SqCC. Patients and Methods We performed massively parallel whole-exome sequencing of 104 Korean lung SqCC patients’ samples with matched normal samples. In addition, copy number analysis and transcriptome analysis were conducted for a subset of these samples. Clinical association with cancer-specific somatic alterations was investigated.

  Study EGAS00001002844

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD43291_Novaseq__WG_

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from lung tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will deeply sample from individuals with smoking-related lung diseases (COPD, pulmonary fibrosis, lung cancer) and those without smoking history. This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumor development.

  Study EGAS00001003502

• Integrative Gene Regulatory Network Analysis Discloses Key Driver Genes of Fibromuscular Dysplasia

  Fibromuscular dysplasia (FMD) is a poorly understood vascular disease that can lead to hypertension, stroke, myocardial infarction and even death. In 2013 we initiated the DEFINE study (ClinicalTrials.gov Identifier: NCT01967511), which has now recruited > 440 subjects and which aims to unravel the pathobiological mechanisms of this disease. Here, by integrating DNA genotype and RNA sequence data from primary fibroblasts of 83 FMD patients and 71 matched healthy controls from the DEFINE study, and its precursor the CAUSE study, we inferred 18 gene regulatory co-expression networks, four of which were found to act together as an FMD-associated super network in the arterial wall. Molecular studies indicated that this super network, termed SN-A and with the top key driver gene UBR4, governs multiple aspects of vascular cell physiology and functionality, including collagen/matrix production. The effects of UBR4 knockdown were also investigated in commercially available aortic smooth muscle and fibroblast cell lines by RNA sequencing, and these results are included in these datasets.Note, that of the 154 subjects in this analysis, 62 did not provide consent to have their genomic data made publicly available. Therefore the human subject data available here is from the 92 study participants who provided written informed consent to share their deidentified genomic data publicly.

  Study phs003674

• The_Genomic_Advances_in_Sepsis__GAinS__RNA_seq

  Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 34 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected on the first, third and/or fifth day following ICU admission. RNA was extracted from leukocytes isolated at the bedside using LeukoLOCK kits. We have previously identified sepsis response signatures (SRSs), transcriptomic endotypes that are associated with differential early mortality (Davenport et al, Lancet Respir Med, 2016; Burnham et al, AJRCCM, 2017) and response to treatment in a clinical trial (Antcliffe et al, AJRCCM, 2018). We generated RNA sequencing data on 903 samples, including 134 samples repeated from our previously released microarray data. Libraries were prepared using NEB Ultra II Library Prep kits (Illumina) and sequenced on a NovaSeq 6000. Reads were aligned to the reference genome (GRCh38) using STAR and gene counts quantified using featureCounts (annotation Ensembl v99). Counts were TMM-normalised and log-transformed. Following QC, processed data were available on 864 samples from 667 unique patients.

  Study EGAS00001003772

• Host pathogen interaction long read transcriptome

  Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

  Study EGAS00001006779

• Feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric brain tumors for classification

  Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation from cfDNA for tumor classification.

  Study EGAS50000000871

• M116 scRNA-seq

  scRNA-seq was performed using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Briefly, M116's PBMCs were thawed and quantified in order to calculate the number of cells to be loaded. Then, barcoded Single Cell 3ʹ Gel Beads, a master mix containing PBMCs, and Partitioning Oil were combined onto the Chromium Next GEM Chip G to generate Gel Beads-In-Emulsion (GEMs), where polyadenylated mRNAs were reverse transcribed. This way, all generated cDNAs from the same cell shared a common 10X Barcode. Following the reverse transcription, GEMs were broken and cDNAs were amplified and cleaned up with SPRIselect beads (Beckman Coulter®). Next, a portion of these cDNAs were enzymatically fragmented and subjected to adaptor ligation before using them as a PCR template for the incorporation of i5/i7 indexes. Finally, libraries were purified with SPRIselect beads, quantified and quality checked by using the 2200 TapeStation (Agilent®), and subjected to paired-end 150-bp sequencing (Novaseq systems, Illumina®) following standard practices at external facilities (Novogene®). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001289

• scRNA seq and scTCR seq data from 5 melanoma patients

  The Chromium Controller and Chromium X platfor of 10X Genomics were used for single cell partitioning and barcoding. Each cell's transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5' Gene Expression (GEX), V(D)J and Feature Barcode (FB) Libraries were prepared according to the manufacturer's protocols (CG000330 and CG000331, 10X Genomics). All libraries were quantified and normalized on library QC data generated on the Bioanalyzer system according to manufacturer's protocols (G2938-90321 and G2938-90024, Agilent Technologies). Based on the expected target cell counts, a balanced library sub-pool of samples was compsed for SC5'GEX, V(D)J and FB libraries. Library sub-pools were quantified by qPCR, accodring to the KAPA Library Quantification Kit Illumina(R) Platforms protocol (KR0405, KAPA Biosystems). Based on qPCR results a final sequencing pool was composed. Paired end sequencing was performed on a NovaSeq 6000 Instrument (Illumina) using NovaSeq 6000 Reagent Kits v1.5 100 cycles (cat. no. 20028401, 20028319, 20028316 Illumina), using 28 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 90 cycles for Read 2.

  Dataset EGAD50000001155

• Psoriasis Patient PBMC scRNA-seq data

  This dataset contains raw and processed data of four scRNA-seq PBMC samples from four Psoriasis patients (Pso3 = male, Pso4 = female, Pso7 = female, Pso8 = male). Raw sample libraries were prepared with 10x 5'-kit v2 multiplexing the individual samples using TrueSeq barcoded antibodies to stain the cells. Resulting sequencing data consists of four FASTQs (2 x antibody multiplex to demultiplex the samples + 2 x transcriptome data containing the typical cell x UMI barcode data for count matrix generation). The raw sequencing data was processed with cellranger 6.0.1 with the GRCh38 3.0.0 reference and cell to sample assignment was subsequently done with couhto 1.1.0 (https://github.com/dmalzl/counhto) employing the same algorithm as cellranger multi (couldn't be used here though as multi does not handle 5'-chemistry data). Processed data contains all main outputs of cellranger count in raw text format or in h5 formats including the used feature reference for (i.e. antibody barcode to sample assignment) as well as the computed cell to sample assignment computed by counhto. For further details including all used code in the analysis of the data please consult https://doi.org/10.5281/zenodo.13846873

  Dataset EGAD50000001102

• ScRNA-seq of human kidney immune cells of patients with ANCA-associated glomerulonephritis, Lupus Nephritis against a healthy nephrectomy control

  ANCA-associated glomerulonephritis (AGN) associates with a high risk of end-stage kidneydisease. The role of kidney immune cells in local inflammation remains unclear. This study investigates kidney immune cell diversity and function. Kidney tissue from AGN patients (n=5) and a lupus nephritis (LN) patient (n=1) were aquired during a biopsy procedure for a clinical indication. Needle-core biopsies were obtained for histopathological examination, and an additional pass was performed to retrieve kidney tissue for scRNA-seq. Healthy kidney tissue (n=1) was obtained from a kidney that was surgically removed do tue due to a (non-invasive) papillary urothelial carcinoma. Immediately after collection, kidney tissue was processed into a single-cell suspension and sorted using a 4-color flow cytometry panel to isolate living, CD45+immune cells. To aid in the multi-omic characterization, surface markers and T and B cell repertoires were sequenced in 2 samples (1 AGN patient and the nephrectomy control). These samples were incubated with an oligo-antibody TotalSeq-C cocktail containing 130 unique cell surface antigens.

  Dataset EGAD50000000229

• 300BCG study ATAC-seq data: human population variation of trained immunity

  ATAC-seq dataset for the paper: Title Multi-omics analysis of human population variation in immune function and in vivo response to BCG vaccination Abstract Immune responses are tightly regulated, yet highly variable between individuals. To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live attenuated vaccine induces not only an adaptive immune response against tu-berculosis, but also triggers innate immune activation and memory. We established personal immune profiles and chromatin accessibility maps over a time course of BCG vaccination in 323 individuals. This large resource uncovered genetic and epigenetic predictors of baseline immunity and BCG vaccine response. We found that BCG vaccination enhances the innate immune response only in individuals with dormant immune states at baseline, suggesting that exogeneous induction of trained immunity is not a universal booster of innate immunity, but specifically elevates weak innate immune responses. This study advances our understanding of BCG’s heterologous immune-stimulatory effects and trained immunity in humans. Moreover, our results highlight the value of epigenetic cell states as an “endo-phenotype” that connects immune function with genotype and the environment.

  Dataset EGAD50000000123

• Ibrutinib induces a global chromatin reorganisation in chronic lymphocytic leukaemia

  Chronic lymphocytic leukaemia (CLL) is the most common haematological malignancy in developed countries. Ibrutinib (PCI-32765), a specific and irreversible inhibitor of Bruton's Tyrosine Kinase (BTK) represents a major step forward in the treatment of CLL. We have undertaken a detailed analysis of the changes happening to the chromatin structure in CLL cells from patients continuously receiving oral doses of ibrutinib. ChIP-seq has been performed for H3K4me3, H3K27ac, H3K27me3 and EZH2 . We observed that Ibrutinib-dependent lymphocytosis correlates with a global and transient recruitment of EZH2 to active cis-regulatory elements and increased H3K27me3.

  Study EGAS00001002827