14983 results for "cancer studies using rna-seq"

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• Determination_of_cell_specific_regulatory_enhancers_in_hematopoetic_models

  The BLUEPRINT project is a large-scale project investigating epigenetic mechanisms involved in blood formation, in health and disease. The human variation workpackage (WP10) of the project seeks to characterize the effect of common sequence variation on the epigenome status of a cell. To do this, the project will use highly purified blood cells to minimise “experimental noise” and therefore enhance the power to discover modest effects. Two peripheral blood cell types, the CD14+CD16- monocyte (an important central orchestrator of adaptive immunity and a bridge between innate and adaptive immunity) and the CD65+CD9- neutrophilic granulocyte (the frontline cell for innate immunity) have been selected for this purpose. The two types of cells will be obtained at high purity from adult blood (AB) of 200 healthy males and females, respectively. Cells will be purified by using already validated and fully operational protocols that are based on density gradient centrifugation of the buffy coat obtained from whole blood, followed by magnetic bead-based purification using monoclonal antibodies against Cluster of Differentiation (CD) lineage-specific cell surface markers. This data set contains functional genomics data for gene expression and chromatin state.

  Study EGAS00001000586

• H3Africa - An integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasis

  The objective of the TrypanoGEN project is to discover genetic variants associated with different responses to sleeping sickness infection. The project was designed in two phases:Phase 1) Variant discovery; 222 samples were sequenced to approximately 10X coverage on an Illumina 2500 with 2x150bp reads, at the University of Liverpool Center for Genomic Research. In addition, 77 samples from Cameroon and Zambia were sequenced to approximately 30X Coverage at Baylor College of Medicine. The sequenced reads were mapped onto the 1000 genomes project human_g1k_v37_decoy reference genome using BWA. The SNP calling on all the samples was done using the genome analysis tool kit GATK v3.4. Samples were selected from seven populations where Trypanosomiasis is endemic: Nilo-Saharan speakers from North-West Uganda and Niger-Congo speakers from South-East Uganda, DRC, Ivory Coast, Guinea, Cameroon and Zambia. The samples included 182 controls, 97 cases, 17 latent infections and 3 suspect cases. Phase 2) Variants discovered in Phase 1 will be used in the development of the H3Africa SNP chip. This chip will then be used in a GWAS study to identify variants associated with trypanosomiasis.

  Study EGAS00001002602

• Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

  Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.

  Study EGAS00001003190

• Duplexseq_of_the_interstrand_crosslinks_WGS

  One of the most dangerous forms of DNA damage are interstrand crosslinks (ICLs), which covalently crosslink the two strands of the DNA double helix. The repair of these lesions is crucial for cellular survival due to their ability to block transcription and DNA replication. Initially, the major pathway that has been described in ICL repair involves a network of 22 genes that are mutated in a severe human genetic disease known as Fanconi Anemia (FA). Using synthetic lethality screens in the near-haploid human HAP1 cell line, we recently identified two potentially novel regulators of ICL repair, C1orf112 and THAP12. Loss of C1orf112 and THAP12 causes hypersensitivity to ICL-inducing DNA damaging agents, such as Mitomycin C (MMC). Additionally, C1orf112-depleted cells show elevated levels of micronuclei and accumulation of DNA damage in S-phase. To better understand how C1orf112 and THAP12 mediate the repair of ICLs, we want to perform mutational signature analysis, using the BotSeq method. Therefore, WT, C1orf112 and THAP12 knockout cells were cultured in vehicle or MMC treated conditions for 10 days and the genomic DNA was isolated. FANCA and FANCD2 knockout cells are taken along as controls in this experimental setting.

  Study EGAS00001006545

• Genomic_Advances_in_Sepsis__GAinS__genotyping

  This cohort comprises a subset of pateints 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 35 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected over the first five days of ICU admission. DNA was extracted from buffy coat or whole blood samples using the Qiagen DNA extraction protocol, the automated Maxwell Blood purification kit (Promega), or the QIAamp Blood Midi kit protocol (Qiagen). Genotyping data were generated using the Illumina HumanOmniExpress BeadChip (295 patients), the Infinium CoreExome BeadChip (655 patients), and the Infinium Global Screening Array BeadChip (307 patients). Genotyping QC and imputation into the Haplotype Reference Consortium was perfomed within each batch. The datasets were combined and following post-imputation filtering data were available on 1168 samples. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001007786

• NOUS-209 off-the-shelf immunotherapy has the potential to hit primary and metachronous colorectal and urothelial cancer in Lynch syndrome

  Lynch syndrome is an inherited cancer predisposition characterized by the development of microsatellite-instable tumors, most commonly colorectal and urothelial cancers. These cancers harbor recurrent frameshift mutations (FSMs) that generate shared neoantigens, creating opportunities for targeted immunotherapy. NOUS-209 is a viral-vector–based cancer vaccine encoding 209 of these shared neoantigen peptides. This study investigated the presence and evolution of NOUS-209 target FSMs in Lynch syndrome–associated tumors, revealing their persistence across primary and metachronous cancers and supporting the rationale for NOUS-209 as a preventive immunotherapy.

  Study EGAS50000001336

• Competitive selection of somatic mutant clones in normal human skin varies with body site

  The risk of getting non-melanoma skin cancer varies over 40-fold across the body. Here we map mutations in normal skin in high and low risk sites in normal donors and those with an increased risk of skin cancer. The density of mutations varied widely, with evidence of positive and negative genetic selection.  Regional differences in mutational signatures in high and low cancer risk sites and preferential selection of mutants of TP53 in high risk skin and FAT1 in lower risk skin were observed. 10% of clones had copy number changes in cancer associated genes and the largest had multiple driver mutations with loss of heterozygosity. In hair follicles, a proposed site of origin of skin cancers, mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. We conclude cancer risk reflects the efficiency of transformation of oncogenic mutants rather than the density of mutant clones.

  Dataset EGAD00001006194

• Whole-Genome Shotgun Metagenomic Analysis of Rectal Mucus for Colorectal Cancer Detection

  This study evaluates the use of rectal mucus as a minimally invasive biospecimen for colorectal cancer (CRC) detection through whole-genome shotgun metagenomic sequencing. 408 rectal mucus samples were collected from patients suspected to have colorectal cancer and sequenced. These samples were analyzed to characterize microbial community composition and its association with CRC stage and anatomical site. These data provide insights into tumor-proximal microbiome signatures and demonstrate the potential of rectal mucus sampling for early and accurate CRC diagnosis. This is 1 of 4 sequencing experiments on the same sample type.

  Study EGAS50000001310

• Canadian Prostate Cancer Genome Network

  Over 5 years, CPC-GENE will sequence the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE will also sequence multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

  Study EGAS00001000900

• Novel Epigenetic Markers for Toxicity after Intraoperative and Conventional Radiotherapy for Breast Cancer

  Ionizing radiation is a common treatment option for cancer but its use is limited by the unpredictable and highly heterogeneous onset of late side effects, especially radiation-induced fibrosis. Clinically applicable biomarkers and effective treatments for radiation fibrosis are currently unavailable. In order to identify novel markers we ran a genome-wide DNA methylation screen in primary dermal fibroblasts obtained from breast cancer patients before intraoperative radiotherapy. Cells from patients developing fibrosis within a three-year follow up were compared to those without fibrosis (12 individuals per group). Illumina Infinium HumanMethylation450 BeadChip Technology was used.

  Study EGAS00001001279

• molecular profiles of serum-derived extracellular vesicles in high-grade serous ovarian cancer

  Patients with high-grade serous ovarian cancer (HGSC) who have no visible residual disease (R0) after primary surgery have the best clinical outcomes, followed by patients who undergo neoadjuvant chemotherapy (NACT) and have response enabling interval cytoreductive surgery. Clinically useful predictive biomarkers for such distinctions are still lacking. Extracellular vesicles (EVs) have been recognized as liquid biopsy-based biomarkers for early cancer detection and disease surveillance in other disease settings. In this study, we performed extensive molecular characterization of serum-derived EVs and correlated them with therapeutic outcomes in patients with HGSC.

  Study EGAS00001006350

• WGBS dataset for lymphnode metastasis samples from prostate cancer

  This dataset contains WGBS sequencing data of lymphnode metastasis samples from prostate cancer. Sequencing was performed on Illumina HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000001183

• Multi-omic profiling of patient-derived pancreatic tumor organoids

  We conducted multi-omic profiling of patient-derived pancreatic cancer organoids and genetically engineered normal pancreas organoids.

  Study JGAS000719

• Amplicon sequencing of adenoma to carcinoma paired samples from colon

  Colorectal cancer panel sequencing of 100 adenoma and carcinoma samples . Cancer Hot Spot panel sequencing of 7 samples from one poly.

  Dataset EGAD00001004848

• Paired-end sequenced plasma DNA samples

  Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.

  Dataset EGAD00001002217

• Whole genome sequencing of 8 HER2-Positive Breast Cancer (in complement to EGAD00001001844)

  Whole genome sequencing of 8 HER2-Positive Breast Cancer (in complement to EGAD00001001844)

  Dataset EGAD00001003189

• Epigenomic profile of diverse cancer

  The samples are from patients of multiple cancer types. The library preparation protocol was developed by the laboratory. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001006124

• Ovarian cancer sequencing dataset

  Sequencing data from patients with Ovarian cancer. Data utilised in the 'Enhanced detection of circulating tumor DNA by fragment size analysis' manuscript (Mouliere et al, 2018)

  Dataset EGAD00001004939

• checup

  Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

  Study EGAS00001007403

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  Dataset EGAD00001015387

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  Dataset EGAD00001015388

• Recurrent intra-tumour heterogeneity is a hallmark of metastatic prostate cancer

  The evolution of cancers from low grade to metastatic disease is a major determinant of cancer mortality. Cancer evolution involves a complex interplay between cell intrinsic genetics and transcriptional alterations and the extrinsic microenvironment. To define the key mechanisms underpinning metastatic development, we focused on the most lethal form of prostate cancer, metastatic castration-resistant prostate cancer, and employed single-cell multi-omics and whole-genome sequencing to deeply profile 34 metastatic lesions from 9 patients obtained from rapid autopsy. We found that intra-tumour heterogeneity is an indicator of key evolutionary processes, characterised by recurrent tumour populations acting as critical functional components of the tumour ecosystem, irrespective of clonal and microenvironmental backgrounds. Unexpectedly, microenvironments across metastatic sites played a limited role while clonal evolution primarily promoted transcriptional noise. Intra-patient functional convergence of tumour ecosystems was observed across metastatic sites, pointing towards system-level selection pressures that drive the heterogeneity landscape of mCRPC. Our findings reveal functional evolutionary convergence of metastatic disease into units of intra-tumour heterogeneity identifying critical determinants of metastatic progression for therapeutic targeting. Note: matched WGS for some tumour single-cell experiments, as well as germline WGS for patients CA0027, CA0034, CA0035, CA0043, and CA0076, can be found in EGAS00001006598.

  Study EGAS50000001312

• nanostring_gene_expression

  Two to four sections of 10 µm thickness each (depending on sample size) from the respective formalin-fixed paraffin-embedded (FFPE) tissue sample were used for RNA isolation on 46 resected tumors as well as 17 paired biopsies. Digital gene expression analysis was performed on the NanoString nCounter platform, utilizing the NanoString MAX/FLEX system, with the PanCancer Immune Profiling panel as well as the PanCancer Pathway panel provided by NanoString.

  Dataset EGAD00010002654

• Single-sell RNA sequencing counts from 7 acute myeloid leukemia patients and 3 healthy donors

  This dataset contains count data (from 10X CellRanger) and metadata from 7 acute myeloid leukemia subjects treated with chemotherapy, as well as data from 3 healthy donors. Additionally, the dataset includes VDJ data for all subjects except for 31_base and the 3 healthy donors (TCRseq not performed).

  Dataset EGAD50000000525

• 10X Genomics single-nuclei RNA-sequencing of endometrium from women with and without PCOS

  Chromium Next GEM Single Cell 3’ Gel Bead Kit (Dual Index) v3.1 (10X Genomics) of endometrium from 27 women including 5 without PCOS and 12 with PCOS. Following baseline biopsies, PCOS participants underwent a 16-week randomized controlled trial with metformin (n=7) or lifestyle intervention (n=3). 25,000 raw reads per nucleus

  Dataset EGAD50000001017

• Glioblastoma CRISPR Screen (2016-06-02)

  This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2016-06-02.

  Dataset EGAD00001002158

• Single cell atlas of human glioma

  We profiled 87 primary-recurrentpatient-matched paired GBM specimens with single-nucleus RNA and bulk-DNA sequencing and single-cell open-chromatin and spatial transcriptomics/proteomics assays. We found that recurrent GBMs are characterized by a shift to a mesenchymal phenotype in response to therapy

  Dataset EGAD00001008811

• SMARTer bulk RNA sequencing for highly purified CD271+ BMSCs from NBM and AML

  bulk RNAseq was conducted on highly purified CD45 - CD71 - CD235a - CD31 - CD271 + BMSCs isolated from a cohort of newly diagnosed 62 AML patients, uniformly treated within an intensive chemotherapy clinical trial and selected to represent the mutational landscape of AML

  Dataset EGAD00001011056

• Long read mRNA sequencing of blood cells exposed to different immune stimuli

  Long-read (PacBio) RNA sequencing dataset of in vitro stimulated PBMC cells. 5 samples consisting of 1 RPMI control and 4 stimulus conditions (lipopolysaccharide (LPS), polyI-polyC, S. aureus and C. albicans) all originating from one donor. Files are raw BAM format files generated by Sequel 2 machine.

  Dataset EGAD00001009998

• Glioblastoma CRISPR Screen (2017-04-27)

  This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2017-04-27.

  Dataset EGAD00001003308

• POT1 splice site mutant analysis

  We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.

  Dataset EGAD00001000786

• TTV018 RORC IBD-associated genotype effects on RORgT expression and function in ex vivo T cells

  RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001002233

• Genotype data of human CD4 Treg cell

  Genotype data obtained using the coreExome Illumina SNP chip array for all the individuals included in the study of gene expression regulation in human primary regulatory CD4+ T cells (Tregs)

  Dataset EGAD00010001848

• RCC_HTA2.0_Reustle2020

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) related to Reustle et al, Genome Med 12:2020 32. Preprocessing of microarray data was performed using Robust Multi-array Average (RMA).

  Dataset EGAD00010002323

• Illumina Infinium MethylationEPIC Array IDAT files generated from 11 glioma patient samples

  This dataset includes IDAT files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using the Illumina Infinium MethylationEPIC Array.

  Dataset EGAD00010002157

• Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

  This dataset contains 224 paired fastq files (112 single cells) from the following samples: brains from two Multiple System Atrophy patients and one control, and non-brain controls (fibroblasts, NA12878)

  Dataset EGAD50000000030

• Whole Exome Sequencing Data

  Here, we provide mapped cram files from 35 multiple myeloma patients. Sequencing was performed employing Illumina's short read technology. Resulting sequencing data was mapped against GRCh38 using nfcore/sarek v3.2.3.

  Dataset EGAD50000000578

• Whole Exome Sequencing Data of prDLBCL

  We used sequenced 34 prDLBCL samples using whole exome sequencing (WES) data to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

  Dataset EGAD50000000591

• LBC1936 bam files

  1075 members of the LBC1936 were sequenced using the Illumina HiSeq X platform. This dataset contains the bam files.

  Dataset EGAD50000001740

• WES_dataset3

  Six EATLs and three MEITLs (among which 5 had only tumoral tissue available) were sequenced using the xgen research panels v2.0 from IDT DNA (Newark, New Jersey, USA).

  Dataset EGAD50000001618

• DAC: LUMC NeuroD AON off target analysis

  In this study, we used three different splice-switching AONs targeting three different human transcripts to study their transcriptome-wide, hybridization-dependent off-target effects with short read RNAseq. Using the computational tools rMATS and Whippet, in control human induced pluripotent stem cells

  Dac EGAC50000000726

• Microhaplotype amplicon sequencing of cervical samples and controls

  Microhaplotype amplicon sequencing of cervical samples (n=10), parental DNA (n=20), cfDNA (n=10) and control experiments using HapMap DNA in different spike-in percentages.

  Dataset EGAD00001010120

• Whole exome sequencing datasets for Low-grade Serous Ovarian Carcinoma

  This dataset includes whole exome sequencing reads from 10 normal and 14 cell lines based on Agilent SureSelect XT Human All Exon v6. They are all 2*100bp reads sequenced using Illumina HiSeq4000.

  Dataset EGAD00001006440

• HV31 - PacBio continuous long read (CLR) sequencing

  PacBio continuous long read (CLR) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using DNA from CD14+ monocytes, to a sequencing depth of ~35×. Sequencing was performed at the Wellcome Sanger Institute.

  Dataset EGAD00001007047

• Genome-wide prediction of human embryos

  This dataset includes whole genome sequence information for three individuals (Mother, Father and Newborn) used in this study. Genomes were sequenced using Illumina HiSeq technology. Files included are fastq files in paired read format.

  Dataset EGAD00001002257

• Duplex sequencing data (SaferSeqS)

  Bam files aligned using hg19. Sequencing data generated with Illumina MiSeq, HiSeq 2500, or HiSeq 4000 instruments.

  Dataset EGAD00001009757

• Dataset for WES PCNSL

  WES sequencing of 23 samples from PCNSL tumor and blood control samples. Sequencing was performed on a NovaSeq 6000 and NextSeq 500 using Agilent SureSelectXT HS Human All Exon V7 and V8. Sequencing was always paired.

  Dataset EGAD00001010847

• 200PT : CNA vcf files

  200PT : CNA vcf files. Copy Number Abberation calls generated using TITAN and PhyloWGS, from the CPCGene 200PT Subclonality study

  Dataset EGAD00001004073

• Microbial infections in Multiple Sclerosis Samples

  In this study, we have examined microbial infection in brain tissue from 9 control samples from healthy patients and 10 samples from patients diagnosed with Multiple sclerosis, by Next-generation sequencing NGS using Miseq sequencing platform (Illumina).

  Dataset EGAD00001004085

• WES data of one tumor of B-cell lymphoma

  paired EXOME sequencing on Illumina HiSeq 4000 using Agilent SureSelect V6 of one tumor sample of one patient with B-cell lymphoma. The bam-file was mapped to the hg19 genome.

  Dataset EGAD00001006060