12310 results for "cancer rna-seq"

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• Somatic_mutation_and_clonal_evolution_in_the_human_testes

  In this study we aim to characterise the landscape of Pathogenic variants and clonal dynamics in normal and cancerous testes and their role in cancer predisposition. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from testes. The range of patients studied will include healthy individuals, and patients with testicular cancer.

  Study EGAS00001003021

• Somatic_mutation_and_clonal_evolution_in_the_human_bladder_TGS

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer.

  Study EGAS00001002659

• Somatic_mutation_and_clonal_evolution_in_the_human_testes___WES

  In this study we aim to characterise the landscape of Pathogenic variants and clonal dynamics in normal and cancerous testes and their role in cancer predisposition. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from testes. The range of patients studied will include healthy individuals, and patients with testicular cancer.

  Study EGAS00001003023

• Detection and localization of surgically resectable cancers with a multi-analyte blood test

  Earlier detection is key to reducing cancer deaths. Here we describe a blood test that can detect eight common cancer types through assessment of the levels of circulating proteins and mutations in cell-free DNA. We applied this test, called CancerSEEK, to 1,005 patients with clinically detected cancers of the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast. CancerSEEK tests were positive in a median of 70% of the eight cancer types. The sensitivities ranged from 69% to 98% for the detection of five cancer types (ovary, liver, stomach, pancreas, and esophagus) for which there are no screening tests available for average-risk individuals. The specificity of CancerSEEK was > 99%: only 7 of 812 healthy controls scored positive. In addition, CancerSEEK localized the cancer to a small number of anatomic sites in a median of 83% of the patients.

  Study EGAS00001002764

• FGFR-driven urothelial cancer

  Study EGAS00001007335

• scRNA-seq for 4 reactive lymph node and 12 high grade B cell lymphoma samples

  Dataset includes count matrices, barcode tsvs, and features tsv for each sample, generated using Cell Ranger.

  Dataset EGAD50000001386

• NICHE - DNA-seq of MMR proficient early stage colon cancers

  The dataset includes 152 FASTQ files from paired-end WXS sequencing on Illumina HiSeq2500 or Novaseq 6000 for 31 pMMR patients. This includes 31 tumor DNA and 31 blood germline samples.

  Dataset EGAD50000001247

• DNA-seq from plasma of 14 liver transplantation patients

  We performed DNA sequencing on the plasma of 14 liver transplantation patients to study the liver DNA in the plasma.

  Study EGAS00001003116

• RRBS - MBD4-deficient AML

  Reduced Representation Bisulfite Sequencing for WEHI-AML-1 and WEHI-AML-2. RRBS libraries were made with the NuGEN Ovation RRBS Methyl-Seq System. Bisulfite conversion was performed with the Qiagen Epitect kit. Sequencing was performed on an Illumina HiSeq2500.

  Dataset EGAD00001003567

• DEEP-IHEC-release-2017

  Raw data files for the German Epigenome Project (DEEP), IHEC/EpiRR submission of 2017. metadata available at: http://deep.dkfz.de/#/experiments

  Dataset EGAD00001003974

• DLBCL Validation (FFPE) Cohort

  miRNA-seq Cohort of 140 Formalin Fixed Paraffin Embedded Diffuse Large B-cell Lymphoma Patient Samples

  Dataset EGAD00001001073

• Epigenetic subtypes of neuroblastoma - ChIPseq

  In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 60 primary neuroblastoma samples.

  Dataset EGAD00001006285

• 5hmC enrichment in human monocyte differentiation

  This dataset consists of 5hmC capture-seq data from human monocytes, monocyte-derived dendritic cells. It includes two biological replicates and three time points. Including controls, the dataset comprises 10 samples in total.

  Dataset EGAD00001006603

• CAGE-seq of frontal post-mortem human brain tissue of patients with FTD and healthy controls

  CAGE-sequencing was performed on frontal post-mortem human brain tissue of patients with FTD caused by mutations in GRN, MAPT or C9orf72 and healthy controls.

  Dataset EGAD00001006843

• Dataset for ChIP and Transcriptomic sequencing of neuroblastoma tumor samples(hipo)

  This dataset contains ChIP and Transcriptomic sequencing of 32cneuroblastoma tumor samples. The sequencing was performed on Illumina HiSeq 2000 and Illumina HiSeq 4000 respectively.

  Dataset EGAD00001015808

• Study of 5'UTR Mutations in Prostate Cancer

  The 5' untranslated region (5' UTR) of mRNA controls the translation of specific transcripts through encoded cis-regulatory elements. Yet exceedingly little is known about the prevalence and function of 5' UTR mutations in cancer. We have uncovered many 5' UTR mutations in our analysis of localized and castration resistant prostate cancer patients, and hypothesize that systematic mutations in critical 5' UTR regulatory regions perturb gene expression to drive prostate cancer progression. To elucidate the functional 5' UTR regulatory landscape of prostate cancer, we have taken a multi-faceted approach including ribosome profiling, in vitro reporter assays and the development of a novel high throughput method to functionally access the impact of recurrent 5' UTR mutations on both transcription and translation.

  Study phs001825

• Cancer Registry of Norway - NIPH Data Access Committee for CRCbiome datasets

  The Cancer Registry of Norway - NIPH appointed Data Access Committee for the CRCbiome datasets - The microbiome as a colorectal cancer screening biomarker. https://www.mn.uio.no/sbi/english/groups/rounge-group/crcbiome/.

  Dac EGAC50000000121

• Massachusetts General Hospital Cancer Center DAC for high-throughput microfluidic enrichment from whole leukopak for CTC-based liquid biopsy

  Whole genome sequencing and whole exome sequencing data of circulating tumor cells isolated from patients with metastatic prostate cancer and liver cancer.

  Dac EGAC50000000423

• Colorectal_organoids_and_tumour_tissue

  Whole genome sequencing of single cell derived organoids from normal colon tissue and colorectal cancer.

  Study EGAS00001000881

• Analyses of IACS-010759 treatment resistance on breast cancer bone metastases

  Identification of biological mecanisms involved in resistance of breast cancer bone metastases to IACS treatment.

  Study EGAS00001006429

• RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the SardiNIA cohort.

  We sequenced the polyA+ of the RNA of the leukocytes from 624 sardinian individuals with RNAseq (Illumina 2000, an average of round 60M reads per sample, 51 + 51 nt). Combining the genotype information of the same individuals (already available from the ProgeNIA project) with the transcriptome data we identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs), including 619 novel QTLs that exhibit population-specific trait associations. Using family relationships, we identified 809 segregating expression outliers and provide a new approach to study large effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk.

  Study EGAS00001002105

• RNA sequencing on intestinal biopsies from inflammatory bowel disease patients treated with vehicle control, MEK inhibitor, or infliximab

  By investigating an intergenic haplotype on chr21q22, independently linked to inflammatory bowel disease (IBD), ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis, we discover that the causal gene, ETS2, is a master regulator of inflammatory responses in human macrophages and delineate how the risk haplotype increases ETS2 expression. Using a database of cellular signatures, we identified drugs that could modulate this pathway. To validate the anti-inflammatory activity of one class of small molecules ex vivo, we obtained biopsies from patients with active IBD and cultured these biopsies with a selective, non-ATP competitive MEK inhibitor (PD-0325901), infliximab (positive control), or DMSO (vehicle control) for 18 hours, then performed RNA sequencing.

  Study EGAS00001007534

• minION fastq files of 10 different tumor samples from the Master program (H021)

  Nanopore RNA Sequencing was done for 10 tumor samples. Direct cDNA sequencing was performed using the SQK-DCS109 kit (Oxford Nanopore Technologies). For analysis of a single sample on a MinION flow cell (version R9.4.1), 5 μg RNA was used as input. For multiplexing on a MinION flow cell, 2.5 μg RNA per sample was used as input, and the native barcoding expansion kit EXP-NBD104 was employed in conjunction with SQK-DCS109. After reverse transcription with Maxima H Minus Reverse Transcriptase (Thermo Scientific), second-strand synthesis was performed using the 2x LongAmp Taq Master Mix (New England Biolabs). The resulting double-stranded cDNA was subjected to end-repair and dA-tailing using the NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs). For multiplexed libraries, this step was followed by barcode ligation and library pooling. Next, libraries were quantified with a Qubit Fluorometer 3.0 (Life Technologies). Finally, sequencing adapters were added to the library preparations and ligated with Blunt/TA Ligase Master Mix (New England Biolabs), followed by further quality control using a Qubit. Samples ACC1 and ACC2 were analyzed on individual MinION flow cells, while the remaining eight samples were sequenced as multiplexed libraries on two MinION flow cells by pooling four samples for each run. Five ACC samples were also analyzed individually on Flongle flow cells

  Dataset EGAD00001008970

• Using genetics to identify cell types and mechanisms underlying susceptibility to primary sclerosing cholangitis

  Primary sclerosing cholangitis (PSC) is a T-cell mediated, chronic inflammatory condition of the biliary tree that is strongly associated with inflammatory bowel disease. Genome-wide association studies have identified 22 non-HLA genetic risk variants associated PSC. Identifying the genes impacted by these variants has proven difficult as the majority lie in non-coding regions of the genome. Knowledge of the genes and biological pathways these non-coding variants are perturbing is vital to understanding the disease biology. One means of assessing the impact of non-coding variants within disease associated loci upon genes is via colocalisation with eQTL. Many eQTL are cell-type specific, requiring the analysis of disease relevant cell types to detect colocalisation. We have collected PSC-relevant T-cell-subtypes from the peripheral blood of PSC patients via fluorescence activated cell sorting in preparation for RNA sequencing and mapping of eQTL. Samples were collected at the Norfolk and Norwich University Hopital, for which local ethical approval has been granted. Lysed cell samples will be transferred to WTSI and DNA/RNA will be extracted from lysed cell samples by T143 before genotyping (DNA) and custom library preparation and sequencing (RNA). 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 EGAD00001011815

• Phase I Study of the Oral PI3kinase Inhibitor BKM120 or BYL719 and the Oral PARP Inhibitor Olaparib in Patients with Recurrent Triple Negative Breast Cancer or High Grade Serous Ovarian Cancer

  We analyzed massive parallel sequence data from patients with breast and ovarian cancer and identified single base substitution mutational signature 3 (Sig3) - extracted using SigMA - as a biomarker of homologous recombination deficiency (HRD) and predictive for response to PARP inhibitors. Participants were patients enrolled in clinical trials as 2 independent datasets: (1) high-grade serous ovarian cancer and triple-negative breast cancer (TNBC) from a Phase 1b trial of the PARP inhibitor olaparib in combination with the PI3K inhibitor buparlisib (BKM120) (NCT01623349), and (2) TNBC patients who received neoadjuvant olaparib in the Phase II PETREMAC trial (NCT02624973).

  Study phs003019

• TRACERx100 metastatic samples

  Whole exome sequencing of 10 metastatic biopsies from four TRACERx100 patients (see EGA dataset EGAS00001002247), collected either after relapse or death. The data from these samples are initially published with Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early stage lung cancer evolution. Nature, http://dx.doi.org/10.1038/nature22364 (2017). Abstract: Earlier detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a patient-specific approach to ctDNA profiling in the first 100 lung TRACERx (TRAcking Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release in early-stage non-small cell lung cancer and perform tumor volume limit of detection analyses. Through blinded profiling of post-operative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients destined to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastases, providing a new approach for ctDNA driven therapeutic studies.

  Dataset EGAD00001003301

• Detection of Cancer Mutations by Urine Liquid Biopsy in Bladder Cancer Patients

  The management of bladder cancer faces multiple challenges concerning the diagnostics and fol-low-up approaches. The standard diagnostic test is invasive cystoscopy. Urine cytology and re-cently proposed urine-based biomarkers still could not replace cystoscopy, thus prompting calls for improvements. Here, we explore urine liquid biopsy to detect cancer mutations for therapeutic and prognostic assessment and subsequently evaluate the utility of urine as a suitable specimen in diagnosing bladder cancer. Our findings show that the analysis of pre-and post-operative urine enables the characterization of specific tumor mutations, which can be used to diagnose and evaluate a patient’s prognosis and therapy response.

  Study EGAS00001005758

• Small Genomic Insertions Form Enhancers that Misregulate Oncogenes

  ChIP-Seq data from 102 cell lines were processed to identify insertions relative to the human reference genome. To confirm the ability of a computational pipeline to identify insertions that are actually present in these genomes, we PCR-amplified and deeply sequenced regions where insertions were predicted to exist in MOLT4 T-cell acute lymphoblastic leukemia cells. The current study release makes available sequences of amplicons from a tumor cell genome (MOLT4) where a computational pipeline predicted small insertions from orthogonal data.

  Study phs001242

• Decade-Long Leukemia Remissions with Persistence of CD4+ CAR T-Cells

  Two patients with chronic lymphocytic leukemia (CLL) were treated with CD19 targeted CAR T therapy and followed over several years. Peripheral blood from both patients at multiple time points was collected, and 5' CITE-Seq with TCR profiling was performed on sorted CD3+CAR+ T cells at multiple time points. Here, we deposit the raw sequencing data for these single-cell experiments. Processed and de-identified data (e.g. cellranger output, Seurat objects) have been made available on a separate public data repository.

  Study phs002931

• High-throughput determination of the antigen specificities of T cell receptors in single cells

  High-throughput linking of T cell receptor (TCR) sequences to their binding antigens is vital for immune profiling, yet challenging. We present Tetramer associated TCR Sequencing (TetTCR-Seq) to address this challenge. Binding is determined using a library of DNA-barcoded antigen tetramers that are rapidly and inexpensively generated using an in vitro transcription/translation platform. We included CMV+ donors (CMV seropositive donors who are infected with Cytomegalovirus) to screen for CMV specific TCRs.

  Study phs001678

• ATACseq of primary fibroblasts and iPSC-derived endoderm cells in CPRF patients with LSD1 mutations and healthy controls

  Primary fibroblasts or iPSC-derived endoderm cells from two CPRF patients carrying distinct heterozygous point mutations in histone demethylase LSD1/KDM1A and their healthy fathers were expanded and split into two cell culture wells and independently passaged twice before cell collection. Nuclei were isolated from the two biological replicates of each individual-derived fibroblasts and used for bulk ATAC-seq library preparation. Libraries were sequenced in paired-end mode on Illumina NextSeq 500. 

  Study EGAS00001008238

• Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted from 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 (KI_3mo).

  Study EGAS50000000469

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  Data generated through single nuclei ATAC sequencing on whole ganglionic eminences from 3 human fetuses (two of 16 and one of 17 gestational weeks). Tissue was acquired from the MRC-Wellcome Trust Human Developmental Biology Resource with ethical approval. snATAC-Seq libraries were prepared from ~8,000 nuclei per sample using Chromium Next GEM Single Cell ATAC (v1.1) reagents (10X Genomics). Quality control of libraries was performed using the Agilent 5200 Fragment Analyzer before sequencing on an Illumina NovaSeq 6000 to a depth of at least 617 million read pairs per library. Raw sequencing data were converted into FASTQ files. For a full description of data generation, please see Cameron et al, Schizophrenia Bulletin 2024, https://doi.org/10.1093/schbul/sbae083. Please note that 10X generated BAM files, rather than FASTQ files, have been uploded. FASTQ files can be regenerated using the 10X Genomics bamtofastq tool. https://support.10xgenomics.com/docs/bamtofastq

  Dataset EGAD50000000601

• LCM-ATACseq on human lung macrophages

  In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation), and processed for ATAC-seq.

  Study EGAS00001006167

• COVID_19_Challenge_Project_Single_Cell_Profiling

  Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection

  Study EGAS00001005696

• cfMethyl-Seq

  cfMethyl-Seq libraries were generated for 479 cfDNA samples and were sequenced with 150 bp paired-end reads.

  Dataset EGAD00001009003

• RNA Sequencing of Control and Myotonic Dystrophy Type 1 Cells During Myogenic Differentiation

  RNAseq data of 30 muscle cell samples (proliferating myoblasts to differentiating myotubes) of immortalized control cells, and myotonic dystrophy type 1 (DM1) patient-derived cells and their edited versions.

  Dac EGAC50000000592

• EAC-scRNA

  This dataset contains single cell RNA-sequencing of EAC samples by 10x Genomics. Total number of files - 24. File format - FASTQ.

  Dataset EGAD50000000752

• BE-scRNA

  This dataset contains single cell RNA-sequencing of BE samples by 10x Genomics. Total number of files - 28. File format - FASTQ.

  Dataset EGAD50000000753

• Single-cell Full Transcriptome RNA sequencing

  Single cell full transcriptome sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD50000000201

• Dataset for RNA sequencing of Glioblastoma samples

  This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD50000000081

• Genomic alterations in MM - CEL

  RNA from the same tumor sample (n=98) was also processed using the 3' IVT kit (Affymetrix) and hybridized to U133 Plus 2.0 arrays (Affymetrix).

  Dataset EGAD00010001577

• Single-cell Full Transcriptome RNA sequencing

  Single cell full transcriptome sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD00001006325

• Single cell targeted RNA sequencing

  Single cell hybrid-capture targeted sequencing of CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma.

  Dataset EGAD00001006327

• Alveolar Rhabdomyosarcoma sequencing data

  This dataset comprises DNA sequencing for tumor and matched normal from an Alveolar Rhabdomyosarcoma patient. It also include RNA sequencing data from the tumor sample.

  Dataset EGAD00001006622

• Single cell sequencing of newly-diagnosed and recurrent GBM

  Single cell RNA and CITE sequencing of newly-diagnosed and recurrent GBM

  Dataset EGAD00001006778

• Combinatorial Indexed 10x Genomics Single-Cell ATAC-seq on Human Cerebral Cortex

  Single-cell chromatin accessibility profiling (scATAC) using droplet fluidics (10x Genomics) is inherently limited in throughput due to the number of available indexed droplets. This study leverages single-cell combinatorial indexing workflows with modified adapter designs to enable indexed tagmentation and superloading of pre-indexed nuclei into the 10x Genomics scATAC workflow, enabling a substantial increase in the number of cell profiles that can be obtained per channel. This workflow, 10x single-cell combinatorial indexed ATAC-seq (txsciATAC), is demonstrated on human brain tissue (middle frontal gyrus), along with mouse brain tissue to enable doublet and crosstalk assessment. This study includes all human data and includes a single preparation taken through nuclei isolation and indexed tagmentation using 96 indexes then split to produce two datasets, one targeting 20k cells and one targeting 70k, each using a single channel of the 10x Chromium controller.

  Study phs003497

• BLUEPRINT ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  ChIP-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000326

• Genome-wide DNA methylation profiles by MeDIP-seq of cord blood cells and cord blood mononuclear cells obtained from twins conceived through in vitro fertilization and naturally conceived controls

  The study included 47 newborn twins conceived though in vitro fertilisation (IVF) and 60 non-IVF-conceived twins from the Peri/postnatal Epigenetic Twins Study (PETS). Cord blood was collected at birth and used to process mononuclear cells. Whole blood cells (WBCs) from cord blood of 98 twins (40 IVF and 58 non-IVF) and cord blood mononuclear cells (CBMCs) of 82 twins (35 IVF and 47 non-IVF) were subjected to DNA methylation profiling. Methylated DNA immunoprecipitation followed by deep sequencing (MeDIP-seq) was applied to generate genome-wide DNA methylation profiles in a total of 180 samples. Single-end reads were mapped onto hg19 using BWA. Methylation levels were quantified using MEDIPS and used to identify IVF-associated differentially methylated regions.

  Study EGAS00001002248

• ATAC-Seq of healthy and IBD blood samples

  PBMCs from blood samples of 9 age- and gender-matched healthy subjects and 25 IBD patients were isolated through a Ficoll density gradient and used to isolate live CD4 T cells through a magnetic cell isolation kit (Miltenyi Biotec). Twelve thousand live CD4 T cells were then used to prepare ATAC-Seq libraries. Briefly, crude nuclei of live CD4+ T cells were treated with Tagment DNA buffer and Tagment DNA Enzyme (Nextera DNA Library Prep Kit, Illumina), and then the DNA was purified by MinElute PCR Purification Kit (Qiagen). Transposed DNA fragments were amplified using specific adapters followed by purification with MinElute PCR Purification Kit (Qiagen). Fragments from 240-360pb were selected in the PippinHT system (Sage Science). The quality of the library and its DNA concentration were assessed by Bioanalyzer instruments (Agilent Technologies) and ultimately submitted for sequencing using Illumina HiSeq 2500 sequencer, V4 chemistry.

  Study EGAS00001007343