9337 results for "cancer rna-seq"

in 46.94 milliseconds.

• Single-cell analysis for metastatic gastric adenocarcinoma

  Intra-tumoral heterogeneity (ITH) is the fundamental property of cancer, however, the origins of ITH remain poorly understood. Here we performed single-cell RNA sequencing of peritoneal carcinomatosis (PC) from patients with advanced gastric adenocarcinoma (GAC), constructed a transcriptome map of 45,048 PC cells, profiled the transcriptome states of diverse tumor cell lineages and types, incisively explored ITH of PC tumor cells, and identified significant correlates with patient survival.

  Study EGAS00001004443

• Immunogenomic landscape of hematological malignancies

  We integrated over 8,000 transcriptomes and over 2,000 samples with multilevel genomic data of hematological cancers to investigate how immunological features are linked to cancer subtypes, genetic and epigenetic alterations, and patient survival. For more detailed follow-up analyses in acute myeloid leukemia (AML), single-cell RNA sequencing was performed on 8 AML bone marrow samples at diagnosis to profile the phenotypes of blasts and infiltrating immune cells in different disease subtypes.

  Study EGAS00001004444

• Genetic drivers of epigenetic and transcriptional variation of human immune responses to infection (RNA-seq, ATAC-seq and ChIPmentation)

  RNA-seq, ATAC-seq and ChIPmentation data from monocyte-derived macrophages that were infected with Influenza A virus strain PR8WT, or a matching non-infected control.

  Dataset EGAD00001008422

• RNA-Seq of Whole Blood from Pediatric Sickle Cell Anemia (SCA) Patients

  The aim of this study is to define the immune cell transcriptome by next generation RNA sequencing in blood from individuals with SCA, in comparison to healthy African American controls. This study has a cross-sectional case-control design. We will compare the transcriptome profiles of blood mononuclear cells from healthy age-matched African American children without cardiovascular disease or risk factors (“Controls”) to those of children with SCA, age 5 -21 years, who are not receiving chronic red blood cell transfusions or hydroxyurea therapy to identify genes that are differentially expressed in SCA. 

  Study phs002687

• Temporal stability of circulating microRNAs in human serum

  Circulating microRNA biomarkers for disease have been subject to extensive research. However, insufficient consideration of variability in the healthy population has led to few markers achieving the performance necessary in independent follow-up studies to be taken forward to clinical practice. To investigate the natural variation of circulating microRNA over time, we performed small RNA sequencing in a longitudinal study of 66 women with no history of cancer, and determined the distribution and dynamics (via intraclass correlation coefficients, ICCs) of the miRNA profile over 3 time points sampled across 2-5 years. We also investigate abundances in circulation, as well as the impact of normalization, age, BMI, and other sample collection factors on microRNA measurements from small RNA sequencing.

  Study EGAS00001003221

• Whole Genome Comparisons of Breast Cancers and their Xenotransplants

  Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.

  Study phs000611

• an integrated molecular study of clear cell renal cell carcinoma (ccRCC) including whole-genome/exome and RNA sequencing as well as array-based gene expression/copy-number/methylation analyses

  Study EGAS00001000509

• IVAC Melanoma

  Whole exome and transcriptome sequencing of 12 melanoma patients (including technical replicates). linicalTrials.gov Identifier: NCT02035956. Paper: Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer - Nature volume 547, pages 222–226

  Dataset EGAD00001004455

• Ductal keratin 15+ luminal progenitors in normal breast exhibit a basal-like breast cancer transcriptomic signature

  Normal breast luminal epithelial progenitors have been implicated as cell of origin in basal-like breast cancer, but their anatomical localization remains understudied. Here, we combine micro-collection of uncultured organoids and single cell mRNA sequencing (scRNA-seq) of FACS-sorted luminal epithelial cells with multicolor imaging to profile ducts and terminal ductal lobular units (TDLUs) and compare them with breast cancer subtypes. Unsupervised clustering reveals eleven distinct clusters and a differentiation trajectory starting with keratin 15+ (K15+) progenitors enriched in ducts. Spatial mapping of luminal progenitors is confirmed at the protein level by staining with critical duct markers. Comparison of the gene expression profiles of normal luminal cells with those of breast cancer subtypes reveals a strong correlation between normal breast K15+ ductal progenitors and basal-like breast cancer. We propose that K15+ basal-like breast cancers originate in ductal progenitors, which emphasizes the importance of not only lineages but also cellular position within the ductal-lobular tree.

  Study EGAS00001005963

• FASTQ files of total RNA-Seq data of POPS control samples

  Placental biopsies (n = 64 female placentas, n = 67 male placentas) were selected from healthy pregnancies from the POPs cohort. These patients had no evidence of hypertension at booking and during pregnancy, did not experience pre-eclampsia, Hemolysis, Elevated Liver enzymes, and Low Platelets (HELLP) syndrome, gestational diabetes, or diabetes mellitus type I or type II and other obstetric complications. They delivered live babies with a birth weight percentile in the normal range (20-80th percentile), with no evidence of slowing in fetal growth trajectory. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003457

• How to use the EGA search box

  Tips on how to search Tip 1: Use simple and clear keywords No matter what you are searching: a study, a dataset or a committee; the search will look recursively in all the fields of all the entities in the database. Thus, there is no need to specify which type of data you are looking for. Try to use single and specific words and avoid long and complex expressions. Try it out: cancer rna-seq instead of cancer studies using RNA-seq. Tip 2: Narrow your results using search operators Search operators give you more control over the results. They manage the way keywords are used to restrict the search. By default, the search engine applies an OR operator when a space is inserted between two words. Include AND (capitalised) between the keywords in your search in order to show only pages containing both terms. Try it out: Search all the studies based on transcriptomic data, including those ones that use RNA sequencing to obtain this data. Tip 3: Do not worry about details The search engine automatically checks for the most common spelling mistakes of given words and suggests the use of the correct version. It also ignores capital letters and most punctuation so none of these mistakes will hamper the accuracy of your search. Besides, when using a combination of words, the search engine will suggest similar combinations with a higher number of results. Tip 4: Use words that are likely to appear within the text Unfortunately, our search engine is not able to interpret words yet. Therefore, words which do not appear in the body text will not return any result despite them denoting a group of present terms. For instance, if we are looking for studies focused on neurological diseases, using neurological as a keyword would not be the best option. Instead, you should use the name of each neurological disease such as bipolar disorder, schizophrenia or depression. In the same fashion, incomplete words do not return any result. Please include an asterisk (*) before and/or after the incomplete word in order to allow for partial matching. Try it out: canc* instead of canc(without wildcard). Also you can try out *oma, or even *geneti* Tip 5: Narrow down your search by filtering the results You can filter the results by the following options: general, study, and dataset. Under these categories, you will find more sub-filters to refine your search. Make sure that you click on Apply in order to filter the results. You can clear the filtering anytime. Advanced Searches Additional example queries: Search for DUO:0000005 and word lung example query Or write: DUO:0000005 AND lung Search for an exome sequencing study in dbGaP example query Or write: study_type: "exome sequencing" AND repository:dbGaP Search for an exome sequencing study in EGA example query Or write: study_type: "exome sequencing" AND repository:ega Search for a dataset that is at the EGA beacon and with type "Whole genome sequencing" and with number of samples between 100 and 2000 and with technology "Illumina HiSeq 2000" example query Or write: is_in_beacon:true AND dataset_types:"Whole genome sequencing" AND samples:[100 TO 2000] AND dataset_technologies:"Illumina HiSeq 2000" Search for PMIDS example query Or write: pmids:32025007

  Documentation discovery/metadata/search-box

• Study of Controlled Human Malaria Infections to Evaluate Protection After Intravenous or Intramuscular Administration of PfSPZ Vaccine in Malaria-Naive Adults

  The study was performed to evaluate whole-blood transcriptomic profiles via RNA-seq before, during, and after immunization with the PfSPZ Vaccine in malaria-naïve, health adults enrolled in VRC 314 (NCT02015091). VRC 314 was designed as an open-label evaluation of the safety, tolerability, immunogenicity, and protective efficacy of the PfSPZ Vaccine. This study was designed to substantiate the initial results with the IV vaccination route for protection against CHMI that was observed in VRC 312 (NCT01441167). Based on the potential importance of dose and schedule in optimizing sustained immunity with this vaccine, an increase in PfSPZ IV dosage on schedules of 3 to 5 vaccinations was evaluated for protection against CHMI conducted early (about 3 weeks) and late (about 24 weeks) after completion of vaccinations. To assess if a higher dose given by another route confers protection, one group received PfSPZ IM, with half of the amount administered in each arm on a schedule with 4 vaccination. The primary objectives of the study were related to the safety and tolerability of vaccinations by the IV and IM routes of administration and protection against Plasmodium falciparum (Pf) challenge performed via a well-established CHMI procedure early (2-4 weeks) after completing schedules of 3 to 5 vaccinations. The secondary objective was related to the durability of protection at 20-26 weeks after the last vaccination, and exploratory objectives were related to the immunogenicity of the PfSPZ Vaccine and identifying potential immune correlates of protection. To further determine potential molecular correlates of immunogenicity and/or protection, RNA-seq was performed on whole blood collected from subjects in all dose groups at time points before, during, and after immunization.

  Study phs002423

• Glioblastoma_CRISPR_Screen

  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.

  Study EGAS00001001519

• Molecular and clinical diversity in primary central nervous system lymphoma: a LOC network multi-omic PCNSL study

  Primary central nervous system lymphoma (PCNSL) is a distinct extranodal lymphoma presenting with limited stage disease but variable response rates to treatment despite homogenous pathological presentation. The likely underlying molecular heterogeneity and its clinical impact is poorly understood. The present dataset contents paired-ended whole-exome sequencing information (n=115; HyperExome Kapa hyperprep), paired-ended RNA-seq information (n=123; KAPA mRNA HyperPrep Kits), and paired-ended bisulfite sequencing (n=64; TruSeq Methyl Capture EPIC) from fresh-frozen tumor tissue immunocompetent, treatment naïve PCNSL patients. Additionally, the dataset includes single-ended RNA-seq (n=93; QuantSeq 3’ mRNA-Seq Library Prep Kit) from formalin-fixed, paraffin-embedded tissue of immunocompetent, treatment naïve PCNSL patients. All samples were sequenced in an Illumina NovaSeq 6000 instrument.

  Dataset EGAD00001008706

• 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, led by NS) 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. Units of 475 ml of AB will be obtained from consenting volunteers of the Cambridge BioResource (CBR), a panel of 10,000 healthy volunteers local to Cambridge who have already consented to participate in biomedical research and of whom biological samples (DNA, plasma, serum) and lifestyle data have been deposited in a repository and database, respectively. We are requesting funding from the Human Diversity project to sequence the genomes of the 200 CBR volunteers at low pass (6x coverage). Nuclei, DNA and RNA will be recovered from the purified cells and made available for RNA-seq, DNA-seq and ChIP-seq and genomic DNA for entire genome sequencing will be recovered from the DNA repository.

  Dataset EGAD00001002205

• Next Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases

  Putative oncogenic pathways in squamous cell lung cancer have been recently characterized, although their biologic repercussions in patients is largely unknown. This study sought to discover potential clinical manifestations of major pathways in squamous cell lung cancer, particularly the PI3K pathway. Two key findings emerged: patients with stage IV squamous cell lung cancer whose tumors harbored upstream PI3K aberrations had significantly worse survival and a higher burden of metastatic disease. In addition, brain metastases were significantly more common in these patients than in others. Paired lung primary/brain metastasis genotyping, including RNA sequencing and whole exome sequencing, uncovered a high degree of genetic heterogeneity between lung/brain pairs, and identified potential regulators of the metastatic process to brain.

  Study phs000907

• Hypermutation of the inactive X chromosome is a frequent event in cancer

  Mutation is a fundamental process in tumorigenesis. However the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. As part of the ICGC PedBrain and Malignant Lymphoma (MMML-Seq) consortium we performed a cross-cancer comparison of whole genomes comprising a diverse set of childhood and adult tumors including both solid and hematopoietic malignancies. In addition we performed whole genome sequencing of clonally expanded hematopoietic stem/progenitor cells (HSPCs) from healthy individuals to compare somatic mutation rates.

  Study EGAS00001000565

• Single cell RNA sequencing of colorectal cancer patients (KUL3)

  All libraries were sequenced on Illumina HiSeq4000 until sufficient saturation was reached.

  Dataset EGAD00001008584

• RNA sequencing of high-risk paediatric cancers for identifying T-cell infiltration signatures

  Transcriptome profiling of 121 high-risk paediatric cancer samples for identifying T-cell infiltration signatures using poly-A capture by Truseq and sequenced on NextSeq 500

  Dataset EGAD00001010920

• Resolving the immune landscape of human prostate at a single cell level in health and cancer

  The prostate gland produces prostatic fluid, high in zinc and citrate and essential for the maintenance of spermatozoa. Prostate cancer is a common condition with limited treatment efficacy in castration-resistant metastatic disease, including with immune checkpoint inhibitors. We used single-cell RNA-sequencing to perform an unbiased assessment of the cellular landscape of human prostate and identified a previously unappreciated subset of tumour-enriched androgen receptor-negative luminal epithelial cells, with increased expression of cancer-associated genes. We also found a variety of innate and adaptive immune cells in normal prostate that were transcriptionally perturbed in prostate cancer. An exception was a unique, prostate-specific, zinc transporter-expressing macrophage population (MAC-MT), that contributed to tissue zinc accumulation in homeostasis, but showed enhanced inflammatory gene expression in tumours, including T cell-recruiting chemokines. Remarkably, enrichment of the MAC-MT signature in cancer biopsies was associated with improved disease-free survival, suggesting beneficial anti-tumour functions.

  Study EGAS00001005787

• Integrated Genomic Analysis of Chronic Lymphocytic Leukaemia

  Chronic lymphocytic leukaemia (CLL) is a frequent and heterogeneous disease whose genetic alterations determining the clinicobiological behaviour are not fully understood. Here, we describe a comprehensive evaluation of the genomic landscape of 452 CLLs and 54 monoclonal B-lymphocytosis (MBL), a precursor disorder. This study provides an integrated portrait of the genomic landscape of CLL, identifies new recurrent mutations acting as drivers of the disease, and suggests clinical interventions which may improve the management of patients with this neoplasia. The data here included was described in the ICGC-CLL manuscript published by Puente et al (Nature 2015). Note that complementary RNA-seq data generated within the IGCG-CLL can be found in EGAS00001000374.

  Study EGAS00001001306

• Single-cell profiling of the leukemic and non-leukemic immune cell compartments in CD8+ T-cell Large Granular Lymphocytic Leukemia

  We performed a detailed and precise characterisation of the clonally expanded leukemic cells in CD8+ T cell Large Granular Lymphocytic Leukemia (T-LGLL). By combining scRNA+TCRαβ-seq with bulk RNA sequencing data we showed evidence of a strong antigen-driven immune response that shapes the entire immune cell repertoire in T-LGLL. Our study highlights how the whole immune cell repertoire including the hyperexpanded CD8+ T-LGLL cells, the non-leukemic CD8+ cells, CD4+ cells, and monocytes contribute to the CD8+ T-LGLL disease phenotype. Please note that this submission contains the fastq files while the processed count matrices can be found in ArrayExpress by the accession E-MTAB-11170.

  Study EGAS00001005297

• Genomic landscape of Ewing sarcoma (ICGC project)

  The Ewing sarcoma project aims to sequence 100 complete genomes of cells of patients suffering from this disease. It is an initiative of great projection, since this is the second most common bone tumor in children and teenagers. The goal of the project is to establish the catalogue of somatic mutations that may cooperate with EWS-ETS fusion in the development of the tumor. The Ewing sarcoma project aims to perform 100 whole genome sequencing of germline and tumor DNA as well as at least 50 RNA-seq from tumors. Correlations between molecular profiles and clinical features will be established. The mutated genes will be further validated in a series of 500 Ewing sarcoma cases from our Tumor Bank.

  Study EGAS00001000855

• Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

  Cancer-associated fibroblasts (CAFs) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although the extent of CAF heterogeneity has remained undefined. Here we employ single-cell RNA-sequencing to thoroughly characterize the neoplastic and tumor microenvironment content of human PDAC tumors. Six human PDAC tumor specimens from six patients were collected, and processed for single-cell RNA-sequencing analysis. Adjacent-normal pancreas tissue was also collected from two of the patients. Tumor samples were digested, and fluorescence-activated cell sorting was used to isolate viable cells. For one tumor sample, viable, CD45-negative, CD31-negative, and EpCAM-negative cells were also isolated to enrich for CAFs. The 10X Chromium platform was then used to isolate single cells for RNA-sequencing analysis. This work has demonstrated the differences in immune cell populations between adjacent-normal and tumor tissues, and identified subpopulations of epithelial cells and CAFs present in PDAC tumors. This high-throughput analysis is a resource to better understand the cell populations present in PDAC, and may ultimately aid in the development of more effective therapies for this deadly malignancy.

  Study phs001840

• scRNA-seq of HGSC tumor and ascites

  Immune regulatory metabolites are key features of the tumor microenvironment (TME), yet with a few notable exceptions, their identities remain largely unknown. We uncovered the immune regulatory metabolic states and metabolomes of sorted tumor and stromal, CD4+, and CD8+ cells from the tumor and ascites of patients with high-grade serous ovarian cancer (HGSC) using high-dimensional flow cytometry and metabolomics supplemented with single cell RNA sequencing. Flow cytometry revealed that tumor cells show a consistently greater uptake of glucose than T cells, but similar mitochondrial activity. Cells within the ascites and tumor had pervasive metabolite differences, with a striking enrichment in 1-methylnicotinamide (MNA) in T cells infiltrating the tumor compared to ascites. Despite the elevated levels of MNA in T cells, the expression of nicotinamide N-methyltransferase, the gene encoding the enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to nicotinamide, was restricted to fibroblasts and tumor cells. Treatment of T cells with MNA resulted in an increase in T cell-mediated secretion of the tumor promoting cytokine tumor necrosis factor alpha. Thus, the TME-derived metabolite MNA contributes to an alternative and non-cell autonomous mechanism of immune modulation of T cells in HGSC. Collectively, uncovering the tumor-T cell metabolome may reveal metabolic vulnerabilities that can be exploited using T cell-based immunotherapies to treat human cancer.

  Study EGAS00001004829

• RNAseq

  Familial Mediterranean Fever (FMF) is a prototypical periodic fever syndrome caused by genetic variation in MEFV. While it is known that especially IL-1β responses are dysregulated in FMF, its innate immune landscape has not been comprehensively described. Therefore, we extensively characterized the function of monocytes and neutrophils in patients with FMF in between disease attacks, as well as their circulating inflammatory proteome. We found that monocyte IL-1 and IL-6 production was enhanced following a range of stimulations, in concordance with alterations in the plasma inflammatory proteome. In contrast, neutrophil function in FMF was normal. Additionally, ATAC-seq and RNA-seq analyses revealed important epigenetic and transcriptional reprogramming arguing for monocyte function dysregulation. Interestingly, chromatin-accessibility was down-regulated in genomic regions related to cellular responses. This argues that the primary immune dysregulation in monocytes due to MEFV mutations leads to a chronic inflammatory profile that is subsequently associated with counterregulatory epigenetic and transcriptional changes reminiscent of tolerance (rather than trained immunity) induction. These data increase our understanding of the innate immune changes in FMF, that can be used in the design of novel approaches to manage chronic inflammation of these patients.

  Study EGAS00001007165

• Characterization of MCSP+ melanoma DCC and MelDCC lines

  To dissect the sequence of genotypic and phenotypic progression during early metastatic colonization, we searched for the earliest detectable disseminated cancer cells (DCC) and identified MCSP+ melanoma cells as strong candidates for metastasis founder cells (MFC) in lymph nodes. We isolated MCSP+ DCC from various stages of metastatic colony-formation, performed scRNA-seq and unravelled their phenotypic progression. Further we performed bulk sequencing on patient-derived DCC models (MelDCC) and showed that they exhibit an immunosuppressive activity on CD8 T cells.

  Study EGAS00001006702

• RNA-seq of Glioblastoma stem cells

  Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as Glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

  Study EGAS00001003070

• Epigenome mapping in purified cells of the digestive and urogenital organs: Participation in International Human Epigenome Consortium (IHEC) (RNA-Seq)

  The aim of this study is to participate in International Human Epigenome Consortium (IHEC, http://ihec-epigenomes.org/), through disclosure of quality epigenome profiles of various normal cell lineages and diseased cells purified from surgically resected materials of multiple Japanese people.

  Study JGAS000028

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• Single cell RNA-seq from AD and PS patients

  We applied single cell immune profiling to gain a holistic view from immune cells infiltrating the skin to circulating immune cells, facilitating a better understanding of the two diseases in their entirety, and the identification of potential type-2 or type-3-disease-driving mechanisms.

  Study EGAS00001007055

• DNA methylation (RRBS) data for the validation the glioblastoma progression study (GBMatch).

  Genome-wide profiling of DNA methylation levels by RRBS in 150 glioblastoma tumor samples. Patients were selected to represent the general population of glioblastoma patients based on Austrian Brain Tumor Registry. These DNA methylation profiles were created for the validation of the glioblastoma progression study (GBMatch) and consist of 106 profiles from FFPE samples and 44 profiles from fresh-frozen samples. For the 44 fresh-frozen samples also WGS data (43 genomes) and RNA-seq data (37 transcriptomes) have been produced for validation purposes.

  Dataset EGAD00001004074

• Gene expression in CSF and whole blood of adults with proven bacterial meningitis in Malawi

  Dataset of BAM files from patients with proven bacterial meningitis in Malawi. Samples consist of BAM files from PolyA RNA seq runs from patients classifed as admission whole blood or CSF on admission (pre-antibiotics) in the Emergency Department. Subsequent BAM files are identical runs from whole blood from the same patients, taken at either day 10 or day 40 post admission to hospital. All patients have disease, they are divided into survivors and non-survivors at the day 40 time point.

  Dataset EGAD00001004488

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• Single-nucleus transcriptomic profiling of aging Down Syndrome brains

  Down syndrome (DS) – trisomy of human chromosome 21 (HSA21) – is characterized by lifelong cognitive impairments and development of neuropathological hallmarks of Alzheimer’s disease (AD). The cellular and molecular modifications responsible for these effects are not understood. Here we performed single-nucleus RNA-sequencing (snRNA-seq) employing both short (Illumina) and long-read (Pacific Biosciences) sequencing technologies on a total of 29 DS and non-DS control prefrontal cortex samples. In DS, the ratio of inhibitory-to-excitatory neurons was significantly increased, which was not observed in previous reports examining sporadic AD. DS microglial transcriptomes displayed AD-related aging and activation signatures in advance of AD neuropathology, with increased microglial expression of C1q complement genes (associated with dendritic pruning) and the HSA21 transcription factor gene RUNX1. Long-read sequencing detected vast RNA isoform diversity within and amongst specific cell types including numerous novel sequences that differed between DS and normal brains. Notably, over 8,000 genes produced RNAs containing intra-exonic junctions (IEJs), including APP that had previously been associated with somatic gene recombination. These and related results illuminate large-scale cellular and transcriptomic alterations as novel features of the aging DS brain.

  Study EGAS00001005691

• Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory

  Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as LPS. We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time dependent manner. ChIP-seq, RNA-seq, WGBS and ATAC-seq data were generated. This analysis identified epigenetic programs in tolerance and trained macrophages, and the potential transcription factors involved. Experimental set-up Time-course in vitro culture of human monocytes. Two innate immune memory states can be induced in culture through an initial exposure of primary human monocytes to either LPS or BG for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 1 hour, 4 hour, 24 hour and 6 days.

  Dataset EGAD00001002693

• Spatial multi-omic map of human myocardial infarction

  We applied an integrative single-cell genomics strategy with single nucleus RNA sequencing (snRNA-seq) and single nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) together with spatial transcriptomics from the same tissue mapping human cardiac cells in homeostasis and after myocardial infarction (MI) at unprecedented spatial and molecular resolution. We profiled in total 31 samples from 23 patients including four non-transplanted donor hearts as controls and samples from tissues with necrotic tissue areas (ischemic zone, IZ), border zone (BZ), and the non-affected left ventricular myocardium (remote zone, RZ) of patients with acute MI.

  Dataset EGAD00001008952

• Genomic Characterization CS-MATCH-0007 Arm Z1D

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and posttreatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm Z1D is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with MMR deficiency are treated with nivolumab. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001859

• Genomic Characterization CS-MATCH-0007 Arm H

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing and RNA sequencing using pre-and post-treatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm H is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with BRAF V600K/V600E mutations are treated with Dabrafenib and Trametinib. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001888

• Genomic Characterization CS-MATCH-0007 Arm Y

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and post-treatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm Y is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with AKT mutations are treated with AZD5363. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001904

• Korean Advanced Thyroid Cancer Dataset

  Massively-parallel DNA sequencing of 113 advanced thyroid cancers and Massively-parallel RNA sequencing of 25 advanced thyroid cancers

  Dataset EGAD00001004845

• Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (RNA)

  Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. RNAseq (BAM files)

  Dataset EGAD00001006353

• Comprehensive molecular and clinicopathological profiling of lung adenocarcinoma in Japanese never or light smokers

  Studies have yet to characterize the differences in molecular profiles of lung adenocarcinoma (LUAD) among divergent ethnic groups. Herein, we conducted comprehensive molecular profiling of LUAD in never or light smokers from Asia in order to discover novel targetable mutations and prognostic biomarkers of this distinct disease entity. Methods: We analyzed 996 cases of Asian LUAD, and performed whole-exome sequencing and/or RNA-seq in 125 cases of Asian LUAD negative for the driver oncogenes defined by conventional laboratory testing. We also investigated the clinical and pathological characteristics among the 996 cases. Results: Driver oncogenes were identified in 88 cases (70.4%) with specific hotspot mutations differing from those in The Cancer Genome Atlas (TCGA) study. Clustering based on mRNA expression profiles, but not genetic mutational ones, could predict patient prognosis. The risk score generated by the expression of a three-gene set was a strong prognostic marker for overall survival and progression-free survival in our cohort, and was further validated using TCGA cohort. Among the 996 cases, each driver alteration is distributed across all histological subtypes. Adenocarcinoma in situ was identified to harbor driver mutations, suggesting that these alterations are early events in the pathogenesis of LUAD. This study indicates the value of applying gene expression profiling for predicting the prognosis after a surgical operation, and that the identification of actionable mutations is important for optimizing targeted drugs in Japanese LUAD.

  Study JGAS000215

• Comparison of fresh and slow-frozen cancer samples for different applications

  Surplus tissues from multiple solid human cancers directly slow-frozen after resection can subsequently be used for different types of methods including the establishment of 2D, 3D, and ex vivo cultures as well as single cell RNA sequencing (scRNAseq) with similar results when compared to freshly analyzed material.

  Study EGAS00001005891

• Personalised Mapping of Tumour Development in Synchronous Colorectal Cancer Patients

  We performed an in-depth characterisation of 12 tumours from 3 syCRC patients by analysing histopathological, whole genome sequencing and RNA-sequencing data. We assessed the extent of genetic overlap between synchronous tumours and examined associations between clinicopathological information and the molecular, microbial and immune features of each tumour genome.

  Study EGAS00001004413

• Somatic copy-number alterations in plasma circulating tumor DNA from advanced EGFR-mutated lung adenocarcinoma patients

  This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-seq) for calling of somatic copy number alterations as well as focal amplifications from patients with lung cancer.

  Dataset EGAD00001007505

• Custom long non-coding RNA capture enhances detection sensitivity in different human sample types.

  Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.

  Study EGAS00001005418

• Sequencing of an adolescent patient with germline RET mutant alveolar rhabdomyosarcoma

  An adolescent patient presented with an alveolar rhabdomyosarcoma made more unique by the presence of a germline RET mutation ordinarily associated with and a known driver of multiple endocrine neoplasia type 2A (MEN2A) cancer. To better understand the role of this germline RET mutation in the genetics and phenotypic response of this unique alveolar rhabdomyosarcoma, we performed DNA and RNA sequencing of the patients in addition to functional studies on patient-derived cultures and genetically similar similar cell models.

  Study EGAS00001004359

• RNA-sequencing of primary urothelial bladder cancer samples

  Paired-end RNA-sequencing of tumour tissue samples (n=85) from primary urothelial bladder cancer patients. Sequencing was performed using either HiSeq (n=27) or NextSeq (n=58) Illumina platforms. Of the 85 samples, 78 are Non-muscle invasive (NMIBC) and 7 are Muscle invasive (MIBC).

  Dataset EGAD00001007005

• A Phase I Study With a Personalized Neoantigen Cancer Vaccine in Glioblastoma Multiforme

  Neoantigens, which are derived from tumor-specific protein-coding gene mutations, are exempt from central tolerance, can generate robust immune responses and function as bona fide antigens that facilitate tumor rejection. A strategy of using multi-epitope and personalized neoantigen vaccination has previously been tested in patients with high-risk melanoma. We demonstrated that this strategy is feasible for glioblastoma (GBM) which typically has a relatively low mutation load and an immunologically 'cold' tumor microenvironment. We conducted whole exome sequencing (WES) of tumor and normal cells from individual GBM patients to identify tumor-specific mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor, and used personalized neoantigen-targeting vaccines to immunize newly diagnosed GBM patients following surgical resection and conventional radiotherapy in a phase I/Ib study. Patients who did not receive dexamethasone, a highly potent corticosteroid that is frequently prescribed to treat cerebral oedema in GBM patients, generated circulating polyfunctional neoantigen-specific CD4+ and CD8+ T cell responses that were enriched in a memory phenotype and showed an increase in the number of tumor-infiltrating T cells. Using single-cell T cell receptor analysis, we provided an evidence that neoantigen-specific T cells from the peripheral blood can migrate into an intracranial GBM tumor. Neoantigen-targeting vaccines thus have the potential to favorably alter the immune environment of GBM.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-Seq) on two GBM samples. We discovered novel or unannotated open reading frames (nuORFs) and their expression levels as well as somatic mutations within the nuORFs, which could be used to predict potential neoantigens.

  Study phs001519