11932 results for "cancer rna-seq"

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• Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort.

  Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort (n=18).

  Dataset EGAD00001011068

• 3D-GSC_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG-derived glioma stem cell (GSC) models. Twenty-two primary GSC models derived from biopsies collected at diagnosis were cultured in an ECM-mimicking compound before for RNA extraction and subsequent rRNA-depletion and sequencing .

  Dataset EGAD00001011079

• RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C)

  RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C). Samples used were Whole Blood. Febrile illness controls include children with bacterial and viral infections and healthy controls. This dataset contains samples from patients recruited into the DIAMONDS study.

  Dataset EGAD00001011134

• H3K4me3, IgG, and Input ChIP-seq in overexpression of pLV Control, CS-FL and CS-ΔEx4 in SW1116 cells.

  none

  Study EGAS00001008121

• RNA Sequencing of Surgically Resected Colorectal Liver Metastases

  Dac EGAC00001000904

• RNA sequencing of sorted human RCC immune populations

  Dac EGAC00001002861

• CNA differences between RNA-based subtypes of PDAC

  Dac EGAC50000000730

• scRNA-seq of human follicular lymphoma and lymph node

  Cryopreserved cells from human nodal follicular lymphoma and lymph node samples were thawed and processed for scRNA-seq analysis. CD3+ CD19− 7-AAD− live T cells (six FL samples from the Original cohort) or 7-AAD− whole live hematopoietic cells (five lymph node and nine FL samples from Validation cohort 1) were sorted using a FACS Aria II or III instrument (BD Biosciences). To generate single-cell emulsions, 6,000–10,000 live cells were loaded into the 10X Genomics Chromium Controller for single-cell partitioning, along with the reverse transcriptase reagent mixture and 3' or 5' gel beads. Sorted T or whole hematopoietic cells were converted to barcoded scRNA-seq libraries using 10X Genomics Chromium single cell 3' reagent kits (v3) for the Validation cohort 1, 5' reagent kits (v1) for the Original cohort, according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten or NovaSeq X Plus system, mapped to the human genome (build GRCh38), and demultiplexed using CellRanger pipelines (v3.1.0, 10x Genomics).

  Dataset EGAD50000001143

• Human scMultiome data (GEX and ATAC paired) from CD34+ Bone Marrow (BM) and mobilized peripheral blood (mPB), including CITE-Seq data from mPB CD34+ samples

  We analyzed healthy CD34+ samples from Bone Marrow (BM) and mobilized Peripheral Blood (mPB) in gene therapy experiments within the X-PAND project. BM samples underwent scMultiome analysis, providing paired GEX and ATAC data. For the mPB samples, both scMultiome and CITE-Seq were performed on the same donors, offering additional protein marker information. These datasets allow for an in-depth exploration of chromatin accessibility, gene expression, and surface protein profiling in hematopoietic progenitor cells from healthy donors.

  Study EGAS50000000750

• Genome-wide identification of distinct miRNA-mRNA target regulation pairs in Non-Hodgkin lymphomas: a report from the ICGC MMML-Seq consortium

  We obtained miRNA profiles by miRnome sequencing from ICGC MMML-Seq patients diagnosed with Burkitt lymphoma, diffuse large B-cell lymphoma and follicular lymphoma and provide evidence of subtype-specific miRNA expression differences. We describe differentially expressed, mutated, edited and not previously annotated miRNAs. Addditionally, by performing argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) experiments, we obtained a set of biochemically-validated miRNA binding sites and identified miRNA-mRNA interaction pairs with a negative correlation in patient RNASeq data.

  Study EGAS00001001394

• Single cell RNA-seq mapping of nasal and tracheobronchial airways in human healthy volunteers

  The respiratory tract constitutes an elaborated line of defense based on a unique cellular ecosystem. Single-cell profiling methods enable the investigation of cell population distributions and transcriptional changes along the airways. We have explored cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12th division of the airway tree. The resulting atlas is composed of a high percentage of epithelial cells (89.1%), but also immune (6.2%) and stromal (4.7%) cells with peculiar cellular proportions in different sites of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type specific gene expression was stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuro-endocrine (PNEC) and brush cells, which are likely derived from a common population of precursor cells. We also report a population of KRT13 positive cells with a high percentage of dividing cells which are reminiscent of “hillock” cells previously described in mouse. Robust characterization of this unprecedented large single-cell cohort establishes an important resource for future investigations. The precise description of the continuum existing from nasal epithelium to successive divisions of lung airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.

  Study EGAS00001004082

• HiChIP fastq files

  HiChIP experiments with two sequencing libraries each. Illumina HiSeq 4000/2500.

  Dataset EGAD00001006278

• High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. These tumors were profiled using whole-genome sequencing (WGS) or whole-exome sequencing (WES) to identify somatic mutations, WGS or low-pass WGS to detect copy number alterations, targeted capture sequencing to assess MYC and BCL2 structural variants, and RNA sequencing. The genetic features of HGBCL-NOS were compared to those of diffuse large B-cell lymphoma (DLBCL-NOS) and EBV-negative adult Burkitt lymphoma (BL). DLBCL-NOS tumors underwent targeted capture sequencing using a panel of 125 genes recurrently mutated in aggressive B-cell lymphomas. BL biopsies were drawn from the Burkitt Lymphoma Genome Sequencing Project and had available WGS (dbGaP Study Accession: phs000527.v18.p6).

  Study EGAS50000000932

• GATA6 expression distinguishes classical and basal-like subtypes in advanced pancreatic cancer.

  PURPOSE: To determine the impact of basal-like and classical subtypes in advanced PDAC and to explore GATA6 expression as a surrogate biomarker. EXPERIMENTAL DESIGN: Within the COMPASS trial patients proceeding to chemotherapy for advanced PDAC undergo tumour biopsy for RNA sequencing. Overall response rate (ORR) and overall survival (OS) were stratified by subtypes and according to chemotherapy received. Correlation of GATA6 with the subtypes using gene expression profiling, in situ hybridization (ISH) were explored. RESULTS: Between December 2015-May 2019, 195 patients (95%) had enough tissue for RNA sequencing; 39 (20%) were classified as basal-like and 156 (80%) as classical. RECIST response data were available for 157 patients; 29 basal-like and 128 classical where the ORR was 10% vs. 33% respectively (p=0.02). In patients with basal-like tumours treated with modified FOLFIRINOX (mFFX) (n=22) the progression rate was 60% compared to 15% in classical PDAC (p= 0.0002). Median OS in the intention to treat population (n=195) was 9.3 months for classical vs. 5.9 months for basal-like PDAC (HR 0.47 95% CI 0.32-0.69, p=0.0001). GATA6 expression by RNAseq highly correlated with the classifier (p<0.001) and ISH predicted the subtypes with sensitivity of 89% and specificity of 83%. In a multivariable analysis, GATA6 expression was prognostic (p=0.02). In exploratory analyses, basal-like tumours, could be identified by keratin 5, were more hypoxic and enriched for a T cell inflamed gene expression signature. CONCLUSIONS: The basal-like subtype is chemoresistant and can be distinguished from classical PDAC by GATA6 expression.

  Dataset EGAD00001006081

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Study EGAS50000000342

• RNA sequencing of surgically removed lung adenocarcinoma afterwards treated with immune checkpoint inhibitors

  Patients with lung adenocarcinoma (LUAD) from The Cancer Genome Atlas (TCGA) database were enrolled in the training cohort to establish a prognostic signature based on the expression of tumor-specific amino acid metabolism related genes. The established signature was further investigated against an original cohort, KCC-ICI, of chemotherapy combined with immune checkpoint inhibitors. The signature consisting of nine genes, KYNU, PSPH, PPAT, MIF, GCLC, ACAD8, TYRP1, ALDH2, and HDC, could effectively stratify the OS in LUAD patients. The KCC-ICI cohort confirmed the predictive ability of the established signature in the clinical response to immune checkpoint blockade therapy, which correlated with the infiltration of immune cells (e.g., T lymphocytes and nature killer cells). We discovered that the high signature risk score patients showed a significantly lower concentration of plasma-free ??-aminobutyric acid (AABA).

  Study JGAS000675

• Single-Cell RNA-Sequencing of Bone Marrow and Circulating Tumor Cells from Patients with Multiple Myeloma and its Precursor Conditions

  We performed single-cell RNA and V(D)J-sequencing of tumor cells from bone marrow and peripheral blood specimens and patients with Monoclonal Gammopathy of Undetermined Significance (MGUS), Smoldering Multiple Myeloma (SMM), and Multiple Myeloma (MM), as well as healthy donors. In this study we aimed to shed light on the mechanisms underlying tumor cell circulatory capacity and dissemination.

  Study phs003855

• DNA and RNA sequencing data from Ovarian Carcinosarcoma patients from the Glasgow Cohort.

  In this study, we analysed DNA and RNA sequencing data from Ovarian Carcinosarcoma patients, from isolated carcinoma and sarcoma components and investigated DNA variants as well as gene expression. Genomic analyses from this data and further investigation from preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate anti-tumour immunity.

  Study EGAS00001006605

• Characterization of Structural Variants in Acute Myeloid Leukemia Patients

  Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and is expected to increase in frequency as the population ages. Most subtypes of AML are difficult to treat, in part due to a lack of understanding of possible molecular targets. Furthermore, the peak incidence of AML is in the sixth decade, and patients over the age of 65 do not tolerate chemotherapeutic regimens well. Moreover, AML has been highly studied as a model for other cancers. An RNA Biology Program is established aiming to develop comprehensive datasets through the profiling of all different classes of RNA expression, RNA editing, alternative splicing, and non-coding RNAs in CD34+ normal hematopoietic stem cells (HSC), their differentiated progeny, and AML clinical samples that could be utilized to understand leukemia. These datasets will allow us to computationally identify and characterize various RNA species and processes to enable the development of effective therapeutics to AML, leukemia and other types of cancers. Epigenetic factors such as methylation and histone modifications will also be characterized from these clinical samples allowing for integrated dataset analysis to look at the cross-talk between RNA and DNA/epigenomics in leukemia. The following is a subsidiary study of the above study description where whole genome sequencing was performed on two collected AML patients' samples using Illumina and Oxford Nanopore sequencing technologies. The aim is to characterize the roles of structural variants (SV) in RNA biology which are potentially important for AML development using our own established long-read SV characterization tool, NanoVar. The advent of Oxford Nanopore sequencing technologies has opened a new avenue for better SV characterization by having longer sequencing reads. NanoVar is an accurate and rapid SV characterization tool that utilizes low-depth Nanopore sequencing data. NanoVar makes use of split-reads and hard-clipped reads for SV discovery and employs a simulation-trained neural network classifier for true positive enrichment. NanoVar exhibited higher accuracy and faster computational speed amongst other long-read SV detection tools in simulated data. In AML patient data, NanoVar displayed excellent accuracy in SV characterization (16/16 SVs validated in two patients) by using only 4x depth sequencing data. In summary, NanoVar improves the accuracy and speed of SV characterization at a lower sequencing cost, an approach compatible with clinical studies.

  Study phs001847

• Raw sequencing files from WGS and RNA-Seq

  Acute leukemias are the most common malignancies in children with an onset of the disease among 0-6 years-old. The early development of theses malignancies has been proposed as an indicator of their prenatal origin, hypothesis that has been confirmed especially in the case of acute lymphoblastic leukemia. For acute myeloid leukemia (AML), comprising an heterogenous group of different cytogenetics subtypes, this prenatal origin has also been confirmed specially for MLL-rearranged and t(8;21) subgroups. AMLs carrying t(7;12) constitute up to 30% of cases under 2-years-old, frequently being associated with a trisomy of chromosome 19 and an overexpression of MNX1 gene. An in utero origin of this specific subgroup has been suggested but not clearly confirmed. Here, we present the case of a 5-months-old AML patient with t(7;12) in which we have fully characterized a novel breakpoint occurring among ETV6 and NOM1 genes. We demonstrate the presence of this specific ETV6-NOM1 fusion in CD34+ hematopoietic stem and progenitor cells isolated from the cord blood unit from the same patient and stored at birth. Moreover, trisomy +19 present at diagnosis was not detected at birth. Together, our results demonstrate the prenatal origin of the t(7;12) in infant AML, and establish trisomy +19 as a secondary event in this leukemia.

  Study EGAS50000000186

• SiMSen‑Seq

  High resolution amplicon-bases sequencing o screen for PIK3CA hot spot mutations

  Dataset EGAD50000001668

• Rapid Idiosyncratic Mechanisms of Clinical Resistance to KRAS G12C Inhibition

  Using deep RNA and whole exome sequencing of pre- and post-treatment autopsy samples, we reveal diverse clonal populations that occurred through altered cell intrinsic, tumor microenvironment and immunologic remodeling mechanisms of resistance.

  Study phs002734

• Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

  RNA-sequencing, ATAC-sequencing, CUT&Tag-sequencing, data from CMML patient and aged-matched healthy donor CD34+ cells. RNA-sequencing data from patient CD34+ cells after treatment for 4 days with decitabine or UNC0638 inhibitors, alone or together, or left untreated

  Dataset EGAD50000000542

• RNASeq profiles from Indian HFrEF Cohort

  The dataset contains whole transcriptomics profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Total transcriptome libraries were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kit and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001196

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Bulk RNA Sequencing of 33 epithelioid sarcomas (EpS) and 3 extracranial extra-renal rhabdoid tumors (EERT) Whole-exome sequencing of 30 EpS and 3 EERT Single-cell RNA Sequencing of 8 EpS Visium Spatial Transcriptomics of 3 EpS

  Dataset EGAD50000001419