15028 results for "cancer studies using rna-seq"

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• The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation

  Assessment of dexamethasone response in human lung through scRNA-seq analysis of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19.

  Study EGAS50000000203

• CITE-seq data of six CK-AML patient samples

  We performed cellular indexing of transcriptomes and epitopes (CITE-seq) of six primary leukemia samples from CK-AML patients. The dataset contains BAM files for each individual sample (D1922 and R0836) or for the hashed pool (HIAML47-HIAML85, P9D-P9R)

  Dataset EGAD50000000633

• scRNA-seq and Amplicon data for MPN/HC samples

  This data set contains scRNA-seq data from MPN patients and healthy individuals. It is accompanied by amplicon data for the JAK2V617F mutation. For each individual an INFa treated and untreated sample is included.

  Dataset EGAD50000001321

• Raw scRNA-seq data for “Characterization of intestinal immune responses in generalized human and murine lipodystrophy”

  Raw 10X 5' v3 scRNA-seq data (GEX) for PBMC of 3 helthy donors and two AGLCD patient timepoints as well as of LPMC of 3 Crohns disease patients and one timepoint of the AGLCD patient.

  Dataset EGAD50000002190

• Raw scTCR-seq data for “Characterization of intestinal immune responses in generalized human and murine lipodystrophy”

  Raw 10X 5' v3 scTCR-seq data (TCR) for PBMC of 3 helthy donors and two AGLCD patient timepoints as well as of LPMC of 3 Crohns disease patients and one timepoint of the AGLCD patient.

  Dataset EGAD50000002191

• BLUEPRINT September 2016, ATAC-seq for osteoclast from venous blood, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for osteoclast from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002907

• BLUEPRINT September 2016, ATAC-seq for naive B cell from tonsil, on Genome GRCh38

  ATAC-seq data for 3 sample(s) for naive B cell from tonsil, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002903

• BLUEPRINT September 2016, ATAC-seq Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002920

• BLUEPRINT September 2016, ATAC-seq for plasma cell from tonsil, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for plasma cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002912

• BLUEPRINT ChIP-Seq from two mantle cell lymphoma patients

  BLUEPRINT ChIP-Seq from two mantle cell lymphoma patients

  Dataset EGAD00001002655

• BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  Dataset EGAD00001002682

• Epigenomic data of HEMa_LP

  To profile the epigenomic landscape of Human Epidermal Melanocytes , adult, lightly pigmented(HEMa-LP), whole genome bisulphite sequencing (WGBS) and ChIP-seq of histone marks data were generated.

  Study EGAS00001004016

• CTD-ILD BALF and blood scRNA-seq dataset

  CTD-ILD BALF and blood scRNA-seq dataset consists of single-cell transcriptome data of bronchoalveolar lavage fluid (BALF) and blood derived from 30 connective tissue disease-associated interstitial lung disease (CTD-ILD) and 12 idiopathic interstitial pneumonia (IIP) patients.

  Dataset EGAD00001011334

• Kids First and INCLUDE: Down Syndrome, Heart Defects, and Acute Lymphoblastic Leukemia

  This project is a collaboration with the trans-NIH INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE (INCLUDE) Project, which seeks to improve health and quality-of-life for individuals with Down syndrome, and NHLBI's TransOmics for Precision Medicine (TOPMed) program, which seeks to apply omics technologies to improve scientific understanding of the fundamental biological processes that underlie heart, lung, blood, and sleep (HLBS) disorders. The data is also available at the INCLUDE Data Hub. Down syndrome (DS), which occurs due to trisomy 21, is one of the strongest risk factors for both congenital heart disease (CHD) and acute leukemia. For instance, children with DS have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL). An important and innovative aspect of the Kids First program is understanding the overlap between structural birth defects and childhood cancer. Notably, the background of DS predisposes children to both of these phenotypes, however, the genomic architecture of risk remains largely undiscovered. In this joint Kids First/TOPMed/INCLUDE project, we are currently including >2,000 samples for whole-genome sequencing, including: 1) paired germline-tumor samples from children with DS-ALL; and 2) samples from families with DS-CHD. This work will advance our understanding of the developmental pathways that may lead to both structural birth defects and childhood cancer. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS. Therefore, the aims of our study are: 1) compare whole-genome sequencing (WGS) data between children with documented DS-AVSD and children with DS who have structurally normal hearts to identify genetic variants that perturb heart development; and 2) compare WGS data between children with documented DS-ALL and children (from Aim 1) with DS who do not have a known history of ALL. We will also examine associations between germline mutations and somatic genomic features. This study will address the fundamental question of why children with DS have an elevated risk of AVSD and ALL. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these children. Additionally, our findings may inform targeted therapies or interventions for children without DS who are at risk for structural birth defects and cancer. Additional Pediatric Cardiac Genetics Consortium (PCGC) data from children affected with Down syndrome and congenital heart disease are accessible through two separate dbGaP studies: phs001138 (Kids First) and phs001194 (TOPMed).

  Study phs002330

• T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases

  Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumour infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T cell infiltration in CLM using T cell receptor (TCR) repertoire sequencing. Eighty-five resected CLM from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T cell fractions were calculated, repertoire clonality was analysed based on Hill evenness curves, and TCR sequential convergence was assessed using network analysis. Increased T cell fractions (10.6% vs 6.3%) were detected in CLM exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT exposed tumours independently of the timing of NACT administration and surgery. While private clones made up >90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence. TCR repertoire sequencing can be used to quantify T cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T cell clonal expansion in CLM in a clinical context.

  Study EGAS00001007136