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ChimeraScan: A tool for identifying chimeric transcription in sequencing data

ABSTRACT: Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29098 | GEO | 2011/09/01

SECONDARY ACCESSION(S): PRJNA140329

REPOSITORIES: GEO

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ChimeraScan: A tool for identifying chimeric transcription in sequencing data

Project description:Next Generation Sequencing technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts. Three cancer cell lines with known gene fusions

2011-09-01 | E-GEOD-29098 | biostudies-arrayexpress

Finding new Chimeric RNAs in RNA-seq data, a test study in Acute Myeloid Leukemia patient cells

Project description:In this strudy, we seek out new chimeric RNA in RNA-seq data from acute myeloid leukemia (AML) patient cells as new biomarkers to improve diagnosis and prognosis in cancer. Total RNA were extracted from bone marrow or peripheral blood mononuclear cells in three AML patients. polyA+ cDNAs were sequenced to generate stranded paired-end reads. RNA-seq analyses were performed using Crac and CracTools software. In particular using these tools, we classified chimeric RNA in four classes, finding new chimeric RNAs. By analysis a larger cohort by qPCR, we were able to define new chimeric RNA as new biomarkers in AML patients.

2017-06-28 | E-MTAB-5767 | biostudies-arrayexpress

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.

Project description: Not available

| S-EPMC3187648 | biostudies-literature

Discovery of Novel Determinants of Endothelial Lineage: Insights from Chimeric Heterokaryons

Project description:Discovery of Novel Determinants of Endothelial Lineage: Insights from Chimeric Heterokaryons

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Chimeric contribution of human extended pluripotent stem cells to monkey embryos

Project description:Pluripotent stem cells (PSCs) represent the earliest stages of organismal development, and have the potential to differentiate into cell types from all three primary germ layers. To date, however, chimeric competency of human EPS cells has not been determined in other animal hosts. Leveraging on a recently developed in vitro culture system that enabled the development of monkey embryos up to 20 days in vitro, in this study, we injected human PSCs (hPSCs) cells into cynomolgus monkeys (Macaca fascicularis) morula embryos and examined their contribution to different lineages at different timepoints during in vitro culture.

2021-04-15 | GSE155381 | GEO

Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice

Project description:We investigated the effects of per- and polyfluroralkyl substance exposure on FRG liver-chimeric humanized mice on a NOD background. These PFAS included PFOA, PFOS, and GenX. These mice were exposed to water ad libitum for 28 days to reach human relevant serum concentrations. We then performed RNA-Sequencing on isolated whole liver lysate to determine differentially expressed genes.

2023-07-14 | GSE208636 | GEO

Chimeric EGFR ChIP-seq of an MCF-10A clone expressing chimeric EGFR and Erbb2 receptors

Project description:Synthetic activation of chimeric EGFR-Erbb2 receptors causes nuclear translocation of the heterodimers at long time scales. To identify genomic loci bound by nuclear EGFR-Erbb2, chromatin from an MCF10A-5E clone coexpressing chimeric EGFR and Erbb2 was prepared with or without synthetic activation and immunoprecipitated for chimeric EGFR by its GluGlu epitope tag.

2023-03-22 | GSE216242 | GEO

chimeric eCLIP identifying the target genes of 5' tRNA-fMet1 half mediated by AGO2 in cystic fibrosis airway epithelial cells

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ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

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Identification of gene fusion events in Mycobacterium tuberculosis that encode novel chimeric proteins

Project description:Mycobacterium tuberculosis is a facultative intracellular pathogen, responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38-71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen we further develop software that detects potential gene fusion events from multigene deletions using whole-genome sequencing data. With this software we could identify a number of other putative gene-fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel proteins and functions can arise.

2020-05-12 | PXD017298 | Pride

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