Project description:The development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes. Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.
Project description:Motivation: The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results: We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains. VDJPuzzle successfully reconstructed BCRs from 98.3% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing. Availability: VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2
Project description:This aim of this study is to understand changes in gene expression in PBMC-derived macrophages (from healthy individuals) in response to lipid A or TNF alpha stimulation