Project description:Using Smart-seq2 single cell sequencing we reported that plasmablasts from dengue-infected individuals separate into 4 distinct clusters with distinct function.
Project description:We used DART-seq to map m6A methylation of RNA in single HEK293T cells. We also used DART-seq to map m6A from bulk RNA from HEK293T cells. Using the 10X Genomics and SMART-seq2 platforms, we sequenced a total of 19,533 experimental and control cells using the 10X Genomics platform, and 1,471 experimental and control cells using SMART-seq2. We then used a Bullseye, a computational pipeline developed within the lab, to identify m6A sites from the C-to-U mutations in bulk and single-cell datasets. We find that most m6A methylation is highly heterogenous from cell-to-cell. RNAs containing m6A methylation, are infrequently methylated, and that most individual sites are rarely methylated within the population. Additionally, we are able to identify differentially methylated RNAs in different cellular states from within a single population, and use m6A methylation information to perform clustering of single cells to find a source of novel cellular heterogeneity.
Project description:Single cell RNA sequencing using either an adapted Smart-seq2 protocol on Chx10-GFP (+) retinal progenitor cells; 10x Genomics Chromium Single Cell system across 10 timepoints of mouse retinal development to examine retinal progenitor cell heterogeneity across retinal development and global changes in gene expression from early retinal neuroepithelial cells through specification and differentiation of retinal cell types; 10X Genomics Chromium Single Cell on P14 Nfia/b/x het control or Nfia/b/x tCKO (Chx10-Cre-GFP) retinas
Project description:Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align. Four mouse retinas (labeled 1la, 1Ra, and 2la, 2Ra respective from the two mice) were used, and 96 single cells from each were processed using Smart-seq2. Total 384 cells Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP mice (Kcng4tm1.1(cre)Jrs mice [Duan et al., Cell 158, 793-807, 2015] crossed to the cre-dependent reporter Thy1-stop-YFP Line#1 [Buffelli et al., Nature 424, 430-434, 2003])
Project description:To investigate the transcriptional profile of human circulating T cells with skin tissue-resident memory phenotype (cTRM) in GVHD we performed bulk RNA sequencing from SMART-seq2 of sorted human cTRM (CD3+ CD4+ CLA+ CD103+) and conventional T cells (CD3+ CD4+ CD103-), and single cell RNA sequencing from 10X Genomics of sorted human CD45+, both from isolated blood PBMCs of patients with active acute GVHD.
Project description:10X genomics single cell analysis of yHSC vs oHSC from Gfplc3/Gfplc3 mice with index sorted SMART-Seq2 sequencing to map AThi oHSC vs ATlo oHSC based on GFP-LC3 marker levels. 10X Genomics data harmonized by nearest neighbor integration and uniform manifold approximation and projection (UMAP) representation distinguished yHSC from oHSC, with the largest transcriptional differences observed in the G0/G1 cell cycle phase cluster. Within oHSCs, AThi oHSCs were almost exclusively observed in the G0/G1 cluster, whereas ATlo oHSCs were spread across the activation continuum, with cells still in the G0/G1 cluster found more proximal to S cluster cells.
Project description:In this study, we used SMART-Seq2 single cell analysis to delineate the molecular mechanisms underlying gene expression changes during endocrine pancreas differentiation
Project description:We investigated the abundances and transcriptomic changes of immune cells at several time points over the course of dengue virus infection. The PBMC samples were obtained from one dengue fever (DF) and one dengue hemorrhagic fever (DHF) patients (8 samples in total). The samples were harvested at two and one days before defervescence (febrile phase), at defervescence (critical phase), and two-week convalescence. Single-cell RNA-seq libraries were prepared using the 10x genomic protocol and were sequenced using the Illumina Hiseq platform. One healthy control sample analysed by the same protocol was included.
Project description:We performed Smart-seq2 scRNAseq on 156 pancreatic tuft cells . We also profiled FACS sorted EpCAM+;CD45+ immune cells and EpCAM-;CD45- non-immune stroma cells from from 3 caerulein-treated KC and 2 caerulein-treated KPouC pancreata by using the 10X Genomics 3' scRNAseq v3.1 kit.
Project description:Using single-cell RNA-sequencing, we characterized the transcriptomes of Drosophila young and old glial cells from repo+ pan glia and ensheathing glia. scRNAseq was performed using Smart-seq2 platform.