Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types

Abstract

Many subtypes of cortical interneurons (CINs) are found in adult mouse cortices, but the mechanism generating their diversity remains elusive. We performed single-cell RNA sequencing on the mouse embryonic medial ganglionic eminence (MGE), the major birthplace for CINs, and on MGE-like cells differentiated from embryonic stem cells. Two distinct cell types were identified as proliferating neural progenitors and immature neurons, both of which comprised sub-populations. Although lineage development of MGE progenitors was reconstructed and immature neurons were characterized as GABAergic, cells that might correspond to precursors of different CINs were not identified. A few non-neuronal cell types were detected, including microglia. In vitro MGE-like cells resembled bona fide MGE cells but expressed lower levels of Foxg1 and Epha4. Together, our data provide detailed understanding of the embryonic MGE developmental program and suggest how CINs are specified.

SoupX removes ambient RNA contamination from droplet based single-cell RNA sequencing data

“…Our method approaches this problem by trying to identify a set of gene/cell pairs for which the cell endogenous expression can be assumed to be zero. That is, the task is to identify Ω = {c, g|mgc = 0} (7) For genes and cells in Ω we see from equation 2 that ngc = ogc. That is, the observed counts are purely due to background contamination.…”

“…Droplet based single-cell RNA sequencing (scRNA-seq) has enabled quantification of the transcriptomes of hundreds of thousands of cells in single experiments [1,2]. This technology underpins recent advances in understanding normal and pathological cell behaviour [3,4,5,6,7,8]. Moreover, large scale efforts to create a 'Human Cell Atlas' critically depend on the accuracy and cellular specificity of the transcriptional readout produced by droplet based scRNA-seq [9,10].…”

Expression of FoxP2 in the Basal Ganglia Regulates Vocal Motor Sequences in the Adult Songbird

“…The identities 128 of five clusters (12,17,19,21,22), comprising 5.2% of all cells, remain unknown based on gene expression 129 markers. Since the expression profiles of each of these clusters suggests a developmental origin from the 130 medial ganglionic eminence, these clusters may represent novel classes of interneurons, which are the only 131 cell type in the striatum known to originate from the medial ganglionic eminence (Chen et al, 2017). The 132 remaining clusters comprise various glial cell-types such as astrocytes and oligodendrocytes ( Figure 1E).…”

Single-Cell RNA-seq Reveals a Subpopulation of Cells Underlying β Cell Expansion in the Postnatal Islets

“…As a first step we used young adult islet cells from C57BL/6 mice to evaluate the potential utility of this approach. Purified islets were handpicked from 3-month old C57BL/6 mice, dissociated into single cells, and captured using the Fluidigm C1 integrated fluidic circuit for RNA-seq (Chen et al 2017) (Materials and Methods). In total, 159 single cell transcriptome datasets from two independent experiments passed the selection filters designed to exclude dying cells and doublets (Materials and Methods).…”

“…S5). To assess the proliferative potentials of P7.5 INS1 + subpopulations and to exclude the possibility that PDGFRB positive P7.5 islet cells are dying cells, we FACS purified the two GFP + subpopulations, GFP + PDGFRBand GFP + PDGFRB + , and then measured EdU in vitro incorporation rate of each subpopulation with or without exposure to platelet-derived growth factor-A/B (PDGF-A/B), the ligands for PDGF signaling (Chen et al 2017) (Materials and Methods). Remarkably, P7.5 GFP + PDGFRB + islet cells exhibited significantly higher proliferative potential than GFP + PDGFRBislet cells, and this higher proliferation rate was amplified in the presence of PDGF ligands (two-way ANOVA, p < 0.0001), unlike GFP + PDGFRBcells (unpaired t-test, p = 0.8206) ( Fig.…”