Single-cell transcriptomics of Htr3a+ interneurons

Mouse development ages E18, P2, P5

Query the atlas ...

This page contains companion data for our paper published in Nature Communication ( doi:10.1038/ncomms14219 ):

Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing.

Frazer Sarah, Prados Julien, Niquille Mathieu, Cadilhac Christelle, Markopoulos Foivos, Gomez Lucia, Tomasello Ugo, Telley Ludovic, Holtmaat Anthony, Jabaudon Denis, Dayer Alexandre

Query the Atlas

This menu list subtype enriched genes for each developmental age. Select a tab to access enriched genes of a specific cell type. Then select a sub-tab to list enriched genes at a specific developmental age
List of genes enriched in Type-1 at both ages P2 and P5. Columns give average Z-score and Fold Change. Click a gene to add it to the query
List of genes enriched in Type-1 at P2. Click a gene to add it to the query
List of genes enriched in Type-1 at P5. Click a gene to add it to the query
List of genes enriched in Type-2 at both ages P2 and P5. Columns give average Z-score and Fold Change. Click a gene to add it to the query
List of genes enriched in Type-2 at P2. Click a gene to add it to the query
List of genes enriched in Type-2 at P5. Click a gene to add it to the query
List of genes enriched in Type-3 at both ages P2 and P5. Columns give average Z-score and Fold Change. Click a gene to add it to the query
List of genes enriched in Type-3 at P2. Click a gene to add it to the query
List of genes enriched in Type-3 at P5. Click a gene to add it to the query

t-Distributed Stochastic Neighbor Embedding (t-SNE) cluster analysis delineates 3 distinct subtypes of Htr3a-GFP+ INs at P2 and P5 and a E18 cluster. Graph-plot and expression was obtained using the Seurat R package output [Macosko et al. 2015]. Color scale indicates expression level of a given gene.

Violin plots indicating gene expression levels in the 3 main Htr3a-GFP+ interneuron subtypes. Gene expression was obtained using the join posterior estimation from the SCDE R package [Kharchenko et al. 2014].

Graphs showing the temporal dynamics of subtype-enriched transcripts across developmental time-points. Gene expression was obtained using the join posterior estimation from the SCDE R package [Kharchenko et al. 2014].

Show fitting details

Fitting details with individual cells and 95% confidence intervals.

Dayer Lab, University of Geneva, Switzerland
alexandre.dayer@unige.ch