Single-cell transcriptome of commissural and non-commissural dentate gyrus granule cells

Dentate granule cells (GCs) have been characterized as unilaterally projecting neurons within each hippocampus. Using anterograde and retrograde labeling, we identified a unique class, the commissural GCs, which atypically project to the contralateral hippocampus in mice. This data set includes single-cell mRNA sequencing reads from retrogradely-labeled (commmissural) and -non-labeled (non-commissural) GCs from control mice and from mice treated with unilateral intrahippocampal kainic acid microinjections (70 nl, 5 mM; cells were collected two weeks after microinjection); control mice were treated with unilateral intrahippocampal saline microinjections (equal amount to kainic acid; cells were collected two weeks after microinjection). These experiments were performed in adult (2.5-3.5 months old) Rbp4-Cre transgenic mice. Overall design: To label contralateral hippocampus-projecting GCs, we injected retroAAV-EGFP into the right (contralateral) ventral hippocampus, and saline or kainic acid together with AAV.cDIO-mCherry (mCherry is to be expressed in GCs in a Cre-dependent manner to visualize the injection site) into the left (ipsilateral) hippocampus of Rbp4-Cre transgenic mice with symmetrical injection coordinates. Two weeks later, patch-RNA-seq was used to sample EGFP-expressing (EGFP+) and EGFP-non-expressing (EGFP-) GCs in the ipsilateral hippocampus, irrespective of their mCherry expression. Partitioning of the data is as follows (number of sequenced cells / number of cells that passed quality control / number of mice from the cells were collected): (1) saline, EGFP+ cells: 7 / 5 / 3, (2) saline, EGFP- cells: 62 / 57 / 3, (3) kainic acid, EGFP+ cells: 30 / 27 / 9, (4) kainic acid, EGFP- cells: 39 / 36 / 3.