math1 - gfp transgenic mice  (Novartis)

Journal: BMC Biology

Article Title: Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

doi: 10.1186/s12915-021-01071-8

Figure Lengend Snippet: Single-cell transcriptome profiling of postnatal cerebellar cells. a Workflow (top panel) for cerebellum collection by FACS-sorted, single-cell sequencing, and analysis of two samples [one at postnatal days 7 (P7) and the other at P11] from Math1-GFP mice and two samples [one at P7 and the other at P11] from Dcx-DsRed mice. Workflow (bottom panel) for cerebellum section, spatial transcriptomes, and analysis of two samples from WT mice (both at P7). b Strains were established from transgenic Math1-GFP and transgenic Dcx-DsRed mice. Scale bar: 100 μm. c t-SNE visualization of 24,919 cells from FACS-sorted samples ( n = 4; Math1-GFP mice at P7 and P11; Dcx-DsRed mice at P7 and P11). Cells are colored according to clusters with annotation of cell types. d Dot plot for the expression of marker genes in each cell type. Color represents the mean expression in each cell cluster, and size indicates the fraction of cells expressing marker genes. e t-SNE visualization of 24,919 cells from FACS-sorted samples: Math1-GFP + and Dcx-DsRed + samples. f Bar plot showing the proportion of cell types in Math1-GFP + and Dcx-DsRed + samples. P < 0.0001. P values were determined using Pearson’s chi-square test

Article Snippet: Math1 - GFP transgenic mice were provided by Novartis.

Techniques: Sequencing, Transgenic Assay, Expressing, Marker

Journal: BMC Biology

Article Title: Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

doi: 10.1186/s12915-021-01071-8

Figure Lengend Snippet: Identifying distinct states associated with postnatal GN development. a t-SNE visualization of 21,397 granule neuron cells (GNs) from FACS-sorted samples after re-clustering. n = 4 mice. They are Math1-GFP mice at P7 and P11, as well as Dcx-DsRed mice at P7 and P11. Cells are colored according to clusters. b t-SNE visualization of FACS-sorted sample sources including Math1-GFP + and Dcx-DsRed + samples. c Signature gene expression of GNPs ( Math1 ) and differentiating/differentiated GNs ( Dcx ). d t-SNE visualization of cell cycle and differentiation ( Rbfox3 , Grin2b , and Neurod1 ) gene scores. e Scores of GNs (X-axis) for seven modules (Y-axis) derived from Monocle 3 module analysis. Four highly correlated modules are highlighted (modules A, B, C, and D). Cells and modules are hierarchically clustered. Scores of cell cycle genes, and expression of Math1 and Dcx are ordered as on the top. f Four cell states are defined corresponding to the four main modules in e . g Scores of the four main module genes are shown. h Heatmap depicting gene expression levels of markers in the four GN states, with color-coding for the corresponding FACS-sorted sample, clusters, cell types, and cell cycle scores. i Signature gene expression of GNPs (Math1, Srebf1, and Tead2), GNs I (Nhlh1, Ebf3, and Sox4), and GNs II (Grin2b, Cntn1, and Car10). In situ hybridization (ISH) data were obtained from the Allen Developing Mouse Brain Atlas (© 2008 Allen Institute for Brain Science. Allen Developing Mouse Brain Atlas http://developingmouse.brain-map.org ). Scale bar: 100 μm. Mouse cerebellum at P4 are shown

Article Snippet: Math1 - GFP transgenic mice were provided by Novartis.

Techniques: Gene Expression, Derivative Assay, Expressing, In Situ Hybridization

Journal: BMC Biology

Article Title: Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

doi: 10.1186/s12915-021-01071-8

Figure Lengend Snippet: Identification and mapping of GN cell-type subpopulations across cerebellar regions. a t-SNE visualization of spots identified as EGL, ML/PCL, and IGL in Fig. a. b Scores of genes specifically associated with four GN states in ST spots. c Spatial locations of anatomical regions associated with the development of GNs: EGL, ML/PCL, and IGL. Spots are colored according to the layers. d Model at P7 for the cellular architecture of GNs in different development phases: a. GNPs in EGL, b. migrating GNs in the inner of EGL and ML/PCL, and d. mature GNs in IGL. c. Purkinje cells are shown in ML/PCL. e Violin plot for scores of selected genes corresponding to four cell states in three layers’ location. Color represents four cell states. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001. P values were determined using two-sided unpaired Wilcoxon test. f Correlation between four states of GNs and three layers’ location. g Signature gene expression of GNPs (Math1 and Mki67), GNs I (Mvd), and GNs II (Cntn1) in the ST H&E image

Article Snippet: Math1 - GFP transgenic mice were provided by Novartis.

Techniques: Gene Expression

Journal: BMC Biology

Article Title: Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

doi: 10.1186/s12915-021-01071-8

Figure Lengend Snippet: Developmental trajectories within GN lineage cells. a RNA velocities of GNs for Math1-GFP + mouse at P7. b UMAP visualization of the transition probability of particular cells corresponding to four GN states. c The velocity-inferred root/end cells, velocity pseudotime, and cell cycle scores of P7 Math1-GFP + mouse are shown. d Gene expression dynamics resolved along velocity pseudotime show a clear cascade of transcription of top likelihood-ranked TFs (likelihood > 0). e Driver genes are identified by high likelihoods. Expression dynamics along velocity pseudotime for the driver genes characterize their activity

Article Snippet: Math1 - GFP transgenic mice were provided by Novartis.

Techniques: Gene Expression, Expressing, Activity Assay