rsc-rp / mack_d_2023.04.13_ipsc_neuromuscular_scrnaseq Goto Github PK

The goal is to investigate the processes of differentiation in motor neurons (MNs) derived from an iPSC model. Gene expression was assayed using single-cell RNA-sequencing (10x Genomics) and processed with CellRanger at each timepoint. Cells were collected from undifferentiated iPSC, and every 3 days until day 45.

We aim to identify the regional identity and subtypes of iPSC motor neurons and transcriptomic (dis)similarity with native MNs in the fetal spinal cord.

1. Preprocessing and integration: mack_d_iPSC_motor_neurons_day0-day50.Rmd
2. Integrated primary spinal cord reference: mack_d_iPSC_motor_neurons_ref_data.Rmd
3. Cell type annotation with SCANVI: mack_d_iPSC_motor_neurons_day0-day50_celltype_annotation.Rmd
4. Cell trajectory analysis: mack_d_iPSC_motor_neurons_day0-day50_trajectories.Rmd

Other Notebooks

• Preprocessing and integration: mack_d_iPSC_motor_neurons_EDA_day0-day45.Rmd
• Figures for CMTR: mack_d_iPSC_motor_neurons_day0-day50_figures.Rmd

@jennylsmith

Jenny L. Smith

https://orcid.org/0000-0003-0402-2779