iNeuron Morphogens

Code and analysis for Human neuron subtype programming through combinatorial patterning with scRNA-seq readouts.

Contents

1. Main screen analysis: NGN2 + ASCL1-DLX2, pre and post patterning a) Analysis of original morphogen screen (QC+clustering). b) Annotation of dataset by mapping with Seurat + marker genes c) Analysis of morphogen effects using transcriptional distance and Random Forest models. d) Morphogen-GRN networks with pySCENIC. e) Analysis of neurotransmitter (NT) and neuropeptide (NP) expression.
2. Primary atlas a) Collection of datasets for primary neuron atlas. b) Annotation of primary neuron atlas (NT). c) Comparison with iNeurons.
3. Patterned progenitors (single-cell multiome + bulk) a) Single-cell multiome analysis of NGN2 patterned progenitors. b) Bulk RNA-seq comparison between NGN2 and ASCL1-DLX2 patterned progenitors.
4. Reproducibility + stability a) Notebooks for analysis of repdrocibility across cell lines using bulk RNA-seq. b) Notebooks for analysis of stability using time-series bulk RNA-seq (d0 to d49).
5. Perturbations of TFs linked to morphogens using OE and KD a) Notebooks for analysis of overexpression (OE) experiments b) Notebooks for analysis of knock-down (KD) experiments.