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. f) Final metadata: Combined cell and cluster annotations for all samples (main_screen_analysis/final_metadata/)
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.

Final Processed Data

Main Screen Analysis Metadata

Location: main_screen_analysis/final_metadata/

Contains the final processed metadata files with combined cell and cluster annotations:

• GSM7950265_NGN2_post_dr_clustered_raw_merged_meta.tsv.xz - NGN2 post-patterning metadata
• GSM7950267_NGN2_pre_dr_clustered_raw_merged_meta.tsv.xz - NGN2 pre-patterning metadata
• GSM7950268_ASCL1_post_dr_clustered_raw_merged_meta.tsv.xz - ASCL1-DLX2 post-patterning metadata
• GSM7950269_ASCL1_pre_dr_clustered_raw_merged_meta.tsv.xz - ASCL1-DLX2 pre-patterning metadata
• 00_Combine_Cell_Cluster_annotation.ipynb - Notebook for combining annotations

These files contain the complete cell-level metadata including cluster assignments, cell type annotations, morphogen treatments, and quality control metrics for all samples used in the main screen analysis.

Note: Metadata files are compressed with XZ compression (.xz) for optimal file size. Use xz -d filename.tsv.xz to decompress or most modern tools can read them directly.