NOTCH1-cardiac-lineage-scRNAseq

This is the repository for the manuscript: Impaired Human Cardiac Cell Development due to NOTCH1 Deficiency.

If you have any questions or feedback regarding this repository, please contact Cankun Wang via cankun.wang@osumc.edu.

Directory structure

• 10x_code: HPC scripts to run CellRanger workflow
• 10x_qc_report: web_summary.html output from 10x CellRanger workflow
• 10x_counts: Gene-cell expression count matrix generated from CellRanger workflow
• velocyto_code: HPC scripts to run velocyto to generate velocity matrix into loom format
• velocity_loom: velocity matrices generated from Velocyto workflow
• rmarkdown: analyses using R
• jupyter: RNA velocity analysis in Jypyter Notbooks (Python)

Download data

• Merged count matrix and metadata for cells: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196632 (Supplementary file section)
• Processed Seurat object: https://bmblx.bmi.osumc.edu/downloadFiles/NOTCH1/NOTCH1_seurat_obj.rds
• Count matrices generated from CellRanger: https://bmblx.bmi.osumc.edu/downloadFiles/NOTCH1/NOTCH1_scRNAseq_10x_counts.zip
• RNA velocity matrices: https://bmblx.bmi.osumc.edu/downloadFiles/NOTCH1/NOTCH1_velocity_loom.zip
• Raw FASTQ reads: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA806200

Author

• Cankun Wang