Hyperactive synaptic circuits in a human neuronal model of childhood dementia.

Data Access and Information

This GitHub contains the RScripts used for the analysis of transcriptomic data found in Hyperactive synaptic circuits in a human neuronal model of childhood dementia.

hiPSC-derived cortical neural lines (n = 5 donors, 2 clones per donor) were cultured for 120-days in vitro prior to sequencing. Single cell RNA sequencing was performed using the 10x Genomics Chromium platform.

Dates of data collection: 2023

Location: Adelaide, South Australia

Files within this repository

1. RScripts: This folder contains all the R scripts used to process transcriptomic data for this project

   • Differential_Expression_Analysis_120D.Rmd: Comparisons between excitatory and inhibitory neuronal cell types.
   • Neuronal_Glial_Types_Analysis_120D.Rmd: Code for cell type identification within Healthy and MPSIIIA snRNA-seq datasets.
   • QualityControl_120Day.Rmd: Quality Control parameters of Healthy and MPSIIIA snRNA-seq transcript data.

2. reference sheets: contains files used to generate figures.

   NOTE: 'NA' values within each of the files in the reference sheets folders indicate empty cells

• housekeepers.txt: Housekeeping genes used for quality control.

  • Reference study: Tirsoh et al, 2016 (https://www.science.org/doi/abs/10.1126/science.aad0501) Variables: 1
  • Number of cases/rows: 98
  • Linked RScript: QualityControl_120Day.Rmd

• cellcycle_tirosh.tsv: Cell cycle genes used to calculate proliferation scores.

  • Reference study: Tirosh et al, 2016 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465819/)
  • Variables: 2
  • Number of cases/rows: 55
  • Variable list:
    • G1/S (Gap 1/Synthesis): Genes defining the G1S cell cycle phase.
    • G2/M (Gap 2/Mitosis): Genes defining the G2M cell cycle phase.
  • Linked RScript: Neuronal_Glial_Types_Analysis_120D.Rmd

Code and Software

Sequenced fastq files were processed using standard CellRanger 7.0.0 pipelines. Demultiplexing analyses were performed using demuxafy (https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/)

Human genome reference: GRCh38-2020-A (10X Genomics)

Requirements for downstream data analysis:

• R
• RStudio
• Seurat

All other required R packages are listed within RScripts.