mcrewcow/pan_et_al_dfchen_igfpl1_paper

IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

IGFBPL1 is a Master Driver of Microglia Homeostasis and Resolution of Inflammation that Limits Glaucomatous Neurodegeneration

This repository has the information on the single-cell RNA-seq analysis described in the paper for IGFBPL1 WT/KO and glaucoma PBS/IGFBPL1 mouse microglia datasets.

The analysis is separated into the following parts:

1. Igfbpl1 WT/KO - glaucoma PBS/Igfbpl1 Seurat R processing - basic Seurat pipeline, availabe upon request ([email protected])
2. ForceAtlas2 + scanpy processing (Jupyter Notebook)
3. RNA Velocity - bash preprocessing to .loom - file: fastq_to_loom_processing.sh
   - scvelo utilization (Jupyter Notebook) Files: Glaucoma datasets analysis, IGFPL1 WT/KO datasets analysis
   
4. Python to R data transformation Files: Saving the object in Python, Building the Seurat object in R

The datasets are uploaded on GEO:
WT/IGFBPL1

The processed datasets are available upon request.

If you have any questions regarding the data, analysis or further improvements, here are the contacts:
[email protected] - PI
[email protected] - Bioinformatics, part 1 + data availability
[email protected] - Bioinformatics, part 2-4 + data availability