Promiscuous, mimetic and Aire-dependent gene regulation in medullary epithelial thymus cells

This repository contains all the code for reproducing the figures and processed data of Aire-WT & -KO mTECs Multiome analysis. The analysis of the RNA data is done with the metacells python package, whereas the ATAC data analysis is done with the mcATAC R package.

Quick links

Metacells paper: Ben-KiKi et al. 2022 Genome Biology
Metacells package Vignette
mcATAC R package
mTECs paper: Bornstein, C., Nevo, S., Giladi, A. et al. 2018 Nature

Usage

To begin, please clone this repository to your working directory. make sure that you will not be limited by disk quota, as the necessary files will be quite large.

The repository contains:

a Dockerfile - a docker image created to execute the complete code on your OS without the need of individual package installation.
2 Jupyter notebooks (see below)
some helper scripts

next, pull the docker image and run it, so it will be available on the local web browser (see "Docker" instructions below).

Running the notebooks

the analysis pipeline and workflow is divided into 2 sections - RNA and ATAC - where the RNA section is meant to be executed first. Since the RNA notebook is the first to run, a command for downloading the data and extracting it is already embedded at the beginning of it, so you can simply start there and keep going for genreating the figures (however, if you're interested in doing so manually - see below "Downloading the data" section).

once you finish running through the RNA notebook, simply switch to the ATAC notebook.

Required modules (python >=3.7):

metacells
Anndata
Scanpy
standard modules (numpy, pandas, scipy, matplotlib, seaborn)

Required packages (R):

metacell
mcATAC
prego
chameleon
visualization packages (ggplot2, pheatmap)

Downloading the data

the processed data, as well as the objects generated through the analysis pipeline and other dependencies (e.g. genomic tracks) are all available to download as a .tar.gz file (mtecs_multiome_data.tar.gz).

NOTE: A command for downloading the data and extracting it is already embedded at the beginning of the RNA Jupyter notebook (make sure you don't download it again).

if you want to manually download it outside of the notebook, please run the following bash command from a designated working directory created for the project:

wget https://mtec-multiome.s3.eu-west-1.amazonaws.com/mtecs_multiome_data.tar.gz

and then run:

tar xvzf mtecs_multiome_data.tar.gz

you should have the following directories created:

mtecs_multiome/
├── data
├── figs
├── gdb
└── objs

you'd probably want to remove the .tar.gz file at this point as it takes up a lot of space

Docker

Pull the docker image

docker pull tanaylab/mtecs_multiome:latest

Download the data (see above).
Run the docker container:

docker run -v $(pwd):/mtecs_multiome -p 8888:8888 tanaylab/mtecs_multiome:latest

Connect to the jupyter server running at port 8888.

tanaylab / mtecs_multiome