anjahess / hlo-scrnaseq

Single cell RNA-sequencing analysis of human liver organoid models of MASLD

Stratification of Human Liver Organoid Models for MASLD

Author: Anja Hess

Date: 2023-MAY-27

1. Description

Command line interface and scripts to reproduce results from the scRNA-seq study of human liver organoid models of MASLD. For publication details see below. The main start script located in bin points to a folder containing ALL 10X samples of interest or an .h5ad file.

2. Before you start

Check out our Jupyter notebook guiding through the analysis!

These scripts are written for python => 3.6.

Jobs were run in a Unix environment (required memory **~ 40-60 GB**). Please make sure you installed dependencies for the individual packages (e.g. scanpy, cpdb).

3. Usage

cd ./bin
python3 start.py path/to/FOLDER/ run_name
python3 start.py file.h5ad run_name

4. Required folder architecture:

4.1 For 10X cellranger outs:

FOLDER
-- SAMPLE1
    -- .mtx.gz
    -- .tsv.gz
    -- .tsv.gz
-- SAMPLE2
    -- ...

4.2 For individual AnnData objects to be merged

FOLDER
-- sample1.h5ad
-- sample2.h5ad

4.3 For an already concatenated AnnData object

python3 start.py file.h5ad run_name

5. Data access

Raw sequence data for scRNA-seq performed in this study are publicly available on GEO under the accession GSE207889.

Previously published scRNA-seq data that were used for analyses: MacParland et al.: GSE115469, Wesley et al.: E-MTAB-8210 (accessed 2023-MAY-28 through https://collections.cellatlas.io/liver-development)

6. Citation

Hess, A. et al. Single-cell transcriptomics stratifies organoid models of metabolic dysfunction-associated steatotic liver disease. The EMBO Journal (2023). https://doi.org/10.15252/embj.2023113898