Nutritional Lung Immunity

A description of the monocyte derived macrophages bioinformatics pipelines.

In vitro time-series RNAseq data from monocyte derived macrophages exposed to A. fumigatus conidia.

Description: Monocyte derived macrophages from six different human donors (M-CSF differentiated) were exposed to Aspergillus fumigatus conidia with cell:conidia ratio=1:1 for 0, 2, 4, 6, 8 hours. Purity of macrophages was confirmed by flow cytometry using surface markers CD14+/CD68+/CD163+.

Preprocessing pipeline

The FASTQ files were aligned using a custom Nextflow pipeline for preprocessing of data and alignment of reads against the GRCh38 reference genome version 96. An overview of the pipeline is below. Click on the image to be taken to the Github repository containing the Nextflow pipeline.

Differential Expression Github Repository

Contains R scripts for performing differential expression analysis of macrophagess exposed to A. fumigatus and control DCs using DESeq2.

Processed Data

Contains post-processed data such as aligned read counts and quality control after alignment trimming.