Scripts and notebooks for the analyses used in our paper Aging affects ciliated cells development in human endometrial epithelium.
In this project, we compared the endometrial transcriptome of young and advanced age females undergoing hormonal replacement therapy (HRT) before frozen embryo transfer, followed by immunohistology analysis and single-cell based deconvolution. RNA was extracted from the biopsies and and single-end sequenced them (75bp) on a NextSeq500 (Illumina).
The align_count_workflow directory contains a snakemake workflow for mapping to the reference genome and counting, the scripts directory contains scripts used for data analysis and figures directory contains scripts and notebooks used for vizualisation.
- Combining expression count matrix for each sample in one joint expression count matrix and processing:
- removal of rows with all 0s and values >=5% in >75% samples
- retrieval of gene names in the place of Ensembl identifiers
- correcting for sequencing run using Combat_seq() from sva package
- Principal component analysis and clustering analysis
- Differential gene expression analysis using DESeq2 package
- Gene ontology analysis
- Preparation of single cell datasets for deconvolution analysis with DWLS method
- Deconvolution analysis with DWLS method
- Normalization of single-cell dataset for later visualization