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RenalBiopsies_DNA_RNA-seq_analysis

Integrated multi-omics analysis for kidney transplant patients to decipher molecular gene signatures for delayed graft function.

Repository sructure

RNA-seq analysis

  • This repository contains script thats reads all raw illumina fastq files from a folder and performs quality control, genome alignment and read summarisation to quantify read counts
  • Genome alignment and read summarisation (gene quantification)
  • Trim galore for trimming low quality reads fastq files
  • Tophat/Bowtie for aligning reads to the updated reference genome (GRCh38) from ensemble
  • Scripts for analysis of RNA-seq data for differential gene expression (DGE) using DESeq2

BS-seq analysis

Scripts for analysis of DNA-seq to extract methylation changes (epigenetic) footprints on CpG islands

Epigenetics

Scripts for mapping differential gene expression signatures and associated methylation status

Glossary notation on samples

  • b - pre perfused kidney patients
  • b1 - post perfused kidney patients
  • DGF - Delayed graft function conditioned patients
  • IGF - No Delayed graft function patients

The analysis of these results are published in Aging cell A molecular signature for delayed graft function

McGuinness, D., Mohammed, S., Monaghan, L., Wilson, P. A., Kingsmore, D. B., Shapter, O., Stevenson, K. S., Coley, S. M., Devey, L., Kirkpatrick, R. B., & Shiels, P. G. (2018). A molecular signature for delayed graft function. Aging Cell, 17(5), e12825. https://doi.org/10.1111/acel.12825