T cell and Monocyte Specific RNAseq Analysis in Septic and Non Septic Critically-Ill Patients and in Patients with Cancer - GSE133822

The purpose of this study was to determine the potential differential effect of sepsis on innate versus adaptive immune effector cells by examining RNA expression in monocyte/macrophages and CD4 and CD8 T cells respectively using next generation sequencing.

mRNA profiles of CD4, CD8 and CD14 cells were generated for sepsis, critically-ill non-septic, cancer patients and age-matched healthy controls using Illumina Hiseq 2500.

Patient Characteristics: Septic = 29; Critically-Ill Non Septic (CINS) = 22; Cancer = 5; Healthy Control = 20.

Patients admitted to a medical or surgical intensive care unit (ICU) who were older than 18 years of age and who fulfilled a consensus panel definition of sepsis were included in the study. Sepsis was defined as the presence of systemic inflammatory response syndrome (SIRS) and a known or suspected source of infection. Patients who had undergone bone marrow irradiation or who had received chemo- or radiation therapy within the last six months, patients with HIV infection, viral hepatitis, or who were receiving immunosuppressive medications (except corticosteroids at a dose of <=300 mg hydrocortisone or equivalent per day) were excluded.

An initial quality check of raw FASTQ data was performed using FastQC.Reads that were either less than 25bp, or had a maximum quality score below Q15, or average quality score below Q10 were discarded. The quality filtered reads were mapped to the human reference genome GRCh38/hg38 (Dec 2013) using STAR.The read counts were called using Subread.Differential gene expression analysis was performed for CD4+, CD8+ and CD14+ samples using DESeq2 in R Bioconductor.Genome_build: hg38Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133822