Whole blood transcriptome analysis of Septic shock patients according to early therapy response - GSE110487

Septic shock is the most severe complication of sepsis, associated with high mortality. The patient’s response to supportive therapy is very heterogeneous and the underlying mechanisms are still elusive. In order to identify which are the actors (genes and pathways) that play a role in establishing the response, we investigate the whole blood transcriptome in septic shock patients with positive and negative responses to early supportive hemodynamic therapy, assessed by changes in SOFA scores within the first 48 hours from ICU admission. We pinpointed genes and pathways that are differently modulated and enriched respectively within 48hrs between responders and non-responders.

We analyzed 31 patients (17 Responders and 14 Not Responders to early therapy). For each patient, 2 samples were collected. In particular the first sample (T1) collected within 16 hours from ICU admission whereas the second (T2) collected within 48 hours from ICU admission. Experimental groups (Responders and Not Responders) are defined accordingly with SOFA scores improvements within 48 hours.

Septic shock (2021 ICD-10-CM code* = R65.21)

Basecalls performed using CASAVA version 1.8.2Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.Genome_build: GRCh38Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58906 genes (rows) [counts matrix]

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110487