DOI: 10.5061/dryad.280gb5mpw
title: Acute effects on the human peripheral blood transcriptome of decompression sickness secondary to scuba diving: Supplementary datasets

description: Decompression sickness (DCS) develops due to inert gas bubble formation in
 the circulation, leading to a wide range of potentially serious clinical
 manifestations. Its pathophysiology remains incompletely understood. In
 this study, we aim to explore changes in the human leukocyte transcriptome
 in divers with cutaneous DCS compared to closely matched unaffected
 controls after uneventful diving. Cases (n = 7) were divers developing the
 typical cutis marmorata rash after diving with a confirmed clinical
 diagnosis of DCS. Controls (n = 6) were healthy divers who surfaced from a
 ≥25 msw dive without decompression violation or evidence of DCS. Blood was
 sampled at two separate time points – within 8 hours of dive completion
 and 40-44 hours later. Transcriptome analysis by RNA-Sequencing followed
 by bioinformatic analysis was carried out to identify differentially
 expressed genes and relate their function to biological pathways. In DCS
 cases, we identified enrichment of transcripts involved in acute
 inflammation, activation of innate immunity and free radical scavenging
 pathways, with specific upregulation of transcripts related to neutrophil
 function and degranulation. DCS-induced transcriptomic events were
 reversed at the second time point following exposure to hyperbaric oxygen.
 The observed changes are consistent with findings from animal models of
 DCS and highlight a continuum between the responses elicited by uneventful
 diving and diving complicated by DCS. This study sheds light on the
 inflammatory pathophysiology of DCS and the associated immune response.
 Such data may potentially be valuable in the search for novel treatments
 targeting this disease.  
description: In this study, we aim to explore the evolution of leukocyte gene
 expression in human subjects with DCS compared to closely matched divers
 after uneventful diving using a hypothesis-free RNA sequencing approach
 .Recruitment of DCS cases (n = 7) and controls (n = 6) was carried out
 using specific criteria. For both DCS cases and controls, whole blood was
 sampled at two time points, T1 - within 8 hours of surfacing from diving
 and T2 - at 40-44 hours after surfacing. Prior to sampling at T2, subjects
 were fasted for 10 hours. Specific exclusion criteria included a) age
 &lt; 18 years b) self-reported consumption of alcohol and/or strenuous
 physical activity before T2 c) symptoms suggestive of delayed DCS
 presentation in controls at T2 d) acute life-threatening clinical
 complications or death within 72 hours of surfacing. All cases received
 emergency HBO as per United States Navy Treatment Table Six between T1 and
 T2.For RNA isolation, 2.5mL of whole blood was collected in a PAXgene®
 Blood RNA Tube (PreAnalytiX, Qiagen/BD) from DCS cases and controls at
 both T1 and T2. The quality of RNA was evaluated by RNA Integrity Number
 (RIN) determination using the RNA6000 Nano protocol on an Agilent 2100
 Bioanalyzer system (Agilent, USA). The RIN values for samples undergoing
 transcriptome analysis ranged from 7.8 to 9.3. Depletion of alpha and beta
 globin mRNA was carried out using the GLOBINclear™ kit (ThermoFisher
 Scientific). To minimize batch effects, all samples were processed
 simultaneously by the same investigator. RNA samples were submitted for
 library generation and sequencing by the Beijing Genomics Institute
 (BGI-Shenzhen). Briefly, poly(A) mRNA was enriched using poly(T)
 oligo-attached magnetic beads, followed by fragmentation. First strand
 cDNA synthesis was carried out using random hexamer N6 primers and reverse
 transcriptase. Following adaptor ligation to cDNA fragments, PCR
 amplification and purification, single stranded DNA circles were generated
 in a final library. DNA nanoballs (DNBs) were subsequently generated by
 rolling circle replication, which underwent paired end sequencing (100bp)
 on the BGI DNBseq platform
description: The readme file contains an explanation of each of the files in
 the dataset.