Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Blood transcriptome responses to apnea

ABSTRACT: Illumina HT-12 v4 genome-wide gene expression microarrays are used to measure peripheral blood transcriptome responses to voluntary apnea in healthy humans. The analyses are done on blood total RNA from free-diving athletes. Samples were collected on PAXgene tubes shortly before and at two time points (1 and 3 hrs) after a series of eight apneas during a free-diving competition.

ORGANISM(S): Homo sapiens

SUBMITTER: Ingrid Eftedal

PROVIDER: E-MTAB-3547 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Project description:Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P<1*10-16) with higher variability (P<1*10-16) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ =0.83; ρ =0.79) between the expression levels of detected probes were much lower compared to the two B-cell isolation methods (ρ =0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes before application in large clinical studies. In the present study, we investigated variability and consistency in gene expression profiles between five of the most common post venipuncture methods of cell and RNA isolation: whole blood (PAXgene (PAX)), PBMCs, Epstein-Barr virus (EBV) transformed LCLs, CD19-specific B-cells subsets (B-cell CD19), CD20-specific B-cells subsets (B-cell CD20). Using samples from six individuals collected during two visits, we evaluated the differences and concordances of global gene expression profiles, the biological and technical variability seen in these approaches, cell-type specific gene expression signatures and their relevance to large-scale biobanking initiatives.

Project description:Decompression sickness (DCS) is a potentially fatal condition usually observed after scuba diving. It involves bubble formation in blood and tissues from dissolved inert gas (usually nitrogen or helium), secondary to decreases in ambient pressure (decompression).To the best of our knowledge, no study has evaluated a DCS-induced transcriptomic signature in humans. 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 < 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.