GSE108666   Details

GSE Accession GSE108666
Title Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [saliva small RNA-seq]
Submission Date 1/2/18
Last Update Date 1/31/20
Pubmed ID
Experiment Type Non-coding RNA profiling by high throughput sequencing
Contributor George,I,Mias; Lavida,R,Brooks; Vikas Singh
Contact Name
Contact E-mail
Organization Name
Organism Homo sapiens
Organism ID 9606
Organism Synonym man; human
Summary The investigation includes findings from our clinical trial, monitoring individualized response to pneumococcal vaccination, where we have carried out integrative profiling assessment of saliva pre and post vaccination in a single individual. This is to our knowledge the most extensive saliva-centered omics dataset on an individual, covering 100 timepoints over the course of one year. The time span covers a healthy period as well as comprehensive monitoring of innate and adaptive immune responses following pneumococcal vaccination. Protein and RNA from saliva were produced at each timepoint (100 timepoints), and mass spectrometry proteomics and RNA-sequencing were carried out for all samples in non-targeted comprehensive profiling. Specifically, a single individual (male, 38) was profiled over multiple timepoints during healthy periods, as well as post treatment with pneumococcal vaccine (PPSV23). Initially pre-immunization samples, including a 24 hour period with hourly sampling (samples P1052515H07-P1052615H08), were collected to provide a comparative baseline. A subsequent 24-hour time course was performed, with again hourly samples taken pre and post vaccination (P1060715H07-P1060815H06). The PPSV23 pneumococcal vaccine was admistered inbetween timepoints at approximately 10.30am, prior to datapoint P1060715H11. Following the vaccination, and after the 24 hour monitoring, daily samples were taken for about a month (up to sample P1070715H08), to capture innate and adaptive responses in saliva. Two more weekly samples followed, with then monthly sample till the end of the investigation.; Omics sample analysis includes: RNA-sequencing of total RNA, small RNA sequencing in saliva extracellular vesicles and saliva mass spectrometry proteomics.; Note on sample naming: The sample identifier/name P1MMDDYYHhh corresponds to: patient index:P1, date MMDDYY and hour hh preceded by H using 24 hour enumeration.
Overall Design Saliva extracellular vesicle small RNA-sequencing summary: Examination of extra cellular vesicle (EV) gene expression dynamics in a single individual in saliva over multiple timepoints. 104 total timepoints spanning two 24-hour periods, one without vaccination, and the second with vaccination. 30 daily samples follow and multiple monthly samples over the course of 1 year total.
Platform ID
Timepoint Count 100
Timepoints gse: [Timepoints, 100]
Disease ID