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Series GSE108664 Query DataSets for GSE108664
Status Public on Jan 31, 2020
Title Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study [Saliva RNA-sequencing]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 samples 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 RNA-sequencing summary: Examination of saliva gene expression dynamics in a single individual in saliva over multiple timepoints. 100 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.
 
Contributor(s) Mias GI, Rogers LR, Singh VV
Citation(s) 33436912
Submission date Jan 02, 2018
Last update date Jan 19, 2021
Contact name George Mias
Organization name Michigan State University
Department Biochemistry and Molecular Biology
Street address 775 Woodlot Drive, Rm1319
City East Lansing
ZIP/Postal code 48824
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (100)
GSM2909567 P1011116H08 [saliva RNA-seq]
GSM2909568 P1021516H08 [saliva RNA-seq]
GSM2909569 P1031416H08 [saliva RNA-seq]
This SubSeries is part of SuperSeries:
GSE108667 Multi-omics profiling for individualized precision wellness
Relations
BioProject PRJNA428256
SRA SRP130925

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE108664_RAW.tar 228.1 Mb (http)(custom) TAR (of FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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