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Series GSE156989 Query DataSets for GSE156989
Status Public on Mar 29, 2021
Title Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMCs up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from native in vivo biology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states.
 
Overall design To study the effects of delays in PBMC processing from whole blood we performed two similar but independent experiments. In Experiment 1, we isolated PBMC from whole blood at 2, 4, 6, 8, and 18 hours after blood draw from healthy donors (n=3) or those diagnosed with systemic lupus erythematosus (SLE, n=3). In Experiment 2, we assayed PBMC isolated from only healthy donors (n=4) starting at 2, 4, 6, 10, 14, and 18 hours after blood draw. In both experiments, the whole blood was held in the dark at room temperature prior to PBMC isolation by Ficoll gradient separation. PBMC were assayed after freeze/thaw by 10x Genomics single-cell RNA-sequencing.

>>> Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns. dbGap: phs002280<<<
Web link https://pubmed.ncbi.nlm.nih.gov/34113805/
 
Contributor(s) Savage AK, Gutschow MV, Chiang T, Henderson KF, Green R, Chaudhari M, Swanson E, Heubeck AT, Kondza N, Burley KC, Genge PC, Lord C, Smith T, Thomson Z, Beaubien A, Johnson E, Goldy J, Bolouri H, Buckner JH, Meijer P, Coffey EM, Skene PJ, Torgerson TR, Li X, Bumol TF
Citation(s) 34113805
Submission date Aug 27, 2020
Last update date Mar 14, 2022
Contact name Allen Institute For Immunology
E-mail(s) xiaojun.li@alleninstitute.org
Phone 2065487135
Organization name Allen Institute
Street address 615 Westlake Ave N, Seattle, WA
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (55)
GSM4749756 NW_TX0005-1_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 2 hours
GSM4749758 NW_TX0005-2_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 4 hours
GSM4749759 NW_TX0005-3_GRCh38_Aged pbmcs derived from a normal subject BRISL2 at 6 hours
Relations
BioProject PRJNA659732

Download family Format
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Supplementary file Size Download File type/resource
GSE156989_RAW.tar 1.8 Gb (http)(custom) TAR (of H5)
Raw data not provided for this record
Processed data provided as supplementary file
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