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Series GSE58335 Query DataSets for GSE58335
Status Public on Oct 27, 2014
Title Transcriptomic profiling of peripheral blood mononuclear cells from healthy individuals
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Substantial effort is currently devoted to identifying cancer-associated alterations using genomics. Here, we show that standard blood collection procedures rapidly change the transcriptional and post-transcriptional landscapes of hematopoietic cells, resulting in biased activation of specific biological pathways, up-regulation of pseudogenes, antisense RNAs, and unannotated coding isoforms, and RNA surveillance inhibition. Affected genes include common mutational targets and thousands of other genes participating in processes such as chromatin modification, RNA splicing, T and B cell activation, and NF-κB signaling. The majority of published leukemic transcriptomes exhibit signals of this incubation-induced dysregulation, explaining up to 40% of differences in gene expression and alternative splicing between leukemias and reference normal transcriptomes. The effects of sample processing are particularly evident in pan-cancer analyses. We provide biomarkers that detect prolonged incubation of individual samples, and show that keeping blood on ice markedly reduces changes to the transcriptome. In addition to highlighting the potentially confounding effects of technical artifacts in cancer genomics data, our study emphasizes the need to survey the diversity of normal as well as neoplastic cells when characterizing tumors.
This study is complemented by GSE61410: transcriptomic profiling of bone marrow cells from healthy individuals.
Overall design Peripheral blood mononuclear cells (PBMCs) were isolated from four healthy individuals, following an ex vivo incubation of variable length at either room temperature or on ice. RNA transcriptomes were measured using the Illumina HiSeq.
Contributor(s) Bradley R, Dvinge H
Citation(s) 25385641
Submission date Jun 09, 2014
Last update date Oct 12, 2019
Contact name Heidi Dvinge
Organization name UW-Madison
Department Biomolecular Chemistry
Lab Dvinge
Street address 440 Henry Mall
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (24)
GSM1407379 PBMC.none.0h.XX.03
GSM1407380 PBMC.none.0h.XY.04
GSM1407381 PBMC.none.4h.XX.03
BioProject PRJNA252189
SRA SRP043080

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

Supplementary file Size Download File type/resource
GSE58335_RAW.tar 4.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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