 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA252189 |
| SRA |
SRP043080 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58335_RAW.tar |
4.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...