↓ Skip to main content

PBMC fixation and processing for Chromium single-cell RNA sequencing

Overview of attention for article published in Journal of Translational Medicine, July 2018
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (88th percentile)

Mentioned by

twitter
16 X users
patent
3 patents

Citations

dimensions_citation
105 Dimensions

Readers on

mendeley
280 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
PBMC fixation and processing for Chromium single-cell RNA sequencing
Published in
Journal of Translational Medicine, July 2018
DOI 10.1186/s12967-018-1578-4
Pubmed ID
Authors

Jinguo Chen, Foo Cheung, Rongye Shi, Huizhi Zhou, Wenrui Lu, CHI Consortium

Abstract

Interest in single-cell transcriptomic analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works investigators have used live cells, which introduces cell stress during preparation and hinders complex study designs. Recent studies have indicated that cells fixed by denaturing fixative can be used in single-cell sequencing, however they did not usually work with most types of primary cells including immune cells. The methanol-fixation and new processing method was introduced to preserve human peripheral blood mononuclear cells (PBMCs) for single-cell RNA sequencing (scRNA-Seq) analysis on 10× Chromium platform. When methanol fixation protocol was broken up into three steps: fixation, storage and rehydration, we found that PBMC RNA was degraded during rehydration with PBS, not at cell fixation and up to 3-month storage steps. Resuspension but not rehydration in 3× saline sodium citrate (SSC) buffer instead of PBS preserved PBMC RNA integrity and prevented RNA leakage. Diluted SSC buffer did not interfere with full-length cDNA synthesis. The methanol-fixed PBMCs resuspended in 3× SSC were successfully implemented into 10× Chromium standard scRNA-seq workflows with no elevated low quality cells and cell doublets. The fixation process did not alter the single-cell transcriptional profiles and gene expression levels. Major subpopulations classified by marker genes could be identified in fixed PBMCs at a similar proportion as in live PBMCs. This new fixation processing protocol also worked in several other fixed primary cell types and cell lines as in live ones. We expect that the methanol-based cell fixation procedure presented here will allow better and more effective batching schemes for a complex single cell experimental design with primary cells or tissues.

X Demographics

X Demographics

The data shown below were collected from the profiles of 16 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 280 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 280 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 63 23%
Student > Ph. D. Student 52 19%
Student > Master 29 10%
Student > Bachelor 23 8%
Student > Postgraduate 12 4%
Other 36 13%
Unknown 65 23%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 90 32%
Agricultural and Biological Sciences 35 13%
Medicine and Dentistry 23 8%
Immunology and Microbiology 19 7%
Neuroscience 10 4%
Other 27 10%
Unknown 76 27%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 12. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 June 2022.
All research outputs
#3,109,617
of 25,552,933 outputs
Outputs from Journal of Translational Medicine
#537
of 4,672 outputs
Outputs of similar age
#56,527
of 323,430 outputs
Outputs of similar age from Journal of Translational Medicine
#11
of 92 outputs
Altmetric has tracked 25,552,933 research outputs across all sources so far. Compared to these this one has done well and is in the 87th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,672 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.0. This one has done well, scoring higher than 88% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 323,430 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 92 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 88% of its contemporaries.