Evidence map›Paper›PMID 32995793›Full record

ArticlebioRxiv : the preprint server for biology2021

Fixed single-cell RNA sequencing for understanding virus infection and host response.

Hoang Van Phan, Michiel van Gent, Nir Drayman, Anindita Basu, Michaela U Gack, Savaş Tay

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 6 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 1 institution in 1 country.

Hoang Van PhanPritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
Michiel van GentDepartment of Microbiology, The University of Chicago, Chicago, IL, USA.
Nir DraymanPritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
Anindita BasuDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Michaela U GackDepartment of Microbiology, The University of Chicago, Chicago, IL, USA.
Savaş TayPritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
University of Chicago · US

Funding

Regulation of Host Innate Immunity Against Viral InfectionR01AI087846 · NIAID · UNIVERSITY OF CHICAGO · PI GACK, MICHAELA ULRIKE · 2010 to 2020
$3.9M
Understanding Mechanisms of Robust Information Processing by NF-kappaBR01GM128042 · NIGMS · UNIVERSITY OF CHICAGO · PI TAY, SAVAS · 2018 to 2022
$1.8M
Ultra-Sensitive Multiplexed Quantification of Proteins Secreted from Single-Cells - Resubmission 01R01GM127527 · NIGMS · UNIVERSITY OF CHICAGO · PI TAY, SAVAS · 2019 to 2022
$1.6M
TRIM protein-mediated innate immune control of KSHV infectionR21AI118509 · NIAID · UNIVERSITY OF CHICAGO · PI GACK, MICHAELA ULRIKE · 2015 to 2016
$435k
NIAID NIH HHS R01 AI087846NIAID NIH HHS R21 AI118509NIGMS NIH HHS R01 GM127527NIGMS NIH HHS R01 GM128042
6 · The paper itself

Abstract

Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited because current high-throughput RNA sequencing methods are incompatible with paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single-cells. We show that FD-seq preserves the mRNA integrity and relative abundances during fixation and subsequent cell retrieval. Furthermore, FD-seq detects a higher number of genes and transcripts than methanol fixation. We applied FD-seq to investigate two important questions in Virology. First, by analyzing a rare population of cells supporting lytic reactivation of the human tumor virus KSHV, we identified

Identifiers

PMID32995793
PMCPMC7523121
OpenAlexW3086681615

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.