Evidence map›Paper›PMID 36595913›Full record

ArticleSTAR protocols2022

Protocol to assess RNA-RNA interactions in situ using an RNA-proximity ligation assay.

Megha G Basavappa, Jorge Henao-Mejia, Sara Cherry

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Megha G BasavappaDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: mbas@pennmedicine.upenn.edu.
Jorge Henao-MejiaDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Sara CherryDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: cherrys@pennmedicine.upenn.edu.

Funding

The role of autophagy in innate anti-viral immunity in DrosophilaR01AI074951 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI CHERRY, SARA · 2007 to 2017
$4.2M
Defining the functional interface between the ER and flavivirusesR01AI140539 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI CHERRY, SARA, DIAMOND, MICHAEL S · 2018 to 2022
$3.0M
Regulation of short-lived myeloid cells by the novel long non-coding RNA MorrbidR01HL136572 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI HENAO-MEJIA, JORGE · 2017 to 2021
$2.0M
Antiviral immunity in the gut: how the intestinal epithelium and microbiota regulate infectionR01AI122749 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI CHERRY, SARA · 2016 to 2020
$2.0M
Regulation of adipose tissue inflammation by the miR-181 familyR21DK111755 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI HENAO-MEJIA, JORGE · 2016 to 2018
$604k
Elucidating the functional roles of long noncoding RNAs in Chikungunya virus infectionR21AI151882 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI CHERRY, SARA · 2020 to 2021
$446k
Regulation of group 1 ILCs by a novel lncRNAR21AI128060 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENAO-MEJIA, JORGE · 2017 to 2018
$443k
NHLBI NIH HHS R01 HL136572NIAID NIH HHS R01 AI074951NIAID NIH HHS R01 AI122749NIAID NIH HHS R01 AI140539NIAID NIH HHS R21 AI128060NIAID NIH HHS R21 AI151882NIDDK NIH HHS R21 DK111755
6 · The paper itself

Abstract

Here, we describe a protocol to assess RNA-RNA interactions in situ using an adapted proximity ligation assay (PLA). We detail steps to perform RNA-probe hybridization, in situ rolling circle amplification, and immunofluorescence confocal microscopy. With these tools, it is possible to detect and characterize the intracellular localization of interacting RNA pairs using small cell numbers. This protocol provides a targeted approach to understanding RNA-RNA interactions in intact cells that can complement other established deep-sequencing-based approaches. For complete details on the use and execution of this protocol, please refer to Basavappa et al. (2022).

Indexed as

RNARNAIn Situ HybridizationMicroscopyMolecular BiologySingle Cell

Identifiers

PMID36595913
PMCPMC9722720

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.