Evidence map›Paper›PMID 35103967›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis.

Asmita Jha, Anders S Hansen

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. 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

2 authors.

Asmita JhaDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID https://orcid.org/0000-0002-2612-551X
Anders S HansenDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. ashansen@mit.edu.ORCID https://orcid.org/0000-0001-7540-7858

Funding

DYNAMIC BOTTOM-UP DISSECTION OF CHROMATIN LOOPING AND GENE REGULATIONDP2GM140938 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI HANSEN, ANDERS SEJR · 2020 to 2020
$2.3M
Molecular mechanisms regulating chromatin looping in time and spaceR00GM130896 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI HANSEN, ANDERS SEJR · 2020 to 2022
$747k
NIGMS NIH HHS DP2 GM140938NIGMS NIH HHS R00 GM130896
6 · The paper itself

Abstract

Single-particle tracking (SPT) makes it possible to directly observe single protein diffusion dynamics in living cells over time. Thus, SPT has emerged as a powerful method to quantify the dynamics of nuclear proteins such as transcription factors (TFs). Here, we provide a protocol for conducting and analyzing SPT experiments with a focus on fast tracking ("fastSPT") of TFs in mammalian cells. First, we explore how to engineer and prepare cells for SPT experiments. Next, we examine how to optimize SPT experiments by imaging at low densities to minimize tracking errors and by using stroboscopic excitation to minimize motion-blur. Next, we discuss how to convert raw SPT data into single-particle trajectories. Finally, we illustrate how to analyze these trajectories using the kinetic modeling package Spot-On. We discuss how to use Spot-On to fit histograms of displacements and extract useful information such as the fraction of TFs that are bound and freely diffusing, and their associated diffusion coefficients.

Indexed as

Single Molecule ImagingTranscription FactorsAnimalsDiffusionGene Expression RegulationMammalsMotionTranscription FactorsDiffusionDiffusion coefficientFluorescence microscopyLive-cell imagingSingle-moleculeSingle-particle trackingSingle-particle trajectoriesspaSPTSpot-OnTranscription factors

Identifiers

PMID35103967

What OpenQuestion holds

Textmetadata
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.