Evidence map›Paper›PMID 35674897›Full record

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

Image-Based Single-Molecule Analysis of Notch-Dependent Transcription in Its Natural Context.

ChangHwan Lee, Tina Lynch, Sarah L Crittenden, Judith Kimble

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 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
2.2field-weighted citation impact, top 13% of its field
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

5 citing papers in PubMed, 4 citations in OpenAlex.

  1. Whole-organism spatial transcriptomics at single-cell resolution inbioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Review
  4. Analysis of the C. elegans Germline Stem Cell Pool.Methods in molecular biology (Clifton, N.J.) · 2023
    Article
  5. 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

4 authors at 2 institutions in 1 country.

ChangHwan LeeDepartment of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA. chlee@albany.edu.
Tina LynchDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
Sarah L CrittendenDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
Judith KimbleDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
University of Wisconsin–Madison · USUniversity at Albany, State University of New York · US

Funding

Molecular regulation of germline developmentR01GM134119 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI KIMBLE, JUDITH · 2019 to 2022
$2.2M
NIGMS NIH HHS R01 GM134119
6 · The paper itself

Abstract

Notch signaling is crucial to animal development and homeostasis. Notch triggers the transcription of its target genes, which produce diverse outcomes depending on context. The high resolution and spatially precise assessment of Notch-dependent transcription is essential for understanding how Notch operates normally in its native context in vivo and how Notch defects lead to pathogenesis. Here we present biological and computational methods to assess Notch-dependent transcriptional activation in stem cells within their niche, focusing on germline stem cells in the nematode Caenorhabditis elegans. Specifically, we describe visualization of single RNAs in fixed gonads using single-molecule RNA fluorescence in situ hybridization (smFISH), live imaging of transcriptional bursting in the intact organism using the MS2 system, and custom-made MATLAB codes, implementing new image processing algorithms to capture the spatiotemporal patterns of Notch-dependent transcriptional activation. These methods allow a powerful analysis of in vivo transcriptional activation and its dynamics in a whole tissue. Our methods can be adapted to essentially any tissue or cell type for any transcript.

Indexed as

Caenorhabditis elegans ProteinsAnimalsCaenorhabditis elegansGerm CellsIn Situ Hybridization, FluorescenceReceptors, NotchRNACaenorhabditis elegans ProteinsReceptors, NotchRNAConfocalGermline stem cells (GSC) single-molecule visualizationMS2RNA live imagingsmFISHTranscriptional burstingTranscriptional dynamicsWhole worm live imagingWide-field microscopy

Identifiers

PMID35674897
OpenAlexW4286830523

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.