Evidence map›Paper›PMID 36807075›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.

Pierre-Olivier Estève, Udayakumar S Vishnu, Hang Gyeong Chin, Sriharsa Pradhan

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. 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
0.8field-weighted citation impact, top 30% 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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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 1 institution in 1 country.

Pierre-Olivier EstèveGenome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.
Udayakumar S VishnuGenome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.
Hang Gyeong ChinGenome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.
Sriharsa PradhanGenome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA. pradhan@neb.com.
New England Biolabs (United States) · US

Funding

Quantitative and highly versatile chromatin accessibility platformR44HG011006 · NHGRI · EPICYPHER, INC. · PI KEOGH, MICHAEL-CHRISTOPHER · 2020 to 2021
$1.8M
NHGRI NIH HHS R44 HG011006
6 · The paper itself

Abstract

A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme nicks one strand of DNA, and DNA polymerase incorporates biotin-conjugated dCTP, 5-methyl-dCTP, Fluorescein-12-dATP or Texas Red-5-dATP, dGTP, and dTTP. This allows accessible chromatin DNA to be labeled for visualization and on bead NGS library preparation. This technology allows cellular level chromatin accessibility quantification and genomic analysis of the epigenetic information in the chromatin, particularly accessible promoter, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding.

Indexed as

ChromatinDNAAnimalsDNA-Directed DNA PolymeraseGenomicsMammalsNucleosomesChromatinDNADNA-Directed DNA PolymeraseNucleosomesBiotinDNA labelingDNA libraryDNA Polymerase IdNTPsFluorescent dyeMicroscopyNEBNextNicking enzymeOpen chromatinSlides

Identifiers

PMID36807075
OpenAlexW4321478443

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.