Evidence map›Paper›PMID 36807062›Full record

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

Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.

Hang Gyeong Chin, Udayakumar S Vishnu, Zhiyi Sun, V K Chaithanya Ponnaluri, Guoqiang Zhang, Shuang-Yong Xu, Touati Benoukraf, Paloma Cejas, George Spracklin, Pierre-Olivier Estève and 2 more

Abstract read
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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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
1.7field-weighted citation impact, top 18% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. 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

12 authors at 4 institutions in 2 countries.

Hang Gyeong ChinNew England Biolabs Inc., Ipswich, MA, USA.
Udayakumar S VishnuNew England Biolabs Inc., Ipswich, MA, USA.
Zhiyi SunNew England Biolabs Inc., Ipswich, MA, USA.
V K Chaithanya PonnaluriNew England Biolabs Inc., Ipswich, MA, USA.
Guoqiang ZhangNew England Biolabs Inc., Ipswich, MA, USA.
Shuang-Yong XuNew England Biolabs Inc., Ipswich, MA, USA.
Touati BenoukrafFaculty of Medicine, Craig L. Dobbin Genetics Research Centre, Memorial University of Newfoundland, St. John's, NL, Canada.
Paloma CejasCenter for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
George SpracklinProgram in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Pierre-Olivier EstèveNew England Biolabs Inc., Ipswich, MA, USA.
Henry W LongCenter for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
Sriharsa PradhanNew England Biolabs Inc., Ipswich, MA, USA. pradhan@neb.com.
New England Biolabs (United States) · USDana-Farber Cancer Institute · USMemorial University of Newfoundland · CAUniversity of Massachusetts Chan Medical School · 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

Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells using a modified nick translation method, where a nicking enzyme nicks one strand of DNA and DNA polymerase incorporates biotin-conjugated dATP, dCTP, and methyl-dCTP. Once the DNA is labeled, it can be isolated for NGS library preparation. We termed this method as universal NicE-seq (nicking enzyme-assisted sequencing). We also demonstrate a single tube method that enables direct NGS library preparation from low cell numbers without DNA purification. Furthermore, we demonstrated universal NicE-seq on FFPE tissue section sample.

Indexed as

ChromatinDNAChromosome MappingFormaldehydeHigh-Throughput Nucleotide SequencingNucleosomesSequence Analysis, DNAChromatinDNAFormaldehydeNucleosomesBiotin-14-dCTP/dATPDNA library preparationEpigenetic profilingFormaldehyde-crosslinked cellsMethyl-dCTPNicking enzymeNucleosomeOpen chromatin labeling

Identifiers

PMID36807062
OpenAlexW4321478803

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.