Evidence map›Paper›PMID 40402457›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Exploring the Cancer Immune Epigenome by ATAC-Seq.

Chunling Zeng, Yuexiang Wang

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. 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
–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

1 citing paper in PubMed.

  1. Review
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.

Chunling ZengCAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Yuexiang WangCAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. yxwang76@sinh.ac.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a rapid and sensitive method for exploring the cancer immune epigenome. ATAC-seq captures open chromatin sites based on transposing the sequencing adapter directly into native chromatin in vitro. Here we describe an optimized protocol for ATAC-seq with four main steps: nucleus extraction, transposition, library amplification, sequencing and data analysis. The ATAC protocol has the advantages of low sample requirements, high speed, and applicability to a wide range of cell and tissue types.

Indexed as

Chromatin Immunoprecipitation SequencingEpigenesis, GeneticEpigenomeEpigenomicsNeoplasmsChromatinGene LibraryHigh-Throughput Nucleotide SequencingHumansTransposasesChromatinTransposasesATAC-seqCancer immune epigenomeOpen chromatin

Identifiers

PMID40402457

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.