Measuring B Cell Chromatin Accessibility by One-Step ATAC-seq.

Sakeenah L Hicks, Christopher D Scharer

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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

–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

0 citing papers in PubMed.

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

2 authors.

Sakeenah L HicksDepartment of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.

Christopher D ScharerDepartment of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA. cdschar@emory.edu.

Funding

Regulation of Pathogenic Plasma Cells in Human SLEP01AI125180 · NIAID · EMORY UNIVERSITY · PI Ignacio E. Sanz · 2016 to 2026

$28.2M

Epigenetic instruction of memory B cell function and reactivationR01AI148471 · NIAID · EMORY UNIVERSITY · PI SCHARER, CHRISTOPHER D · 2020 to 2024

$1.9M

NIAID NIH HHS P01 AI125180NIAID NIH HHS R01 AI148471

6 · The paper itself

Abstract

The Assay for Transposase Accessible Chromatin (ATAC)-seq protocol is optimized to generate global maps of accessible chromatin using limited cell inputs. The Tn5 transposase tagmentation reaction simultaneously fragments and tags the accessible DNA with Illumina Nextera sequencing adapters. Fragmented and adapter tagged DNA is then purified and PCR amplified with dual indexing primers to generate a size-specific sequencing library. The One-Step workflow below outlines the Tn5 nuclei transposition from a range of cell inputs followed by PCR amplification to generate a sequencing library.

Indexed as

B-LymphocytesChromatinHigh-Throughput Nucleotide SequencingTransposasesAnimalsChromatin Immunoprecipitation SequencingDNAGene LibraryHumansPolymerase Chain ReactionSequence Analysis, DNAChromatinDNATn5 transposaseTransposasesATAC-seqChromatin accessibilityEpigeneticGene regulationSequencing libraryTn5 transposase

Identifiers

PMID39017885

DOI10.1007/978-1-0716-3950-4_5

PMCPMC11789530

What OpenQuestion holds

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Registered trials

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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.