Integrated single-cell sequencing of 5-hydroxymethylcytosine and genomic DNA using scH&G-seq.

Alex Chialastri, Chatarin Wangsanuwat, Siddharth S Dey

Abstract read

In one paragraph

Article in STAR protocols, 2021. 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

3 authors.

Alex ChialastriDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA.

Chatarin WangsanuwatDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA.

Siddharth S DeyDepartment of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA.

Funding

A marker-free technology for mapping the epigenome of cell types in mammalian tissuesR01HG011013 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2020 to 2024

$1.8M

Understanding DNA methylation reprogramming dynamics during preimplantation development using single-cell sequencingR01HD099517 · NICHD · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI DEY, SIDDHARTH SUBHAS · 2019 to 2023

$1.4M

NHGRI NIH HHS R01 HG011013NICHD NIH HHS R01 HD099517

6 · The paper itself

Abstract

The asymmetric distribution of 5-hydroxymethylcytosine (5hmC) between two DNA strands of a chromosome enables endogenous reconstruction of cellular lineages at an individual-cell-division resolution. Further, when integrated with data on genomic variants to infer clonal lineages, this combinatorial information accurately reconstructs larger lineage trees. Here, we provide a detailed protocol for single-cell 5-hydroxymethylcytosine and genomic DNA sequencing (scH&G-seq) to simultaneously quantify 5hmC and genomic DNA from the same cell to reconstruct lineage trees at a single-cell-division resolution. For complete details on the use and execution of this protocol, please refer to Wangsanuwat et al., 2021.

Indexed as

5-MethylcytosineCell DivisionCell LineComputational BiologyDNAHumansSequence Analysis, DNASingle-Cell Analysis5-hydroxymethylcytosine5-MethylcytosineDNABioinformaticsCell isolationGenomicsMolecular BiologySequencingSingle Cell

Identifiers

PMID34950891

DOI10.1016/j.xpro.2021.101016

PMCPMC8672100

What OpenQuestion holds

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LicenceCC BY

Read underepoch 390

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.