Evidence map›Paper›PMID 36807070›Full record

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

Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq.

Samuel H Kim, Georgi K Marinov, S Tansu Bagdatli, Soon Il Higashino, Zohar Shipony, Anshul Kundaje, William J Greenleaf

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. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Using Callus as an Ex Vivo System for Chromatin Analysis.Methods in molecular biology (Clifton, N.J.) · 2025
    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

7 authors.

Samuel H KimCancer Biology Program, School of Medicine, Stanford University, Stanford, CA, USA. samhkim@stanford.edu.
Georgi K MarinovDepartment of Genetics, Stanford University, Stanford, CA, USA.
S Tansu BagdatliDepartment of Genetics, Stanford University, Stanford, CA, USA.
Soon Il HigashinoDepartment of Genetics, Stanford University, Stanford, CA, USA.
Zohar ShiponyDepartment of Genetics, Stanford University, Stanford, CA, USA.
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA, USA.
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA, USA.

Funding

VACCINE INDUCED IMMUNITY IN THE YOUNG AND AGEDU19AI057266 · NIAID · EMORY UNIVERSITY · PI Rafi Ahmed · 2003 to 2026
$81.7M
MEDICAL SCIENTIST TRAINING PROGRAMT32GM007365 · NIGMS · STANFORD UNIVERSITY · PI CHUA, KATRIN F · 1985 to 2021
$33.8M
PRODUCTION CENTER FOR MAPPING REGULATORY REGIONS OF THE HUMAN GENOMEUM1HG009442 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2017 to 2021
$20.1M
Special EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2M
Integration of genetic association mapping and functional data to elucidate genetic mechanisms of diseaseR01HG008140 · NHGRI · STANFORD UNIVERSITY · PI JONATHAN K PRITCHARD · 2016 to 2026
$7.3M
Labeling and sequencing of 5hmC and 5mC in DNA-RenewalR01HG006827 · NHGRI · UNIVERSITY OF CHICAGO · PI HE, CHUAN · 2012 to 2025
$7.2M
High-throughput systematic characterization of regulatory element functionUM1HG009436 · NHGRI · STANFORD UNIVERSITY · PI BASSIK, MICHAEL C, GREENLEAF, WILLIAM JAMES · 2017 to 2021
$5.4M
Decoding the regulatory architecture of the human genome across cell types, individuals and diseaseU01HG009431 · NHGRI · STANFORD UNIVERSITY · PI PRITCHARD, JONATHAN K · 2017 to 2021
$3.5M
NHGRI NIH HHS P50 HG007735NHGRI NIH HHS R01 HG006827NHGRI NIH HHS R01 HG008140NHGRI NIH HHS U01 HG009431NHGRI NIH HHS UM1 HG009436NHGRI NIH HHS UM1 HG009442NIAID NIH HHS U19 AI057266NIGMS NIH HHS T32 GM007365
6 · The paper itself

Abstract

The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and understand biological processes. Recent advancements have focused on increasing sensitivity and throughput to provide richer and deeper biological insights at the cellular level. The next frontier is the development of multiomic methods capable of analyzing multiple features from the same cell, such as the simultaneous measurement of the transcriptome and the chromatin accessibility of candidate regulatory elements. In this chapter, we discuss and describe SHARE-seq (Simultaneous high-throughput ATAC, and RNA expression with sequencing) for carrying out simultaneous chromatin accessibility and transcriptome measurements in single cells, together with the experimental and analytical considerations for achieving optimal results.

Indexed as

ChromatinTranscriptomeHigh-Throughput Nucleotide SequencingRegulatory Sequences, Nucleic AcidSequence Analysis, DNASingle-Cell AnalysisChromatinChromatin accessibilityMultiomicsscATAC-seqscRNA-seqSplit–poolTranscriptomics

Identifiers

PMID36807070

What OpenQuestion holds

Textmetadata
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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.