Evidence map›Paper›PMID 37645998›Full record

ArticlebioRxiv : the preprint server for biology2023

Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization.

Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard Que, Carter Palmer, Yixu Yuan, Yida Zhang, Jinghui Song and 10 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors at 6 institutions in 1 country.

Kian KalhorDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Chien-Ju ChenDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Ho Suk LeeDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Matthew CaiDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Mahsa NafisiDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Richard QueDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Carter PalmerSanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
Yixu YuanDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Yida ZhangDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Jinghui SongDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Amanda KnotenDepartment of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Blue B LakeDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Joseph P GautDepartment of Pathology and Immunology, Washington University School of Medicine, St.
Dirk KeeneUniversity of Washington School of Medicine, Seattle, WA, USA.
Ed LeinAllen Institute for Brain Science, Seattle, WA, USA Louis, MO, USA.
Peter V KharchenkoDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Jerold ChunSanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
Sanjay JainDepartment of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Jian-Bing FanIllumina, San Diego, CA, USA.
Kun ZhangDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
University of California San Diego · USUniversity of Washington · USAllen Institute for Brain Science · USHarvard University · USSanford Burnham Prebys Medical Discovery Institute · USWashington University in St. Louis · US

Funding

Single-cell sequencing and in situ mapping of RNA transcripts in human brainsU01MH098977 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHANG, KUN · 2012 to 2016
$9.8M
Toward a human adult brain cell atlas with single-cell technologiesU01MH114828 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHUN, JEROLD, REN, BING · 2018 to 2022
$8.7M
Organ Specific ProjectU54HL145608 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SOLDATOV, RUSLAN · 2018 to 2021
$5.6M
Altered reverse transcriptase-dependent gene diversification mechanisms in Alzheimer's disease brainsR01AG065541 · NIA · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI CHUN, JEROLD · 2020 to 2024
$4.8M
NHLBI NIH HHS U54 HL145608NIA NIH HHS R01 AG065541NIMH NIH HHS U01 MH098977NIMH NIH HHS U01 MH114828
6 · The paper itself

Abstract

In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical biopsies has been limited due to their large size, general lower tissue quality and high background autofluorescence. Here we report DART-FISH, a versatile padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections at cellular resolution. We introduced an omni-cell type cytoplasmic stain, dubbed RiboSoma that substantially improves the segmentation of cell bodies. We developed a computational decoding-by-deconvolution workflow to extract gene spots even in the presence of optical crowding. Our enzyme-free isothermal decoding procedure allowed us to image 121 genes in a large section from the human neocortex in less than 10 hours, where we successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. Additionally, we demonstrated the detection of transcripts as short as 461 nucleotides, including neuropeptides and discovered new cortical layer markers. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.

Identifiers

PMID37645998
PMCPMC10462101
OpenAlexW4385972390

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.