Evidence map›Paper›PMID 38370833›Full record

ArticlebioRxiv : the preprint server for biology2024

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.

Zhiliang Bai, Dingyao Zhang, Yan Gao, Bo Tao, Shuozhen Bao, Archibald Enninful, Daiwei Zhang, Graham Su, Xiaolong Tian, Ningning Zhang and 8 more

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

Article in bioRxiv : the preprint server for biology, 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, 16 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors at 5 institutions in 1 country.

Zhiliang BaiDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.ORCID 0000-0002-3977-3057
Dingyao ZhangDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
Yan GaoCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Bo TaoDepartment of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
Shuozhen BaoDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
Archibald EnninfulDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
Daiwei ZhangDepartment of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.ORCID 0000-0002-5019-622X
Graham SuDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
Xiaolong TianDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
Ningning ZhangDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
Yang XiaoDepartment of Biomedical Engineering, Columbia University, New York, NY 10027, USA.
Yang LiuDepartment of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
Mark GersteinSection on Biomedical Informatics and Data Science, Yale University, New Haven, CT 06520, USA.
Mingyao LiDepartment of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Yi XingCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jun LuDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
Mina L XuDepartment of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
Rong FanDepartment of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
Yale University · USChildren's Hospital of Philadelphia · USYale Cancer Center · USColumbia University · USUniversity of Pennsylvania · US

Funding

A Multidisciplinary Center for Developing Human and Non-human Primate Brain Cell AtlasesUM1MH130991 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Hao Huang, ARNOLD KRIEGSTEIN · 2022 to 2026
$25.2M
Spatiotemporal Tumor Analytics for Guiding Sequential Targeted-Inhibitor: Immunotherapy Combinations (ST-Analytics)U54CA274509 · NCI · INSTITUTE FOR SYSTEMS BIOLOGY · PI Rong Fan · 2022 to 2026
$15.6M
Tech Core 2U54CA268083 · NCI · JOHNS HOPKINS UNIVERSITY · PI Pei-Hsun wu · 2022 to 2026
$10.2M
Yale Cooperative Hematology Specialized Core CenterU54DK106857 · NIDDK · YALE UNIVERSITY · PI JOHN HWA, Diane S Krause · 2015 to 2026
$9.7M
Yale TMC for Cellular Senescence in Lymphoid OrgansU54AG076043 · NIA · YALE UNIVERSITY · PI FAN, RONG, HALENE, STEPHANIE · 2021 to 2025
$7.0M
Yale Murine-TMC on Immune Cell Senescence Derived InflammationU54AG079759 · NIA · YALE UNIVERSITY · PI DIXIT, VISHWA DEEP, MONTGOMERY, RUTH R · 2022 to 2025
$6.5M
High-throughput in vivo and in vitro functional and multi-omics screens of neuropsychiatric and neurodevelopmental disorder risk genesRM1MH132648 · NIMH · YALE UNIVERSITY · PI Kristen Jennifer Brennand, Rong Fan · 2023 to 2026
$5.6M
Highly scalable and sensitive spatial transcriptomic and epigenomic sequencing of brain tissues from human and non-human primateRF1MH128876 · NIMH · YALE UNIVERSITY · PI FAN, RONG, SESTAN, NENAD · 2021 to 2021
$2.9M
Ex vivo analysis of human brain tumor cells in a microvascular niche modelR01CA245313 · NCI · YALE UNIVERSITY · PI FAN, RONG, ZHOU, JIANGBING · 2020 to 2024
$2.6M
Novel Bioinformatics Tools for Quantitative Prediction of Primary MicroRNA ProcessingR01GM138856 · NIGMS · YALE UNIVERSITY · PI DING, YE, LU, JUN · 2020 to 2023
$1.8M
High-throughput single-cell co-sequencing of small and large RNAs to identify molecular circuitry in cancerR33CA246711 · NCI · YALE UNIVERSITY · PI FAN, RONG, LU, JUN · 2020 to 2022
$1.2M
High-spatial-resolution ECM-inclusive multi-omics sequencing of human PFA and FFPE tissue slidesUH3CA257393 · NCI · YALE UNIVERSITY · PI FAN, RONG · 2022 to 2023
$1.2M
NCI NIH HHS R01 CA245313NCI NIH HHS R33 CA246711NCI NIH HHS U54 CA268083NCI NIH HHS U54 CA274509NCI NIH HHS UH3 CA257393NHGRI NIH HHS R56 HG012310NIA NIH HHS U54 AG076043NIA NIH HHS U54 AG079759NIDDK NIH HHS U54 DK106857NIGMS NIH HHS R01 GM138856NIMH NIH HHS RF1 MH128876NIMH NIH HHS RM1 MH132648NIMH NIH HHS UM1 MH130991
6 · The paper itself

Abstract

Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining

Identifiers

PMID38370833
PMCPMC10871202
OpenAlexW4391792424

What OpenQuestion holds

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LicenceCC BY-ND
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.