Evidence map›Paper›PMID 42124641›Full record

ArticlebioRxiv : the preprint server for biology2026

Unified Transcriptome and Mechanics Map of the Intact Mammalian Preimplantation Embryo In Situ.

Ehsan Habibi, Anubhav Sinha, Haiqian Yang, Payman Yadollahpour, Yiwei Li, Lani Lee, David A Wollensak, Zachary D Chiang, Denny Sakkas, Edward S Boyden and 3 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

13 authors.

Ehsan HabibiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Anubhav SinhaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Haiqian YangDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Payman YadollahpourBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yiwei LiDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Lani LeeDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
David A WollensakBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Zachary D ChiangBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Denny SakkasBoston IVF-Eugin Group, Waltham, MA 02451, USA.
Edward S BoydenDepartment of Media Arts and Sciences, MIT, Cambridge, MA, USA.
Ming GuoDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Aviv RegevKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Fei ChenBroad Institute of MIT and Harvard, Cambridge, MA, USA.

Funding

Tool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI ARLOTTA, PAOLA, HUANG, Z JOSH · 2017 to 2021
$64.5M
COVID19 Slide-seqR01HG010647 · NHGRI · BROAD INSTITUTE, INC. · PI Fei Chen, Evan Z Macosko · 2019 to 2026
$6.0M
Expansion MicroscopyR01EB024261 · NIBIB · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S. · 2017 to 2025
$4.6M
Neuroimaging Training ProgramT32EB001680 · NIBIB · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BRUCE R ROSEN · 2003 to 2026
$3.8M
Multiplexed Nanoscale Protein Mapping Through Expansion Microscopy and Immuno-SABERRF1MH124606 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BOYDEN, EDWARD S., YIN, PENG · 2020 to 2020
$2.7M
NHGRI NIH HHS R01 HG010647NIBIB NIH HHS R01 EB024261NIBIB NIH HHS T32 EB001680NIMH NIH HHS RF1 MH124606NIMH NIH HHS U19 MH114821
6 · The paper itself

Abstract

The development and maintenance of multicellular tissues requires that cell states be closely coupled to their local environment, including geometric and mechanical cues. However, studying this coupling in intact tissues has been challenging, because existing measurement technologies cannot simultaneously assess mechanical properties and molecularly defined cell states. To address this gap, we introduce the Unified Transcriptome and Mechanics Map (UTMM), a method for concurrent measurement of the transcriptome and cytoplasmic stiffness (high-frequency elastic modulus) within intact 3D multicellular structures. UTMM relies on two innovations: (1) a targeted in situ RNA sequencing approach for intact 3D embryos (3DISS), and (2) a strategy that leverages high-frequency intracellular organelle fluctuations to infer cell-level stiffness

Identifiers

PMID42124641
PMCPMC13160130

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.