2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
May 8th, 2025
Version: 1
The Rockefeller University
genomics
biorxiv

EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing

Liao, A.Open in Google Scholar•Zhang, Z.Open in Google Scholar•Sziraki, A.Open in Google Scholar•Abdulraouf, A.Open in Google Scholar•Xu, Z.Open in Google Scholar•Lu, Z.Open in Google Scholar•Zhou, W.Open in Google Scholar•Cao, J.Open in Google Scholar

Large-scale single-cell atlas efforts have revealed many aging- or disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular and dynamic analyses. To address this, we developed EnrichSci - a highly scalable, microfluidics-free platform that combines Hybridization Chain Reaction RNA FISH with combinatorial indexing to profile single-nucleus transcriptomes of targeted cell types with full gene-body coverage. When applied to profile oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures that are missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.

Similar Papers

biorxiv
Fri May 09 2025
Natural variation in chalcone isomerase defines a major locus controlling radial stem growth variation among Populus nigra populations
Poplar is a promising resource for wood production and the development of lignocellulosic biomass, but currently available varieties have not been optimized for these purposes. Therefore, it is critical to investigate the genetic variability and mechanisms underlying traits that affect biomass yield. Previous studies have shown that target traits in different poplar species are complex, with a sma...
Durufle, H.
•
Dejardin, A.
•
Jorge, V.
•
Pegard, M.
...•
Segura, V.
biorxiv
Fri May 09 2025
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection
Water buffalo is a cornerstone livestock species in many low- and middle-income countries, yet major gaps persist in its genomic characterization, complicated by the divergent karyotypes of its two sub-species (swamp and river). Such genomic complexity makes water buffalo a particularly good candidate for the use of graph genomics, which can capture variation missed by linear reference approaches....
Arshad, F.
•
Jayaraman, S.
•
Talenti, A.
•
Owen, R.
...•
Prendergast, J. G.
biorxiv
Fri May 09 2025
Spatially varying graph estimation for spatial transcriptomics cancer data
Modern spatial transcriptomic profiling techniques facilitate spatially resolved, high-dimensional assessment of cellular gene transcription across the tumor domain. The characterization of spatially varying gene networks enables the discovery of heterogeneous regulatory patterns and biological mechanisms underlying cancer etiology. We propose a \\textit{spatial Graphical Regression} (\\texttt{sGR...
Acharyya, S.
•
Kang, J.
•
Baladandayuthapani, V.
biorxiv
Thu May 08 2025
High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform
We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellul...
Lopez, T.
•
Honigfort, D.
•
Mah, A.
•
Thompson, C.
...•
biorxiv
Thu May 08 2025
All of Us diversity and scale improve polygenic prediction contextually with greatest improvements for underrepresented populations
Recent studies have demonstrated that polygenic risk scores (PRS) trained on multi-ancestry data can improve prediction accuracy in groups historically underrepresented in genomic studies, but the availability of linked health and genetic data from large-scale diverse cohorts representative of a wide spectrum of human diversity remains limited. To address this need, the All of Us research program ...
Tsuo, K.
•
Shi, Z.
•
Ge, T.
•
Mandla, R.
...•
Martin, A. R.
biorxiv
Thu May 08 2025
Cryptic diversity arises from glacial cycles in Pacific herring, a critical forage fish
Forage fishes are biological drivers throughout the Pacific Ocean, from the Arctic to nearly subtropical latitudes. As a critical trophic link, the health and stability of Pacific herring (Clupea pallasii) populations have implications for other marine species, including several targeted by large, productive fisheries. Previous research has indicated marked divergence between Pacific herring in th...
Timm, L. E.
•
Almgren, S. A.
•
Lopez, J. A.
•
Glass, J. R.
biorxiv
Thu May 08 2025
Identification of a novel transcriptome signature for predicting the response to anti-TNF-α treatment in rheumatoid arthritis patients
Objectives: To identify and validate a transcriptomic signature capable of predicting the response to antitumour necrosis factor (TNF) therapy in patients with rheumatoid arthritis (RA) before treatment initiation. Methods: We performed a retrospective transcriptomic analysis using two public datasets, RNA-seq data from peripheral blood mononuclear cells in GSE138746 and microarray data from whole...
Pena, R. D.
biorxiv
Thu May 08 2025
Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity
The 3\' untranslated regions (3\'UTRs) of mRNAs play a critical role in controlling gene expression and function because they contain binding sites for microRNAs and RNA binding proteins (RBPs) that alter mRNA stability, localization, and translation. Most mRNA 3\' ends contain multiple polyadenylation sites (PAS) that can be utilized in condition-specific manners, a process known as alternative p...
Gazzara, M. R.
•
Cater, T.
•
Mallory, M. J.
•
Barash, Y.
•
Lynch, K. W.
biorxiv
Thu May 08 2025
Identity-by-descent captures Shared Environmental Factors at Biobank Scale
The apple does not fall far from the tree is an old idiom that encapsulates a key concept: being related extends beyond merely sharing genetic material. It often implies sharing a common environment, including culture, language, dietary habits, and geographical location. In this study, we show that the analysis of genetic relatedness can serve as an indicator of health conditions by capturing the ...
Marsico, F.
•
Buonaiuto, S.
•
Amos-Abanyie, E.
•
Chinthala, L.
...•
Colonna, V.