Search Results - "Spatial Transcriptomics methods"

Multiplexed spatial transcriptomics methods and the application of expansion microscopy

Authors: Andra Fortner Octavian Bucur

Source: Front Cell Dev Biol
Frontiers in Cell and Developmental Biology, Vol 12 (2024)

Subject Terms: 0301 basic medicine, transcriptomics, ExSeq, Cell and Developmental Biology, 0303 health sciences, 03 medical and health sciences, QH301-705.5, spatial omics, Biology (General), expansion microscopy, MERFISH, FISSEQ

Access URL: https://pubmed.ncbi.nlm.nih.gov/39105173
https://doaj.org/article/23e24aa8140741e89b2cb2a673b0fcec

Development and application of spatial transcriptomics methods

Authors: Andrusivova, Zaneta Lundeberg, Joakim, Professor Shin, Jay W., Doktor

Contributors: Andrusivova, Zaneta Lundeberg, Joakim, Professor Shin, Jay W., Doktor

Source: TRITA-CBH-FOU.

Subject Terms: RNA, Spatial Transcriptomics, RNA sequencing, Biotechnology, Bioteknologi

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-334467
https://kth.diva-portal.org/smash/get/diva2:1789758/FULLTEXT01.pdf

Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

Authors: Natalie Charitakis Agus Salim Adam T. Piers et al.

Source: Genome Biology, Vol 24, Iss 1, Pp 1-12 (2023)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/1b4f8dd834724091bdaa2bce84d5993b

Additional file 3 of Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

Authors: Charitakis, Natalie Salim, Agus Piers, Adam T. et al.

Additional file 1 of Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods

Authors: Charitakis, Natalie Salim, Agus Piers, Adam T. et al.

The local cellular response to Human Papillomavirus focuses on basal layer restoration as visualized in situ by specific cellular neighborhoods near infected cells.

Authors: Slieker, Roderick C. Abdulrahman, Ziena Santegoets, Saskia et al.

Source: Frontiers in Immunology; 2025, p1-13, 13p

Subject Terms: HUMAN papillomavirus, VULVAR diseases, TRANSCRIPTOMES, CELL physiology, IMMUNE response, INFLAMMATION

Multiplexed RNA imaging and in situ profiling in living cells.

Authors: Mi L Khajouei S You M

Source: Chemical science [Chem Sci] 2025 Nov 06; Vol. 16 (45), pp. 21152-21173. Date of Electronic Publication: 2025 Nov 06 (Print Publication: 2025).

Publication Type: Journal Article; Review

Journal Info: Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 101545951 Publication Model: eCollection Cited Medium: Print ISSN: 2041-6520 (Print) Linking ISSN: 20416520 NLM ISO Abbreviation: Chem Sci Subsets: PubMed not MEDLINE

From spots to cells: Cell segmentation in spatial transcriptomics with BOMS.

Authors: Kamboj, Ocima Park, Jeongbin Stegle, Oliver et al.

Source: PLoS ONE; 6/12/2025, Vol. 20 Issue 6, p1-24, 24p

Subject Terms: GENETIC regulation, TRANSCRIPTOMES, MESSENGER RNA, MOLECULES

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.

Authors: Gandin, Valentina Kim, Jun Yang, Liang-Zhong et al.

Source: Science; 4/18/2025, Vol. 388 Issue 6744, p1-13, 13p

Subject Terms: BIOLOGICAL specimen analysis, CELL imaging, GENETIC barcoding, TRANSCRIPTOMES, EXPANSION microscopy, RNA analysis

Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology.

Authors: Pang, Jia‐Min B Byrne, David J Bergin, Alice R T et al.

Source: Histopathology; Mar2024, Vol. 84 Issue 4, p577-586, 10p

Subject Terms: TRANSCRIPTOMES, MOLECULAR pathology, ANATOMICAL pathology, PATHOLOGISTS, MORPHOLOGY, SURGICAL pathology

Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy.

Authors: An, Junsha Lu, Yajie Chen, Yuxi et al.

Source: Frontiers in Immunology; 2025, p1-19, 19p

Subject Terms: GENE expression, TRANSCRIPTOMES, BREAST cancer research, BREAST cancer, RNA sequencing

In preprints: unfolding the spatial genomics frontier of mouse gastrulation.

Authors: Nowotschin, Sonja Hadjantonakis, Anna-Katerina

Source: Development (09501991); Apr2025, Vol. 152 Issue 8, p1-3, 3p

Subject Terms: HISTORY of biology, DEVELOPMENTAL biology, GENE regulatory networks, TRANSCRIPTION factors, EMBRYONIC stem cells, GASTRULATION

ESTABLISHMENT OF U-251 MG CELL SUBLINES WITH ECTOPIC OVEREXPRESSION OF CHI3L1 mRNA VARIANTS AS A MODEL SYSTEM OF THE ISOFORMS TRIALS IN GLIOMAGENESIS.

Alternate Title: ОТРИМАННЯ СУБЛІНІЙ КЛІТИН U-251 MG З ЕКТОПІЧНОЮ НАДЕКСПРЕСІЄЮ ДВОХ ВАРІАНТІВ мРНК CHI3L1 ЯК МОДЕЛЬНОЇ СИСТЕМИ ДОСЛІДЖЕННЯ ІЗОФОРМ У ГЛІОМАГЕНЕЗІ.

Authors: Areshkov, P. O. Anopriienko, O. V. Shloma, A. R. et al.

Source: Biopolymers & Cell. 2025, Vol. 41 Issue 4, p275-282. 8p.

Subject Terms: *PROTEIN isoforms, *CELL lines, *GLIOMAS, *GENES, *TUMOR microenvironment, *RNA sequencing, *GLIOBLASTOMA multiforme

Imaging the spatial organization of healthy human brain and glioblastoma

Authors: Mossi Albiach, Alejandro

Index Terms: info:eu-repo/semantics/doctoralThesis

URL: http://hdl.handle.net/10616/48967
I. Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH. Lars E. Borm, Alejandro Mossi Albiach, Camiel C.A. Mannens, Jokubas Janusauskas, Ceren Özgün, David Fernández-García, Rebecca Hodge, Francisca Castillo, Charlotte R.H. Hedin, Eduardo J. Villablanca, Per Uhlén, Ed S. Lein, Simone Codeluppi & Sten Linnarsson. Nature Biotechnology. 2022 September. ::doi::10.1038/s41587-022-01455-3 ::pmid::36138169 ::isi::000858803100002
II. Transcriptomic diversity of cell types across the adult human brain. Kimberly Siletti, Rebecca Hodge, Alejandro Mossi Albiach, Lijuan Hu, Ka Wai Lee, Peter Lönnerberg, Trygve Bakken, Song-Lin Ding, Michael Clark, Tamara Casper, Nick Dee, Jessica Gloe, C. Dirk Keene, Julie Nyhus, Herman Tung, Anna Marie Yanny, Ernest Arenas, Ed S. Lein, Sten Linnarsson. Science. 2023 October. ::doi::10.1126/science.add7046 ::pmid::37824663 ::isi::001112161200001
III. Glioblastoma is spatially organized by neurodevelopmental programs and a glial-like wound healing response. Alejandro Mossi Albiach, Jokubas Janusauskas, Ivana Kapustová, Egle Kvedaraite, Simone Codeluppi, Johannes B. Munting, Lars E. Borm, Jesper Kjaer Jacobsen, Alia Shamikh, Oscar Persson, Sten Linnarsson. Biorxiv. 2023 September. Preprint. [Manuscript] ::doi::10.1101/2023.09.01.555882

Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology

Authors: Pang, JMB Byrne, DJ Bergin, ART et al.

Index Terms: Journal Article

URL: http://hdl.handle.net/11343/344535
NHMRC/1193630

Comparison of spatial transcriptomics technologies using tumor cryosections.

Authors: Rademacher A Huseynov A Bortolomeazzi M et al.

Source: Genome biology [Genome Biol] 2025 Jun 20; Vol. 26 (1), pp. 176. Date of Electronic Publication: 2025 Jun 20.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

MeSH Terms: Gene Expression Profiling*/methods , Medulloblastoma*/genetics , Medulloblastoma*/pathology , Transcriptome*, Humans ; Tumor Microenvironment

Technological Innovations and Applications of Spatial Transcriptomics in Livestock and Poultry Research.

Authors: Wang, Mingyu Guo, Ao Zhang, Lin et al.

Source: Animal Research & One Health. Feb2026, Vol. 4 Issue 1, p14-27. 14p.

SpatioFreq: A Deep Learning Framework for Decoding Cellular and Tissue Landscapes Across Organisms Using Spatial Transcriptomics.

Authors: Wang Z Dai R Wang M et al.

Source: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2026 Mar 06. Date of Electronic Publication: 2026 Mar 06.

Publication Type: Journal Article

Journal Info: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1867-1462 (Electronic) Linking ISSN: 18671462 NLM ISO Abbreviation: Interdiscip Sci Subsets: MEDLINE

SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics.

Authors: Kinsler G Fagan C Li H et al.

Source: Nature methods [Nat Methods] 2026 Feb; Vol. 23 (2), pp. 328-333. Date of Electronic Publication: 2025 Dec 18.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Single-Cell Analysis*/methods , Gene Expression Profiling*/methods , Transcriptome*, Animals ; Mice ; Clone Cells ; Humans

Super-resolved, three-dimensional spatial transcriptomics reveals cell-type and brain-region-specific modulation of key epitranscriptomic switches following adolescent alcohol exposure.

Authors: Tandukar J Islam A Malovic E et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Jan 23. Date of Electronic Publication: 2026 Jan 23.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE