NGI Spatial omics (10 publications)

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Ended: Current

Year 2024

Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.

Condello V, Paulsson JO, Zedenius J, Näsman A, Juhlin CC

Endocr. Pathol. - (-) - [2024-01-27; online 2024-01-27]

NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2023

PubMed DOI Crossref

Solid-phase capture and profiling of open chromatin by spatial ATAC.

Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL

Nat. Biotechnol. 41 (8) 1085-1088 [2023-08-00; online 2023-01-05]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

The spatial landscape of gene expression isoforms in tissue sections.

Lebrigand K, Bergenstråhle J, Thrane K, ..., Waldmann R, Lundeberg J

Nucleic Acids Res. 51 (8) e47 [2023-05-08; online 2023-03-18]

NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.

Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E

Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]

BioImage Informatics [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref

Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.

Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J

Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]

NGI Short read [Service] NGI Spatial omics NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Spatially resolved clonal copy number alterations in benign and malignant tissue.

Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J

Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]

NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.

Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J

Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.

Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL

Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]

NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

The spatial transcriptomic landscape of the healing mouse intestine following damage.

Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ

Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]

NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2021

PubMed DOI Crossref

Genome-wide spatial expression profiling in formalin-fixed tissues.

Gracia Villacampa E, Larsson L, Mirzazadeh R, ..., Carlson J, Lundeberg J

Cell Genomics 1 (3) 100065 [2021-12-08; online 2021-12-08]

NGI Short read [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]