NGI Spatial omics

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Started: -

Ended: Current

Year 2025

PubMed DOI Crossref
Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.
Kaldhusdal V, Boger MF, Tjernlund A, ..., Czarnewski P, Broliden K
Sci Rep 15 (1) 1014 [2025-01-06; online 2025-01-06]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2024

PubMed DOI Crossref
The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.
Li D, Liu Z, Zhang L, ..., Sommar P, Xu Landén N
Nat Commun 15 (1) 8637 [2024-10-05; online 2024-10-05]
Bioinformatics Support for Computational Resources [Service] 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
Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.
Sonavane S, Hassan S, Chatterjee U, ..., Reimegård J, Rising A
Sci Adv 10 (33) eadn0597 [2024-08-16; online 2024-08-14]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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. 35 (2) 122-133 [2024-06-00; online 2024-01-27]
Bioinformatics Support for Computational Resources [Service] 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 (NBIS) [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 (NBIS) [Collaborative] 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]
SciLifeLab Data Centre
Publications 9.5.1