In Situ Sequencing

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SciLifeLab Infrastructure Unit Since 2019.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2019

Ended: Current

Year 2024

DOI Crossref
A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods
Samakovlis C, Firsova A, Salas SM, ..., Nilsson M, Nawijn M
- - (-) - [2024-10-07; online 2024-10-07]
In Situ Sequencing [Service]
PubMed DOI Crossref
Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.
Andersson A, Escriva Conde M, Surova O, ..., Nilsson M, Nyström H
Clin. Cancer Res. 30 (19) 4517-4529 [2024-10-01; online 2024-07-26]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing [Service]
PubMed DOI Crossref
BirthSeq, a new method to isolate and analyze dated cells in different vertebrates.
Rueda-Alaña E, Grillo M, Vázquez E, ..., Nilsson M, García-Moreno F
Development 151 (13) - [2024-07-01; online 2024-07-10]
In Situ Sequencing [Service]
PubMed DOI Crossref
A community effort to track commercial single-cell and spatial 'omic technologies and business trends.
De Jonghe J, Opzoomer JW, Vilas-Zornoza A, ..., Cribbs AP, Taylor-King JP
Nat. Biotechnol. 42 (7) 1017-1023 [2024-07-00; online 2024-07-18]
In Situ Sequencing [Collaborative]
DOI Crossref
Evolutionary convergence of sensory circuits in the pallium of amniotes
Rueda-Alaña E, Senovilla-Ganzo R, Grillo M, ..., De Pitta M, García-Moreno F
- - (-) - [2024-05-02; online 2024-05-02]
In Situ Sequencing [Service]
PubMed DOI Crossref
Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.
Kukanja P, Langseth CM, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G
Cell 187 (8) 1990-2009.e19 [2024-04-11; online 2024-03-20]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2023

DOI Crossref
Open-source, high-throughput targeted in-situ transcriptomics for developmental biologists
Lee H, Langseth CM, Salas SM, ..., Grillo M, Nilsson M
- - (-) - [2023-10-11; online 2023-10-11]
In Situ Sequencing [Technology development]
DOI Crossref
BirthSeq, a new method to isolate and analyze dated cells from any tissue in vertebrates
Rueda-Alaña E, Grillo M, Vazquez E, ..., Nilsson M, García-Moreno F
- - (-) - [2023-10-10; online 2023-10-10]
In Situ Sequencing [Service]
PubMed DOI Crossref
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J
Nat. Biotechnol. - (-) - [2023-09-04; online 2023-09-04]
In Situ Sequencing [Collaborative] Spatial Mass Spectrometry [Collaborative]
DOI Crossref
Single cell-resolutionin situsequencing elucidates spatial dynamics of multiple sclerosis lesion and disease evolution
Langseth CM, Kukanja P, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G
- - (-) - [2023-06-30; online 2023-06-30]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [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 [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.
Magoulopoulou A, Salas SM, Tiklová K, ..., Hilscher MM, Nilsson M
Annu Rev Genomics Hum Genet - (-) - [2023-04-05; online 2023-04-05]
In Situ Sequencing [Collaborative]
DOI Crossref
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
Salas SM, Czarnewski P, Kuemmerle LB, ..., Ishaque N, Nilsson M
- - (-) - [2023-02-14; online 2023-02-14]
In Situ Sequencing [Technology development]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] In Situ Sequencing [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref
Metabolic reprogramming and membrane glycan remodeling as potential drivers of zebrafish heart regeneration.
Spelat R, Ferro F, Contessotto P, ..., Kilcoyne M, Pandit A
Commun Biol 5 (1) 1365 [2022-12-13; online 2022-12-13]
In Situ Sequencing [Service]
PubMed DOI Crossref
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Liu I, Jiang L, Samuelsson ER, ..., Nilsson M, Filbin MG
Nat. Genet. 54 (12) 1881-1894 [2022-12-00; online 2022-12-05]
In Situ Sequencing [Collaborative]
PubMed DOI Crossref
Spatial and temporal heterogeneity in the lineage progression of fine oligodendrocyte subtypes
Hilscher MM, Langseth CM, Kukanja P, ..., Nilsson M, Castelo-Branco G
BMC Biol. 20 (1) 122 [2022-12-00; online 2022-05-25]
In Situ Sequencing [Collaborative]
PubMed DOI Crossref
Spatial genomics maps the structure, nature and evolution of cancer clones.
Lomakin A, Svedlund J, Strell C, ..., Nilsson M, Yates LR
Nature 611 (7936) 594-602 [2022-11-00; online 2022-11-09]
In Situ Sequencing [Service]
PubMed DOI Crossref
The discovAIR project: a roadmap towards the Human Lung Cell Atlas.
Luecken MD, Zaragosi LE, Madissoon E, ..., Meyer KB, Nawijn MC
Eur. Respir. J. 60 (2) - [2022-08-00; online 2022-08-18]
In Situ Sequencing [Service]
PubMed DOI Crossref
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.
Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G
PLoS Comput. Biol. 18 (8) e1010366 [2022-08-00; online 2022-08-12]
BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing [Collaborative]
PubMed DOI Crossref
Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.
van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G
Dev. Cell 57 (11) 1421-1436.e5 [2022-06-06; online 2022-05-05]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial Resolution of Mycobacterium tuberculosis Bacteria and Their Surrounding Immune Environments Based on Selected Key Transcripts in Mouse Lungs.
Magoulopoulou A, Qian X, Pediatama Setiabudiawan T, ..., Nilsson M, Carow B
Front Immunol 13 (-) 876321 [2022-05-18; online 2022-05-18]
In Situ Sequencing [Collaborative]
PubMed DOI Crossref
Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.
Lee H, Marco Salas S, Gyllborg D, Nilsson M
Sci Rep 12 (1) 7976 [2022-05-13; online 2022-05-13]
In Situ Sequencing [Technology development]
DOI Crossref
Developmental origins of cell heterogeneity in the human lung
Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C
- - (-) - [2022-01-12; online 2022-01-12]
In Situ Sequencing [Service]

Year 2021

PubMed DOI Crossref
A roadmap for the Human Developmental Cell Atlas.
Haniffa M, Taylor D, Linnarsson S, ..., Webb S, Human Cell Atlas Developmental Biological Network
Nature 597 (7875) 196-205 [2021-09-00; online 2021-09-08]
In Situ Sequencing [Collaborative] Spatial Proteomics
PubMed DOI Crossref
Comprehensive in situ mapping of human cortical transcriptomic cell types.
Langseth CM, Gyllborg D, Miller JA, ..., Hilscher MM, Nilsson M
Commun Biol 4 (1) 998 [2021-08-24; online 2021-08-24]
In Situ Sequencing [Technology development]
PubMed DOI Crossref
Molecular architecture of the developing mouse brain.
La Manno G, Siletti K, Furlan A, ..., Lönnerberg P, Linnarsson S
Nature 596 (7870) 92-96 [2021-08-00; online 2021-07-28]
In Situ Sequencing [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.
Marco Salas S, Gyllborg D, Mattsson Langseth C, Nilsson M
BMC Bioinformatics 22 (1) 391 [2021-07-31; online 2021-07-31]
In Situ Sequencing [Technology development]

Year 2020

PubMed DOI Crossref
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.
Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M
Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Technology development]
PubMed DOI Crossref
Probabilistic cell typing enables fine mapping of closely related cell types in situ.
Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M
Nat. Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Service]
PubMed DOI Crossref
In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections
Hilscher MM, Gyllborg D, Yokota C, Nilsson M
Methods Mol. Biol. 2148 (-) 313-329 [2020-00-00; online 2020-05-12]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing [Collaborative]

Year 2019

PubMed DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
Advanced FISH Technologies Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer.
Svedlund J, Strell C, Qian X, ..., Sieuwerts AM, Nilsson M
EBioMedicine 48 (-) 212-223 [2019-10-00; online 2019-09-13]
In Situ Sequencing [Technology development]
PubMed DOI Crossref
Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I
Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-07]
Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma.
Carow B, Hauling T, Qian X, ..., Nilsson M, Rottenberg ME
Nat Commun 10 (1) 1823 [2019-04-23; online 2019-04-23]
In Situ Sequencing [Collaborative]
PubMed DOI Crossref
Placing RNA in context and space - methods for spatially resolved transcriptomics.
Strell C, Hilscher MM, Laxman N, ..., Yokota C, Nilsson M
FEBS J. 286 (8) 1468-1481 [2019-04-00; online 2018-03-31]
In Situ Sequencing [Technology development]
PubMed DOI Crossref
A microfluidic platform towards automated multiplexed in situ sequencing.
Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M
Sci Rep 9 (1) 3542 [2019-03-05; online 2019-03-05]
In Situ Sequencing [Technology development]
PubMed DOI Crossref
Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development
Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T
Nat Commun 10 (1) 581 [2019-02-04; online 2019-02-04]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing [Collaborative]

Year 2018

PubMed DOI Crossref
RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.
Wu C, Simonetti M, Rossell C, ..., Crosetto N, Nilsson M
Commun Biol 1 (-) 209 [2018-11-28; online 2018-11-28]
Advanced FISH Technologies [Technology development] In Situ Sequencing [Technology development]
PubMed DOI Crossref
Expression profiling and in situ screening of circular RNAs in human tissues.
Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L
Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
SciLifeLab Data Centre
Publications 9.5.1