In Situ Sequencing (ISS) (24 publications)

SciLifeLab Infrastructure Unit Since 2019.

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

Started: 2019

Ended: Current

Year 2022

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 (ISS) [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 (ISS) [Collaborative]

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 [Technology development] In Situ Sequencing (ISS) [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 Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 [2022-05-25; online 2022-05-25]

In Situ Sequencing (ISS) [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 (ISS) [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 (ISS) [Technology development]

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 (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [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 Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [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 Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]

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 [2020-05-13; online 2020-05-13]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative]

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 Compute and Storage [Service] In Situ Sequencing (ISS) [Service]

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 Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [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]

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 (ISS) [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 Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]