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In Situ Sequencing (ISS)
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SciLifeLab Infrastructure Unit Since 2019.
Primary
: Shown in the list of current labels.
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 (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [Service]
DOI
Crossref
Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model
Yaghmaeian Salmani B
,
Lahti L
, Gillberg L, ..., Svenningsson P, Perlmann T
-
-
(-) - [2023-06-06; online 2023-06-06]
Bioinformatics Support for Computational Resources [Service]
In Situ Sequencing (ISS) [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]
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 (ISS) [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 (ISS) [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]
In Situ Sequencing (ISS) [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 (ISS) [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 (ISS) [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 (ISS) [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 (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) [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]
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 Support for Computational Resources [Service]
In Situ Sequencing (ISS) [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 (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 Support for Computational Resources [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 Support for Computational Resources [Service]
In Situ Sequencing (ISS) [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 (ISS) [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 (ISS) [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 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 (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]
Bioinformatics Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
In Situ Sequencing (ISS) [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 (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 Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
In Situ Sequencing (ISS) [Technology development]
NGI Uppsala (Uppsala Genome Center) [Technology development]
National Genomics Infrastructure [Technology development]
Publications
9.5.0