Fredrik Salmén
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View article: Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages
Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages Open
View article: Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment
Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment Open
Epigenetic mechanisms, including histone modifications, are key regulators of transcription and influence cellular differentiation. To uncover the interplay between histone modifications and transcription, we developed T-ChIC (Transcriptom…
View article: High-throughput total RNA sequencing in single cells using VASA-seq
High-throughput total RNA sequencing in single cells using VASA-seq Open
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes the detection of many long non-coding, short non-c…
View article: Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo Open
Stress granules are phase-separated assemblies formed around RNAs. So far, the techniques available to identify these RNAs are not suitable for single cells and small tissues displaying cell heterogeneity. Here, we used TRIBE (target of RN…
View article: Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions Open
View article: Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development
Droplet-based Single-cell Total RNA-seq Reveals Differential Non-Coding Expression and Splicing Patterns during Mouse Development Open
In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify the termini of polyadenylated transcripts capturing only…
View article: Identification of the stress granule transcriptome via RNA-editing in single cells and<i>in vivo</i>
Identification of the stress granule transcriptome via RNA-editing in single cells and<i>in vivo</i> Open
Stress granules are phase separated assemblies formed around mRNAs whose identities remain elusive. The techniques available to identify the RNA content of stress granules rely on their physical purification, and are therefore not suitable…
View article: Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships Open
In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functi…
View article: Identification and transfer of spatial transcriptomics signatures for cancer diagnosis
Identification and transfer of spatial transcriptomics signatures for cancer diagnosis Open
Background Distinguishing ductal carcinoma in situ (DCIS) from invasive ductal carcinoma (IDC) regions in clinical biopsies constitutes a diagnostic challenge. Spatial transcriptomics (ST) is an in situ capturing method, which allows quant…
View article: A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart Open
View article: High-definition spatial transcriptomics for in situ tissue profiling
High-definition spatial transcriptomics for in situ tissue profiling Open
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue …
View article: High-definition spatial transcriptomics for in situ tissue profiling
High-definition spatial transcriptomics for in situ tissue profiling Open
View article: High-density spatial transcriptomics arrays for <i>in situ</i> tissue profiling
High-density spatial transcriptomics arrays for <i>in situ</i> tissue profiling Open
Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays either lac…
View article: Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors Open
The comprehensive analysis of tumor tissue heterogeneity is crucial for determining specific disease states and establishing suitable treatment regimes. Here, we analyze tumor tissue sections from ten patients diagnosed with HER2+ breast c…
View article: Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity Open
View article: Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics Open
Periodontitis is a highly prevalent chronic inflammatory disease of the periodontium, leading ultimately to tooth loss. In order to characterize the gene expression of periodontitis-affected gingival tissue, we have here simultaneously qua…
View article: New insights into the human heart development using a combined spatial and single-cell transcriptomics approach
New insights into the human heart development using a combined spatial and single-cell transcriptomics approach Open
New insights into the human heart development using a combined spatial and single-cell transcriptomics approach
View article: An Organ-Wide Gene Expression Atlas of the Developing Human Heart
An Organ-Wide Gene Expression Atlas of the Developing Human Heart Open
View article: Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue Open
Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to imp…
View article: ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
ST Pipeline: an automated pipeline for spatial mapping of unique transcripts Open
Motivation In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sectio…
View article: Correction: Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Correction: Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries Open
Scientific Reports 6: Article number: 37137; published online: 16 November 2016; updated: 13 March 2017 This Article contains errors in Figure 6c. The Pearson correlation values for the automated and manually prepared samples were inadvert…
View article: Spatially resolved and single cell transcriptomics
Spatially resolved and single cell transcriptomics Open
In recent years, massive parallel sequencing has revolutionized the field of biology and has provided us with a vast number of new discoveries in fields such as neurology, developmental biology and cancer research. A significant area is de…
View article: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries Open
View article: Massive and parallel expression profiling using microarrayed single-cell sequencing
Massive and parallel expression profiling using microarrayed single-cell sequencing Open
Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. H…
View article: Spatial Transcriptomics. Digital Pathology to Investigate Intratumor Heterogeneity in Breast Cancer.
Spatial Transcriptomics. Digital Pathology to Investigate Intratumor Heterogeneity in Breast Cancer. Open