Range of methods designed for assigning cell types
Spatial transcriptomics is a method for assigning cell types (identified by the mRNA readouts) to their locations in the histological sections. Recent work demonstrated that the subcellular localization of mRNA molecules, for example, in the nucleus can also be studied.[1]
The first widely-adopted method, described by Ståhl et al., in a landmark 2016 paper in Science[2] implies positioning individual tissue samples on the glass slides or arrays including "spots" of spatially barcoded oligo(dT) tails to capture the poly-adenylated mRNAs.[2] Besides oligo(dT) tail and spatial barcode, which indicates the x and y position on the arrayed slide, the probe contains an amplification and sequencing handle, and unique molecular identifier.[2] Commonly, histological samples are cut using cryotome, then fixed, stained, and put on the microarrays.[2] After that, it undergoes enzymatic permeabilization, so that RNA molecules can diffuse down to the slide, with further hybridization of polyadenilated mRNA molecules to the oligo (dT) probes.[2] Reverse transcription is then carried out in situ.[2] As a result, spatially marked complementary DNA (cDNA) is synthesized, providing information about gene expression in the exact location of the sample.[2] From the cDNA, libraries are synthesised for short-read sequencing. In summary, the first widely-adopted spatial transcriptomics protocol combines paralleled sequencing and staining of the same sample.[2] In the downstream analysis, bioinformatic tools allow to overlapp the tissue image with the gene expression. The output is a map of the transcriptome capture the gene expression of individual cells within a tissue section. It is important to mention that the first generation of the arrayed slides comprised about 1,000 spots of the 100-μm diameter, limiting resolution to ~10-40 cells per spot.[2]
Spatial transcriptomics includes methods that can be divided into two modalities, those based in next-generation sequencing for gene detection, and those based in imaging.[3] Some common approached to resolve spatial distribution of transcripts are microdisection techniques, Fluorescent in situ hybridization methods, in situ sequencing, in situ capture protocols and in silico approaches.[4]
^Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, et al. (March 2019). "Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution". Science. 363 (6434): 1463–1467. doi:10.1126/science.aaw1219. PMC 6927209. PMID 30923225.
^ abcdefghiStåhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, et al. (July 2016). "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics". Science. 353 (6294): 78–82. Bibcode:2016Sci...353...78S. doi:10.1126/science.aaf2403. PMID 27365449. S2CID 30942685.
^Tian L, Chen F, Macosko EZ (June 2023). "The expanding vistas of spatial transcriptomics". Nature Biotechnology. 41 (6): 773–782. doi:10.1038/s41587-022-01448-2. PMC 10091579. PMID 36192637.
Spatialtranscriptomics is a method for assigning cell types (identified by the mRNA readouts) to their locations in the histological sections. Recent...
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Veres A, Li V, et al. (May 2015). "Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells". Cell. 161 (5): 1187–1201. doi:10...
has conducted influential studies in whole-tissue and single-cell transcriptomics. He received his PhD from the University of Cambridge in Applied Mathematics...
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as compared to other arthropod species. Using community annotation, transcriptomics, and genome sequencing, they uncovered that Colorado Potato beetles...
parallel single-cell transcriptomic and epigenomic profiles. Genome Biology, 21(1):25, 2020 Cang Z and Q. Nie. Inferring spatial and signaling relationships...
Whelan A, Deeks JJ, et al. (June 2001). "Enhanced contact tracing and spatial tracking of Mycobacterium tuberculosis infection by enumeration of antigen-specific...
standard analysis scheme of FISH datasets in a similar way to single-cell transcriptomics analysis. Often parents of children with a developmental disability...
including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open...
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