a database for spatially resolved transcriptomes

Spatially resolved transcriptome techniques and datasets

Spatial transcriptomics

Spatial Transcriptomics (ST) is an approach that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue samples. By placing tissue sections on glass slides with arrayed oligonucleotides containing positional barcodes, this method claimed to generate high quality cDNA libraries with precise positional information for RNA-seq. The barcoded microarrays have 1,007 spots of RT-primers with unique barcode sequences. Each spot has a diameter of 100 µm (corresponding to a tissue domain). The center-to-center distance is 200 µm.

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Schematics of Spatial Transcriptomics (ST). Thrane et al. Cancer Res. 2018.

Spatial transcriptome dataset

PMID Title Journal Year Details Browse
27365449 Visualization and analysis of gene expression in tissue sections by spatial transcriptomics Science 2016 Details Browse
29021611 Spatial detection of fetal marker genes expressed at low level in adult human heart tissue Sci Rep 2017 Details Browse
29925878 Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity Nat Comm 2018 Details Browse
30154148 Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma Cancer Res 2018 Details Browse
30948552 Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis Science 2019 Details Browse


Slide-seq is a method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Uniquely DNA-barcoded 10-μm microparticles (“beads”) are packed onto a rubber-coated glass coverslip to form a monolayer termed a “puck”. Each bead’s distinct barcode sequence is determined via SOLiD (sequencing by oligonucleotide ligation and detection) chemistry. Ten micrometer fresh-frozen tissue sections are transferred onto the dried bead surface via cryosectioning. mRNA released from the tissue is captured onto the beads for preparation of 3′-end, barcoded RNA-seq libraries.

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Schematics of Slide-seq. Rodriques et al. Science. 2018.

Slide-seq dataset

PMID Title Journal Year Details Browse
30923225 Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 2018 Details Browse


Laser capture microdissection sequencing (LCM-seq) is a technique in which a laser is used to ablate small groups of cells or even single cells up to relatively large regions within a tissue section mounted on a special support matrix, and subsequently to transfer the captured material into test tubes for downstream RNA sequencing. Spinal cords isolated from mouse pups are sectioned at 12 μm thickness at cervical and lumbar levels. Motor neurons (MNs) are visualized using Histogene staining, captured by a Leica LMD7000 system and collected in PCR tubes. Cells are lysed, cDNA synthesized, amplified and analysed using a Bioanalyzer and sequencing libraries subsequently prepared. The cDNA profile is exemplified by a Bioanalyzer profile of 50 captured MNs.

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Schematics of LCM-seq. Nichterwitz et al. Nat Commun. 2016.

LCM-seq dataset

PMID Title Journal Year Details Browse
24780627 A gene expression atlas of early craniofacial development. Dev Biol 2014 Details Browse
25344199 Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. Genome Biol 2014 Details Browse
27387371 Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling. Nat Comm 2016 Details Browse
30270040 Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 2018 Details Browse


Sequential fluorescence in situ hybridization (seqFISH): In seqFISH, primary probes against genes are hybridized in cells. Overhang sequences on the primary probes correspond to four rounds of barcoding. Only one twentieth of the total genes in each fluorescent channel are labelled by readout probes in each pseudocolour hybridization readout round, lowering the density of transcripts in each image. mRNA dots in each pseudocolour can then be localized by Gaussian fitting and collapsed into a super-resolved image. Each gene is barcoded within only one fluorescent channel.

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Schematics of seqFISH. Eng et al. Nature. 2019.

seqFISH dataset

PMID Title Journal Year Details Browse
27764670 In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron 2016 Details Browse
30371680 Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nat Biotechnol 2018 Details Browse
30911168 Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 2019 Details Browse


Multiplexed error-robust fluorescence in situ hybridization (MERFISH) is a single-molecule imaging method that allows thousands of RNA species to be imaged in single cells by using combinatorial FISH labeling with encoding schemes capable of detecting and/or correcting errors. Combinatorial labeling that identifies each RNA species by multiple (N) distinct signals offers a route to rapidly increase the number of RNA species that can be probed simultaneously in individual cells. Each RNA species is encoded with a N-bit binary word, and the sample is probed with N corresponding rounds of hybridization, each round targeting only the subset of RNAs that should read “1” in the corresponding bit. N rounds of hybridization would allow 2N – 1 RNA species to be probed.

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Schematics of MERFISH. Chen et al. Science. 2015.

MERFISH dataset

PMID Title Journal Year Details Browse
30385464 Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 2018 Details Browse

Liver single cell zonation

Paired-cell sequencing is a method in which mRNA from pairs of attached cells are sequenced and the spatially resolved gene expression from one cell type is used to infer the pairs' tissue coordinates. This method was applied to pairs of hepatocytes and liver endothelial cells (LECs). Using the spatial information from hepatocytes, LEC zonation was reconstructed and a landmark gene panel was extracted which was used to spatially map LEC scRNA-seq data. Magnified area represents a typical porto-central sinusoidal unit. A typical unit consists of 10–15 hepatocytes and is coarse-grained into 8 or 4 concentric layers when analyzing paired cells and single cells, respectively. Paired-cell RNA sequencing utilizes the hepatocyte zonation to determine tissue localization and single-cell RNA-seq of LECs to extract LEC-specific genes. LEC zonation is obtained by averaging expression of LEC genes in the spatially localized pairs. This dataset is also used to extract LEC landmark genes for localizing single LECs.

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Schematics of liver single cell zonation. Halpern et al. Nat Biotechnol. 2018.

Liver single cell zonation

PMID Title Journal Year Details Browse
28166538 Single-cell spatial reconstruction reveals global division of labour in the mammalian liver Nature 2017 Details Browse
30222169 Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells. Nat Biotechnol 2018 Details Browse


Geographical position sequencing (Geo-seq) is a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology.Cells were captured by laser capture microdissection from four quadrants: anterior (A), posterior (P), and lateral (left/right, L/R), of each sample section (S1–S11) of the epiblast of late mid-streak stage (E7.0) C57BL/6 embryos, and analyzed by RNA-seq.

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Schematics of the GEO-seq workflow. Peng et al. Dev Cell. 2016.

Geo-seq dataset

PMID Title Journal Year Details Browse
27003939 Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Dev Cell 2016 Details Browse


Tomo-seq: In Tomo-seq, samples are cryosectioned into thin slices. RNA is extracted from individual slices using the TRIzol reagent, and oligodeoxythymidine primers carrying section-specific barcodes are used to initiate reverse transcription, allowing sample pooling before library preparation. Embryos are cryosectioned into 50–100 slices and sections are collected in individual Eppendorf tubes for spatially resolved transcriptomics. RNA extraction is performed for each individual section, followed by reverse transcription. The samples are then pooled and amplified by in vitro transcription.

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Schematics of Tomo-seq procedures in zebrafish embryos. Junker et al. Cell. 2014.

Tomo-seq dataset

PMID Title Journal Year Details Browse
23028969 Transcriptome tomography for brain analysis in the web-accessible anatomical space. PLoS one 2012 Details Browse
23951250 Sequencing mRNA from cryo-sliced drosophila embryos to determine genome-wide spatial patterns of gene expression. PLoS one 2013 Details Browse
25417113 Genome-wide RNA tomography in the zebrafish embryo. Cell 2014 Details Browse
26748692 Spatially resolved genome-wide transcriptional profiling identifies BMP signaling as essential regulator of zebrafish cardiomyocyte regeneration. Dev Cell 2016 Details Browse
28724751 Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury. Circulation 2017 Details Browse
29400650 Spatially resolved RNA-sequencing of the embryonic heart identifies a role for Wnt/β-catenin signaling in autonomic control of heart rate. Elife 2018 Details Browse
30416013 Spatial transcriptomics of C. elegans males and hermaphrodites identifies sex-specific differences in gene expression patterns. Dev Cell 2018 Details Browse