Journal: bioRxiv
Article Title: Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays
doi: 10.1101/2021.01.17.427004
Figure Lengend Snippet: A. Stereo-seq pipeline. Step 1 , design of the DNB patterned array chip. Step 2 , in situ sequencing to determine the spatial coordinates of uniquely barcoded oligonucleotides placed on each spot of the chip. Step 3 , preparation of capture probes by ligating the UMI-polyT containing oligonucleotides to each spot. Step 4 , subsequent in situ RNA capture from tissue placed on the chip. Step 5 , cDNA amplification, library construction and sequencing. Step 6 , data analysis to generate the spatially resolved transcriptome of the profiled tissue. B. Stereo-seq achieves a smaller spot size (upper left), higher resolution (upper right), higher number of spots per 100 μm 2 (bottom left) and larger capture area (bottom right) than other reported methods. Samples used for the comparison included mouse olfactory bulb (Stereo-seq, Visium, Slide-seqV2 and HDST), E10 mouse embryo (DBiT-seq) and mouse liver (Seq-Scope) ( ; ; ; ; ). Note that since Seq-Scope uses a random array, which contains no patterned spots, the size of each pixel was estimated according to the published dataset. C. Boxplots showing the number of transcripts captured by Stereo-seq at the indicated resolution in comparison with reported HDST, Slide-seqV2, Visium, DBiT-seq and Seq-Scope datasets. Samples in those datasets used for comparison are as in panel B . D. Unsupervised spatially-constrained clustering of the mouse olfactory bulb section analyzed by Stereo-seq data at bin 14 resolution, bins were colored by their annotation. ONL, olfactory nerve layer. OPL, outer plexiform layer. GL, glomerular layer. GCL-D, granular cell zone deep. GCL-E, granular cell layer externa. GCL-I, granular cell layer internal. IPL, internal plexiform layer. ML, mitral layer. SEZ, subependymal zone. Scale bar, 500 μm. E. Left: spatial visualization of Cdhr1 in a mouse olfactory bulb section analyzed by Stereo-seq. Right: Cdhr1 ISH data taken from Allen Brain Atlas. Scale bars, 500 μm. F. Unsupervised spatially-constrained clustering of the mouse brain section analyzed by Stereo-seq at bin 50 resolution, bins were colored by their annotation. Scale bar, 500 μm. G. Left: projection of captured DNB signals of the same region squared in the panel F . Scale bar, 50 μm. Right: superimposed nucleic acid staining and captured DNB signals from the same region squared in the middle panel. Scale bar, 10 μm.
Article Snippet: HDST data ( ) were taken from GSE130682, SLIDE-seqV2 data ( ) from the Single Cell Portal of the Broad Institute, DBiT-seq data ( ) from GSE137986, and Visium data ( ) from GSE153859, Seq-Scope data were taken from GSE169706 ( ).
Techniques: In Situ, Sequencing, Amplification, Comparison, Olfactory, Staining
