Fig. 1: MAGIC-seq enables sensitive, high throughput and consistent profiling of diverse tissue types. | Nature Genetics

Fig. 1: MAGIC-seq enables sensitive, high throughput and consistent profiling of diverse tissue types.

From: Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view

Fig. 1

a, Overview of the MAGIC-seq workflow. Custom microfluidic chips with serpentine channels were designed in three variations, triple-grid chip, nine-grid chip and splicing-grid chip. To create barcoded DNA arrays, two microfluidic PDMS chips were sequentially placed on a glass slide with carboxyl group on its surface. b, Comparison between MAGIC-seq and other spatial transcriptomic methods. c, Violin plot showing the number of genes per spot captured by MAGIC-seq in comparison with DBiT-seq, Decoder-seq and our sequenced 10x Visium datasets. The results have been normalized to 100k or 60k raw reads per 50 μm or 15 μm spot. d, Saturation curves of MAGIC-seq and other spatial transcriptomic methods for median gene counts per spot under different sequencing depths. e, Comparison of capture area and containing spots between MAGIC-seq and other methods. f, Cost comparison between MAGIC-seq and other methods excluding sequencing and downstream analysis. The panels display the cost normalized to per section, per mm2 and per spot (∼50 μm). g, Microfluidic device used for the fabrication of the nine-grid chips. Two PDMS chips (70 channels with a channel width of 50 μm) with serpentine channels perpendicular to each other were sequentially attached to the glass slide, resulting in nine barcoded arrays at their intersections. The blue and red dyes were used for illustrating the channels and resulting arrays. h, Schematic representation of the experimental evaluation of batch effect among different samples (left) and correlation of gene expression between sections (right). i, CV of top 100 gene expressions between different sections. Intraregion shows CV of genes within the same section. Intraslide shows CV of genes between two sections on the same slide. Interslide shows CV of genes between two sections from two slides. j, Spatial profiling and distribution of clusters for nine tissue types by the nine-grid chip. Tissues are colored by inferred cluster domains. For c and i, boxes, interquartile range. Centerlines and points, median. Whiskers, values within 1.5× interquartile range of the top and bottom quartiles. HIP, hippocampus; R, Spearman correlation coefficient; CV, coefficient of variation.

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