Journal: Cancer Cell

Article Title: Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer

doi: 10.1016/j.ccell.2022.11.001

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Article Snippet: Sequencing reads from 10x Genomics Visium libraries were aligned to the human transcriptome reference GRCh38-2020-A using 10x Genomics SpaceRanger (v.1.3.0) and exonic reads were used to produce mRNA count matrices for each sample.

Techniques: Recombinant, Multiplex Assay, Expressing, DNA Extraction, Sequencing, Software

Journal: Advanced Science

Article Title: Spatial Isoforms Reveal the Mechanisms of Metastasis

doi: 10.1002/advs.202402242

Figure Lengend Snippet: Metastatic lymph nodes in ESCC exhibit expansive enrichment of T cells and macrophages. A) Spatial transcriptomic spots of all three samples: Before, After, and AfterLN. The colors indicate the niches of each sample. B) Boxplot of the contact frequency of spatial niches in each sample. P value was calculated by an unpaired two‐tailed Student's t‐test, n (Before) = 21 413, n (After) = 32 618, n (AfterLN) = 33 246. C) CD74, C1QC , and CXCL13 expression were labeled by RNAscope in situ hybridization. Left: HE; Middle: 10X RNAscope; Right: 20X RNAscope. DAPI: blue, C1QC : green, CD74 : pink, CXCL13 : red, Merge: white. D) Boxplot of the colocalization of the cell fraction with CD74 , C1QC , and CXCL13 expression between the tumor and LN samples when the enrichment calculation cutoff is 0.6. P value was calculated by an unpaired two‐tailed Student's t‐test. E) Circular plot of the cell‐cell interactions between niches in the three samples. The colors indicate the niche. The area of each bond indicates the frequency of interaction. F) Spatial trajectory of subclusters in niches 4–6. Arrows show the direction of the trajectory. G) Tree plot of the trajectory of subclusters in niches 4–6.

Article Snippet: Based on a previous SiT workflow, full‐length 10X Genomics Visium cDNA libraries were split for Illumina sequencing and ONT sequencing.

Techniques: Two Tailed Test, Expressing, Labeling, RNAscope, In Situ Hybridization

Journal: Advanced Science

Article Title: Spatial Isoforms Reveal the Mechanisms of Metastasis

doi: 10.1002/advs.202402242

Figure Lengend Snippet: The CD74 isoform ratio revealed enrichment of CD8 + CXCL13 + T cells and C1QC + TAMs. A,H) Spatial distribution of the CD74‐ 201 isoform and CD74 ‐202 isoform in the After and AfterLN samples. The colors indicate the expression levels. B,I) Spatial distribution of the ratio of CD74 ‐202 isoform expression/ CD74 ‐201 isoform expression in the After and AfterLN samples. The color level indicates the ratio of CD74 ‐202 / CD74 ‐201 isoform expression. C,J) Spatial distribution of C1QC + TAMs, CD8 + CXCL13 + Tex cells in the After and AfterLN samples. D,K) C1QC + TAMs and CD8 + CXCL13 + Tex cells’ enrichment score distribution in the After and AfterLN samples. E,L) Pie charts of C1QC + TAMs and CD8 + CXCL13 + Tex cells enriched in low, medium, and high CD74 ‐202/ CD74 ‐201 ratio groups in the After and AfterLN samples. P values were calculated by a chi‐square test. In the After sample, n (low) = 57, n (medium) = 237, n (high) = 27. In the AfterLN sample, n (low) = 324, n (medium) = 969, n (high) = 15. F,M) Boxplots of enrichment scores in low, medium, and high CD74 ‐202 isoform expression/ CD74 ‐201 ratio groups in the After and AfterLN samples. P value was calculated by an unpaired two‐tailed Student's t‐test G,N) Boxplots of CD74 ‐202 / CD74 ‐201 ratio in enrichment spots (enrichment score > 0) and other spots in the After and AfterLN samples. P value was calculated by an unpaired two‐tailed Student's t‐test. O) Pie charts of C1QC + TAMs and CD8 + CXCL13 + Tex cells enriched in low, medium, and high CD74 ‐202/ CD74 ‐201 ratio groups in the validation samples. P value was calculated by a chi‐square test, n (low) = 82, n (medium) = 199, n (high) = 7. P) Boxplots of enrichment scores in low, medium, and high CD74 ‐202 isoform expression/ CD74 ‐201 ratio groups in the validation samples. P value was calculated by an unpaired two‐tailed Student's t‐test. Q) Boxplots of CD74 ‐202 / CD74 ‐201 ratio in enrichment spots (enrichment score > 0) and other spots in the validation samples. P value was calculated by an unpaired two‐tailed Student's t‐test. R) Detection of the CD74‐ 202 and CD74‐ 201 isoforms in the tumor and LN samples labeled by BaseScope hybridization technology. Left: HE; middle: 10X BaseScope; right: 20X BaseScope. Dark purple elements indicate counterstained nuclei. CD74‐ 201: pink, CD74‐ 202: turquoise. S) Boxplot of the ratio of CD74‐ 202 to CD74‐ 201 between tumors and LNs. P value was calculated by an unpaired two‐tailed Student's t‐test. T) Boxplot of the CD74‐ 202 count between tumors and LNs. P value was calculated by an unpaired two‐tailed Student's t‐test.

Article Snippet: Based on a previous SiT workflow, full‐length 10X Genomics Visium cDNA libraries were split for Illumina sequencing and ONT sequencing.

Techniques: Expressing, Two Tailed Test, Labeling, Hybridization