10x visium spatial transcriptomics scrna binning (Spatial Transcriptomics Inc)

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Spatial Transcriptomics Inc 10x visium spatial transcriptomics scrna binning

Mast cells from IBD patients with HαT demonstrate increased MRGPRX2 expression. Spatial <t>transcriptomics</t> <t>(10x</t> Xenium) was performed on 8 descending colon biopsies from the University of Pennsylvania IBD biobank (4 HαT, 4 non-HαT; balanced UC/CD). (A) UMAP embedding showing major cellular populations. (B) Mast cells (MCs), defined as TPSAB1 + MS4A2 + KIT + , are more abundant in HαT samples. (C) Feature map of isolated MCs demonstrating increased MRGPRX2 transcript levels in HαT. (D) Digital droplet PCR (ddPCR) of representative tissues from the same cohort confirms upregulated MRGPRX2 expression in HαT vs. non-HαT. (E) Spatial transcriptomics images showing increased MRGPRX2 transcripts (red dots) in HαT-positive IBD tissue compared with non-HαT tissue. (F) ddPCR validation on matched samples (HαT: n = 4; non-HαT: n = 4) showing elevated MRGPRX2 mRNA. (G) Pseudobulk differential expression demonstrates significantly increased MRGPRX2 in HαT samples. For transcriptomic analyses, differential expression was calculated using DESeq2 with Benjamini–Hochberg FDR correction (FDR < 0.05). Effect sizes are shown as log₂ fold-change with 95% CIs. For ddPCR comparisons, Welch's t -test was used with Cohen's d reported.

10x Visium Spatial Transcriptomics Scrna Binning, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/spatial+transcriptomics+methods+10x+visium/10x+binning+scrna+spatial+transcriptomics+visium/pmc12868144-2-30-32
Average 86 stars, based on 1 article reviews

10x visium spatial transcriptomics scrna binning - by Bioz Stars, 2026-11

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Article Title: MRGPRX2-expressing mast cells are increased in the GI tract of individuals with active inflammatory bowel disease and hereditary α-tryptasemia

Journal: Frontiers in Allergy

doi: 10.3389/falgy.2025.1726096

Mast cells from IBD patients with HαT demonstrate increased MRGPRX2 expression. Spatial transcriptomics (10x Xenium) was performed on 8 descending colon biopsies from the University of Pennsylvania IBD biobank (4 HαT, 4 non-HαT; balanced UC/CD). (A) UMAP embedding showing major cellular populations. (B) Mast cells (MCs), defined as TPSAB1 + MS4A2 + KIT + , are more abundant in HαT samples. (C) Feature map of isolated MCs demonstrating increased MRGPRX2 transcript levels in HαT. (D) Digital droplet PCR (ddPCR) of representative tissues from the same cohort confirms upregulated MRGPRX2 expression in HαT vs. non-HαT. (E) Spatial transcriptomics images showing increased MRGPRX2 transcripts (red dots) in HαT-positive IBD tissue compared with non-HαT tissue. (F) ddPCR validation on matched samples (HαT: n = 4; non-HαT: n = 4) showing elevated MRGPRX2 mRNA. (G) Pseudobulk differential expression demonstrates significantly increased MRGPRX2 in HαT samples. For transcriptomic analyses, differential expression was calculated using DESeq2 with Benjamini–Hochberg FDR correction (FDR < 0.05). Effect sizes are shown as log₂ fold-change with 95% CIs. For ddPCR comparisons, Welch's t -test was used with Cohen's d reported.

Figure Legend Snippet: Mast cells from IBD patients with HαT demonstrate increased MRGPRX2 expression. Spatial transcriptomics (10x Xenium) was performed on 8 descending colon biopsies from the University of Pennsylvania IBD biobank (4 HαT, 4 non-HαT; balanced UC/CD). (A) UMAP embedding showing major cellular populations. (B) Mast cells (MCs), defined as TPSAB1 + MS4A2 + KIT + , are more abundant in HαT samples. (C) Feature map of isolated MCs demonstrating increased MRGPRX2 transcript levels in HαT. (D) Digital droplet PCR (ddPCR) of representative tissues from the same cohort confirms upregulated MRGPRX2 expression in HαT vs. non-HαT. (E) Spatial transcriptomics images showing increased MRGPRX2 transcripts (red dots) in HαT-positive IBD tissue compared with non-HαT tissue. (F) ddPCR validation on matched samples (HαT: n = 4; non-HαT: n = 4) showing elevated MRGPRX2 mRNA. (G) Pseudobulk differential expression demonstrates significantly increased MRGPRX2 in HαT samples. For transcriptomic analyses, differential expression was calculated using DESeq2 with Benjamini–Hochberg FDR correction (FDR < 0.05). Effect sizes are shown as log₂ fold-change with 95% CIs. For ddPCR comparisons, Welch's t -test was used with Cohen's d reported.

Techniques Used: Expressing, Isolation, Biomarker Discovery, Quantitative Proteomics

Individuals with IBD and HαT exhibit increased SIGLEC8 expression in colon tissue. Spatial transcriptomics and pseudobulk analysis were performed on 8 representative descending colon samples (4 HαT, 4 non-HαT; balanced UC/CD). (A) Pseudobulk counts aggregated by sample show higher SIGLEC8 expression in the HαT group (Wilcoxon test; Cohen's d and 95% CI reported). (B) Volcano plot of DESeq2 pseudobulk differential expression analysis contrasting non-HαT (blue) and HαT (red) samples. Genes surpassing FDR < 0.05 (Benjamini–Hochberg correction) are highlighted. SIGLEC8 is prominently upregulated in HαT, consistent with findings from CyTOF and ddPCR validation.

Figure Legend Snippet: Individuals with IBD and HαT exhibit increased SIGLEC8 expression in colon tissue. Spatial transcriptomics and pseudobulk analysis were performed on 8 representative descending colon samples (4 HαT, 4 non-HαT; balanced UC/CD). (A) Pseudobulk counts aggregated by sample show higher SIGLEC8 expression in the HαT group (Wilcoxon test; Cohen's d and 95% CI reported). (B) Volcano plot of DESeq2 pseudobulk differential expression analysis contrasting non-HαT (blue) and HαT (red) samples. Genes surpassing FDR < 0.05 (Benjamini–Hochberg correction) are highlighted. SIGLEC8 is prominently upregulated in HαT, consistent with findings from CyTOF and ddPCR validation.

Techniques Used: Expressing, Quantitative Proteomics, Biomarker Discovery

Spatial Transcriptomics:

Article Title: MRGPRX2-expressing mast cells are increased in the GI tract of individuals with active inflammatory bowel disease and hereditary α-tryptasemia
Article Snippet: .. Spatial transcriptomics cohort , 8 , 4 , 4 , Severe IBD: UC ( n = 4), CD ( n = 4)—balanced across HαT and non-HαT , Descending colon , 10x Visium Spatial Transcriptomics + scRNA-binning , Selected from genotyped cohort; used to evaluate MC abundance and MRGPRX2 expression patterns.. .. CyTOF cohort (UMMC, separate from biobank) , 17 , 5 , 12 , Symptomatic, non-IBD participants with histologically normal small intestine , Small intestine , Mass cytometry (CyTOF) , Independent functional cohort used to assess MC phenotypes associated with HαT. All samples H&E-normal..

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