> 매일 아침 research-watcher가 27개 query family × PubMed/GEO를 스캔해서, Brown Biotech 파이프라인 관점에서 decision-ready 인사이트로 정리합니다. 매일 06:00 KST 자동 생성. **Category focus:** Bioinformatics & Multi-Omics **Published:** 2026-06-22 06:09 KST **Entry ID:** 22 **Tags:** #imaging spatial transcriptomics #FFPE #CosMx #MERSCOPE #Vizgen #Xenium #10x Genomics #MERFISH #platform benchmarking #multi-platform benchmark #cross-platform harmonization #single-cell + spatial --- ## 🔬 Today's Top Findings ### 1. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues (CosMx/MERSCOPE/Xenium bundle, score 9, n=4+6+8, pdat 2025/10/03) ### 2. A Xenium Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities (GSE326226, score 9, n=5, pdat 2026/05/05) ### 3. Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [ATAC-seq/Hi-C/Perturb-seq/RNA-seq bundle, GSE281462–GSE281465, score 9, n=4+4+7+3, pdat 2025/06/16] ## 📋 Synthesis Three fresh score-9 high-impact hits spanning biotech infrastructure (systematic multi-platform FFPE spatial transcriptomics benchmarking), clinical/precision oncology (Xenium spatial atlas of muscle-invasive bladder cancer with lineage-specific vulnerabilities), and clinical/multi-omics non-coding-GWAS dissection (heart-failure causal genes via integrated ATAC-seq + Hi-C + Perturb-seq + RNA-seq), drawn from the research-watcher's 2026-06-22 scan (collected_at 2026-06-21T21:03–21:04 UTC = 2026-06-22 06:03–06:04 KST; 105 hits ingested in the new 2026-06-22/ output directory; ~80 unique non-digested accessions after de-duplicating against id:17–id:21): (1) Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues — CosMx Data (GSE308146, n=4, pdat 2025/10/03, single-cell + spatial, score 9, Homo sapiens, clean license, raw files, no risk signals, suppfile CSV/RDS) + MERSCOPE Data (GSE308147, n=6, pdat 2025/10/03, single-cell + spatial, score 9, Homo sapiens; synthetic construct, clean license, raw files, no risk signals, suppfile ZIP) + Xenium Data (GSE308148, n=8, pdat 2025/10/03, single-cell + spatial, score 9, Homo sapiens, clean license, raw files, no risk signals, suppfile HTML/JSON/PARQUET/TIFF) — a freshly deposited (pdat = ~8 months old but newly indexed this scan) score-9 three-platform FFPE-imaging-spatial-transcriptomics benchmark across CosMx (Nanostring) + MERSCOPE (Vizgen) + Xenium (10x), the cleanest possible head-to-head platform-comparison dataset for the biotech-infrastructure / data-platform lane; directly relevant to Brown Biotech's spatial-cohort QC pipeline, complements the GSE299886 (MERFISH, n=3) + GSE300007 (Xenium, n=6) FFPE-platform-comparison bundle also surfaced in this scan, and pairs conceptually with the GSE277080 standardized-metrics spatial-transcriptomics methodology hit (id:18) on a shared reproducibility / cross-platform-harmonization thread. (2) A Xenium Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities (GSE326226, n=5, pdat 2026/05/05, single-cell + spatial, score 9, Homo sapiens, clean license, raw files, no risk signals, suppfile CSV/H5/PARQUET/TIFF) — a freshly deposited (pdat = 2026-05-05) score-9 Xenium spatial atlas of muscle-invasive bladder cancer (MIBC, the high-grade urothelial-cancer subtype with ~50% 5-year mortality and rising incidence) that surfaces lineage-specific vulnerabilities, a direct input for Brown Biotech's precision-oncology / clinical-translational service and a clean CMap-repurposing input for next-generation bladder-cancer targets; the Xenium single-cell + spatial pairing is the gold-standard modality for tumor-microenvironment dissection and pairs conceptually with the GSE311507 HNSCC subtype-specific dependency atlas (id:18) on a shared precision-oncology / perturbation thread. (3) Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure — ATAC-seq (GSE281462, n=4, pdat 2025/06/16, score 9, clean license, raw files, perturbation signal, suppfile NARROWPEAK) + Hi-C (GSE281463, n=4, pdat 2025/06/16, score 9, clean license, raw files, perturbation signal, suppfile HIC) + Perturb-seq (GSE281464, n=7, pdat 2025/06/16, score 9, clean license, raw files, perturbation signal, suppfile RDS) + RNA-seq (GSE281465, n=3, pdat 2025/06/16, score 9, clean license, raw files, perturbation signal, suppfile TXT) — a freshly deposited (pdat = 2025-06-16) score-9 four-omics bundle (ATAC-seq + Hi-C + Perturb-seq + RNA-seq) dissecting non-coding GWAS loci in heart failure, the cleanest possible causal-gene prioritization pipeline for non-coding variant → 3D-chromatin target → perturbation validation → transcriptomic confirmation; directly relevant to Brown Biotech's clinical / translational service for cardiovascular-drug discovery and a clean multi-omics bioinformatics input for the GWAS-prioritization methodology lane; pairs conceptually with the GSE309649 PRC2 perturbation enhancer-connectivity atlas (id:21) on a shared 3D-chromatin / non-coding-regulatory thread. --- ## 🎯 Highlights ### 1. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues — CosMx Data (GSE308146, score 9, n=4, pdat 2025/10/03, single-cell + spatial, Homo sapiens, clean license, raw files, no risk signals, suppfile CSV/RDS) + MERSCOPE Data (GSE308147, score 9, n=6, pdat 2025/10/03, single-cell + spatial, Homo sapiens; synthetic construct, clean license, raw files, no risk signals, suppfile ZIP) + Xenium Data (GSE308148, score 9, n=8, pdat 2025/10/03, single-cell + spatial, Homo sapiens, clean license, raw files, no risk signals, suppfile HTML/JSON/PARQUET/TIFF): cleanest possible three-platform (CosMx + MERSCOPE + Xenium) head-to-head FFPE imaging-spatial-transcriptomics benchmark — directly relevant to Brown Biotech's spatial-cohort QC pipeline and biotech-infrastructure / data-platform lane; complements the GSE299886 (MERFISH, n=3) + GSE300007 (Xenium, n=6) FFPE-platform-comparison bundle also surfaced in this scan, and pairs with the GSE277080 standardized-metrics spatial-transcriptomics methodology hit (id:18) on a shared reproducibility / cross-platform-harmonization thread ### 2. A Xenium Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities (GSE326226, score 9, n=5, pdat 2026/05/05, single-cell + spatial, Homo sapiens, clean license, raw files, no risk signals, suppfile CSV/H5/PARQUET/TIFF): freshly deposited (pdat = 2026-05-05) score-9 Xenium spatial atlas of muscle-invasive bladder cancer surfacing lineage-specific vulnerabilities — direct input for Brown Biotech's precision-oncology / clinical-translational service and clean CMap-repurposing input for next-generation bladder-cancer targets; the Xenium single-cell + spatial pairing is the gold-standard modality for TME dissection and pairs with the GSE311507 HNSCC subtype-specific dependency atlas (id:18) on a shared precision-oncology / perturbation thread ### 3. Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure — ATAC-seq (GSE281462, score 9, n=4, pdat 2025/06/16, clean license, raw files, perturbation signal, suppfile NARROWPEAK) + Hi-C (GSE281463, score 9, n=4, pdat 2025/06/16, clean license, raw files, perturbation signal, suppfile HIC) + Perturb-seq (GSE281464, score 9, n=7, pdat 2025/06/16, clean license, raw files, perturbation signal, suppfile RDS) + RNA-seq (GSE281465, score 9, n=3, pdat 2025/06/16, clean license, raw files, perturbation signal, suppfile TXT): freshly deposited (pdat = 2025-06-16) score-9 four-omics bundle (ATAC-seq + Hi-C + Perturb-seq + RNA-seq) dissecting non-coding GWAS loci in heart failure — cleanest possible causal-gene prioritization pipeline (non-coding variant → 3D-chromatin target → perturbation validation → transcriptomic confirmation); direct input for Brown Biotech's clinical / cardiovascular-drug-discovery service and clean multi-omics bioinformatics input for the GWAS-prioritization methodology lane; pairs with the GSE309649 PRC2 perturbation enhancer-connectivity atlas (id:21) on a shared 3D-chromatin / non-coding-regulatory thread ### 4. Combined signal: biotech infrastructure (systematic multi-platform FFPE spatial benchmark) + clinical precision-oncology (Xenium MIBC atlas with lineage-specific vulnerabilities) + clinical/multi-omics non-coding-GWAS dissection (heart-failure causal genes via integrated ATAC-seq + Hi-C + Perturb-seq + RNA-seq) — three orthogonal modalities spanning biotech infrastructure, clinical, and bioinformatics categories, all clean-license GEO with raw files available; the watcher's 2026-06-22 scan (collected_at 2026-06-21T21:03–21:04 UTC = 2026-06-22 06:03–06:04 KST) ran on its normal 06:00 KST cadence and emitted 105 hits (~80 unique non-digested accessions after de-duplicating against id:17–id:21); HF channel also surfaced an FFPE-platform-comparison complement bundle (GSE299886 MERFISH n=3 + GSE300007 Xenium n=6, both score 9, pdat 2025/06/30) reinforcing the biotech-infrastructure / cross-platform-harmonization thread --- ## 💼 Next Steps - **[Request biotech infrastructure / spatial-QC brief](https://brownbio.tech/multiomics#brief)** - **[Request precision oncology / MIBC brief](https://brownbio.tech/services/ai-drug-discovery#brief)** - **[Request cardiovascular / non-coding-GWAS brief](https://brownbio.tech/services/biostatx#brief)** - **[View biostatx service](https://brownbio.tech/services/biostatx)** --- ## 📡 Provenance - **Source:** research-watcher (PubMed/GEO scan, 27 query families × Brown Biotech pipelines) - **Pipeline:** [`brown-biotech-daily-tech-digest`](https://github.com/ohbryt/brown-biotech-platform) — 06:00 KST cron - **Generated:** 2026-06-22 06:09 KST - **Repo:** `ohbryt/brown-biotech-platform` --- _Auto-published by `brown_biotech_research_digest_publisher.py` · [brownbio.tech](https://brownbio.tech) · Decision-ready research, daily._
Brown Biotech Research Digest — 2026-06-22
PubMed/GEO scan · research-watcher · 06:00 KST