MERFISH
Multiplexed Error-Robust Fluorescence In Situ Hybridization (Spatial Transcriptomics)
MERFISH（空間トランスクリプトーム：多重エラー耐性蛍光in situハイブリダイゼーション）
1. Biological & Technical Mechanism
MERFISH uses combinatorial binary barcoding and sequential rounds of single-molecule FISH imaging with error-correcting codes to locate and count hundreds to thousands of distinct mRNA transcripts directly within intact tissue sections. Unlike dissociation-based scRNA-seq, MERFISH preserves the exact spatial coordinates, cortical laminar depth, and cell-to-cell neighborhood interactions (e.g., microglia-astrocyte-plaque niches).
MERFISHは、エラー訂正符号を用いた組み合わせバイナリバーコーディングと連続蛍光イメージングにより、脳組織切片内の数千種類のmRNA分子の絶対位置をナノメートル〜マイクロメートル精度で直接マッピングする空間トランスクリプトーム技術です。細胞をバラバラにするscRNA-seqでは失われてしまう「皮質層構造」「神経回路の空間トポロジー」「アミロイド斑や脱髄病変周囲のグリア細胞ニッチ（近傍細胞間相互作用）」を完全に保持して解析できます。
2. Open Science & Clinical Trial Significance
Whole-brain spatial cell atlases (Allen Brain Map BICCN) and Alzheimer's middle temporal gyrus spatial datasets use MERFISH to map how vulnerable neurons degenerate in proximity to pathological plaques and reactive glia.
Allen Brain Mapの全脳空間セルアトラスやSEA-AD（シアトル・アルツハイマー病脳細胞アトラス）において、病理プラークからの空間距離に応じたミクログリア・アストロサイトの応答変化や脆弱ニューロンの層特異的脱落を解明する中核データとして公開されています。
Related Neuroscience Terms & Standards
High-throughput transcriptomic profiling at individual cell or nucleus resolution, enabling identification of disease-associated microglia (DAM), astrocytes, and vulnerable neuronal subtypes.
Standard Python/HDF5 container for single-cell and spatial omics, storing expression matrices (X) alongside cell annotations (obs), gene metadata (var), and embeddings (obsm).
Major lipid carrier in the central nervous system; the APOE ε4 allele is the strongest genetic risk factor for late-onset Alzheimer's disease.
Open Datasets & Research Publications Related to MERFISH
Spatial Transcriptomics of Chronic Active Multiple Sclerosis Lesions Reveals Iron-Laden MIMS Microglia Driving OPC Differentiation Arrest
Subcellular MERFISH and single-nucleus RNA sequencing across human post-mortem white matter lesions map complement C1q signaling and interferon-responsive oligodendrocyte states at paramagnetic lesion rims.
Allen Brain Atlas: Human Brain ISH Autism Study
High-resolution ISH data detailing gene expression with a unique panel of lamina- and cell type- specific markers to phenotype cortical microstructure during the early years after autism onset.... Freely accessible open data product maintained by the Allen Institute for Brain Science.
BICCN Whole Human Brain Single-Cell Transcriptomic Cell Type Atlas
Cell atlas spanning >3 million single nuclei across 100+ human brain regions, mapping distinct vulnerable neuronal and glial sublineages.
Dandiset 000108: Single-Cell Patch-seq Electrophysiology and Morphometry of Human Neocortical Neurons
Over 1,200 human surgical neocortical pyramidal neurons and interneurons characterized simultaneously with patch-clamp electrophysiology, fluorescent morphological reconstruction, and single-cell RNA sequencing in NWB 2.0 format.
Allen Brain Atlas: Visual Coding Optical Physiology
Time series of 2P in vivo neuronal responses to visual stimuli across Cre lines, higher visual areas and cortical layers... Freely accessible open data product maintained by the Allen Institute for Brain Science.
Dandiset 002027: Behavioral Fever and Compound 3 20-30 C
BRAIN Initiative neurophysiology dataset deposited to DANDI Archive.
Disclaimer: This encyclopedia entry is intended for academic neuroscience research and data science reference only, and does not constitute medical advice.