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10x genomics merfish  (10X Genomics)

 
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    10X Genomics 10x genomics merfish
    10x Genomics Merfish, supplied by 10X Genomics, 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/10x+genomics+merfish/10x+genomics+merfish/pmc12834424-7-18-18
    Average 86 stars, based on 1 article reviews
    10x genomics merfish - by Bioz Stars, 2026-10
    86/100 stars

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    other:

    Article Title: Towards Precision Aging Biology: Single-Cell Multi-Omics and Advanced AI-Driven Strategies
    Article Snippet: Allen et al. [ ] , GSE207848 CELL x GENE repository ( https://cellxgene.cziscience.com/collections/31937775-0602-4e52-a799-b6acdd2bac2e ) , Spatial transcriptomics , 10X Genomics MERFISH , Mouse , Frontal cortex and striatum , Juvenile (1 month) Old (21 months).



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    10x genomics merfish  (10X Genomics)
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    platforms e g 10x genomics visium and merfish  (10X Genomics)
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    Overview on the <t>MERFISH</t> method. (A) Preparation of the cellular RNA library. Targeted RNA types are determined and encoded by a barcode each. The encoding probes and readout probes are designed and synthesized. After cell fixation and permeabilization encoding probes are added to the cells, so they hybridize to the cellular RNA. (B) Simplified scheme of the operating principle of MERFISH cycles. For the purpose of simplification, our cell contains four RNAs that have been hybridized to encoding probes. We use four different readout probes in four MERFISH cycles. In each cycle a different type of readout probe is added which hybridizes to the respective readout sequences on the encoding probes. After hybridization, imaging occurs and shows the RNAs that have bound to the respective readout probe. The fluorescence is then removed for the next cycle to start. (C) Decoding of the MERFISH images. The single images from each MERFISH cycle are analyzed to determine the spots in which targeted RNAs are located. A present or lacking fluorescent signal in the respective spot is transformed into the bits 1 or 0. Combining the bits from each MERFISH cycle, the binary code is obtained that indicates which RNA type is located in the respective spot. Created with BioRender.com.
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    Overview on the MERFISH method. (A) Preparation of the cellular RNA library. Targeted RNA types are determined and encoded by a barcode each. The encoding probes and readout probes are designed and synthesized. After cell fixation and permeabilization encoding probes are added to the cells, so they hybridize to the cellular RNA. (B) Simplified scheme of the operating principle of MERFISH cycles. For the purpose of simplification, our cell contains four RNAs that have been hybridized to encoding probes. We use four different readout probes in four MERFISH cycles. In each cycle a different type of readout probe is added which hybridizes to the respective readout sequences on the encoding probes. After hybridization, imaging occurs and shows the RNAs that have bound to the respective readout probe. The fluorescence is then removed for the next cycle to start. (C) Decoding of the MERFISH images. The single images from each MERFISH cycle are analyzed to determine the spots in which targeted RNAs are located. A present or lacking fluorescent signal in the respective spot is transformed into the bits 1 or 0. Combining the bits from each MERFISH cycle, the binary code is obtained that indicates which RNA type is located in the respective spot. Created with BioRender.com.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: Overview on the MERFISH method. (A) Preparation of the cellular RNA library. Targeted RNA types are determined and encoded by a barcode each. The encoding probes and readout probes are designed and synthesized. After cell fixation and permeabilization encoding probes are added to the cells, so they hybridize to the cellular RNA. (B) Simplified scheme of the operating principle of MERFISH cycles. For the purpose of simplification, our cell contains four RNAs that have been hybridized to encoding probes. We use four different readout probes in four MERFISH cycles. In each cycle a different type of readout probe is added which hybridizes to the respective readout sequences on the encoding probes. After hybridization, imaging occurs and shows the RNAs that have bound to the respective readout probe. The fluorescence is then removed for the next cycle to start. (C) Decoding of the MERFISH images. The single images from each MERFISH cycle are analyzed to determine the spots in which targeted RNAs are located. A present or lacking fluorescent signal in the respective spot is transformed into the bits 1 or 0. Combining the bits from each MERFISH cycle, the binary code is obtained that indicates which RNA type is located in the respective spot. Created with BioRender.com.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Synthesized, Hybridization, Imaging, Fluorescence, Transformation Assay

    NGS-based sequencing with region capture by the VISIUM platform. (A) A capture area consists of 5,000 small spots in which capture probes are fixed to the bottom of the wells. (B) Structure of the capture probes. (C) mRNAs are captured inside the spots by the capture probes. Reverse transcription is performed, and second strand synthesis provides cDNA that is then amplified by PCR. (D) Amplified oligonucleotides are prepared for Illumina sequencing by the attachment of various oligonucleotides (TruSeq Read two sequence, indices, P5 and P7). These can be processed by the Illumina sequencer to read out the spatial barcode and UMI for spatial mapping and the RNA coding sequences for RNA identification. This data enables reconstruction of the cellular RNA map. Created with BioRender.com.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: NGS-based sequencing with region capture by the VISIUM platform. (A) A capture area consists of 5,000 small spots in which capture probes are fixed to the bottom of the wells. (B) Structure of the capture probes. (C) mRNAs are captured inside the spots by the capture probes. Reverse transcription is performed, and second strand synthesis provides cDNA that is then amplified by PCR. (D) Amplified oligonucleotides are prepared for Illumina sequencing by the attachment of various oligonucleotides (TruSeq Read two sequence, indices, P5 and P7). These can be processed by the Illumina sequencer to read out the spatial barcode and UMI for spatial mapping and the RNA coding sequences for RNA identification. This data enables reconstruction of the cellular RNA map. Created with BioRender.com.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Sequencing, Reverse Transcription, Amplification

    Comparison of VISIUM, Slide-seqVs, stereo-seq and seq-scope.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: Comparison of VISIUM, Slide-seqVs, stereo-seq and seq-scope.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Comparison

    Selection of Studies applying spatial transcriptomics technology.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: Selection of Studies applying spatial transcriptomics technology.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Selection, Electron Microscopy

    Cell type and tissue compatibility of spatial transcriptomics methods with and without ExM technology.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: Cell type and tissue compatibility of spatial transcriptomics methods with and without ExM technology.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Cell Culture, Derivative Assay

    Comparison of ISS methods, ISH methods and NGS-based sequencing with region capture.

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet: Comparison of ISS methods, ISH methods and NGS-based sequencing with region capture.

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Comparison, Sequencing, RNA Detection, Microscopy, Amplification, Hybridization, Multiplexing, In Situ, Microarray, Cell Culture

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: Multiplexed spatial transcriptomics methods and the application of expansion microscopy

    doi: 10.3389/fcell.2024.1378875

    Figure Lengend Snippet:

    Article Snippet: However, it can be observed that the adoption of many new methodologies is constrained to their specific research settings they have been developed in, whereas those achieving wider outreach frequently leverage commercial platforms (e.g., 10x Genomics VISIUM and MERFISH).

    Techniques: Imaging, Microscopy, Sequencing, Formalin-fixed Paraffin-Embedded, Fluorescence, In Situ Hybridization, In Situ, RNA Sequencing Assay, Next-Generation Sequencing, Saline, Polymerase Chain Reaction, Amplification, Reverse Transcription, Real-time Polymerase Chain Reaction, Ligation