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permeabilization buffer  (Complete Genomics Inc)


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    Structured Review

    Complete Genomics Inc permeabilization buffer
    Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) <t>Permeabilization,</t> in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions
    Permeabilization Buffer, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 99/100, based on 495 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/permeabilization+buffer+set/Stereo-seq+Transcriptomics+Set+for+FFPE/pmc12709731-202-13-17
    Average 99 stars, based on 495 article reviews
    permeabilization buffer - by Bioz Stars, 2026-11
    99/100 stars

    Images

    1) Product Images from "ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq"

    Article Title: ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq

    Journal: Genome Biology

    doi: 10.1186/s13059-025-03900-3

    Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) Permeabilization, in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions
    Figure Legend Snippet: Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) Permeabilization, in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions

    Techniques Used: Blocking Assay, Incubation, Imaging, Staining, In Situ, cDNA Synthesis, Amplification, Sequencing, Gene Expression, Biomarker Discovery

    Related Articles

    Spatial Transcriptomics:

    Article Title: A pan cancer multi omics analysis of OLR1 reveals its association with tumor immunity metabolic pathways and clinical prognosis
    Article Snippet: .. Spatial transcriptomics datasets were obtained from the STOmics database (https://db.cngb.org/stomics/) and the GEO database (https://www.ncbi.nlm.nih.gov/geo/), including STDS0000027, STDS0000033, STDS0000046, GSM5924031, and GSM6505133. ..

    Article Title: Spi1-Soat1 Transcriptional axis drives microglial lipid droplet accumulation and secondary brain injury after intracerebral hemorrhage
    Article Snippet: .. Cholesterol metabolic pathway activation and microglia-specific upregulation of Soat1 are tightly associated with lipid droplet accumulation after ICH To define the core metabolic pathways and key regulators driving microglial LD accumulation after ICH, we analyzed the day 7 perihematomal tissue subset of a spatial transcriptomics dataset (STOmics DB, ID:STT0000047), with a focus on lipid metabolic cascades underlying LD biogenesis (Fig. 3A). ..

    Analysis:

    Article Title: Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions.
    Article Snippet: .. Indeed, using Stereo-seq (STOmics) spatial transcriptomic analysis, which profiles host and microbial RNA, we found that Yersinia transcripts were localized to the basal region of the PG and did not extend to the enterocytes overlaying the PG (Supplementary Fig. 10g). ..

    Sequencing:

    Article Title: Multi-omics integration and machine learning identify an ACKR1 + endothelial cell-based lactate-immune signature associated with carotid plaque vulnerability and progression.
    Article Snippet: .. The internal singlecell and spatial transcriptomes were deposited with our previous study (Lai et al., Nat Cardiovasc Res, 2025) in the Genome Sequence Archive for Human at the National Genomics Data Center under accession HRA006030 (https://ngdc.cncb.ac.cn/gsa-human), with backups in the China National GeneBank: spatial transcriptomes in the STOmics Database (STT0000052, https://db.cngb.org/stomics/) and single-cell data in the China National Sequence Archive (CNP0004894, https:// db.cngb.org/cnsa/). ..

    Single Cell:

    Article Title: Multi-omics integration and machine learning identify an ACKR1 + endothelial cell-based lactate-immune signature associated with carotid plaque vulnerability and progression.
    Article Snippet: .. The internal singlecell and spatial transcriptomes were deposited with our previous study (Lai et al., Nat Cardiovasc Res, 2025) in the Genome Sequence Archive for Human at the National Genomics Data Center under accession HRA006030 (https://ngdc.cncb.ac.cn/gsa-human), with backups in the China National GeneBank: spatial transcriptomes in the STOmics Database (STT0000052, https://db.cngb.org/stomics/) and single-cell data in the China National Sequence Archive (CNP0004894, https:// db.cngb.org/cnsa/). ..

    Activation Assay:

    Article Title: Spi1-Soat1 Transcriptional axis drives microglial lipid droplet accumulation and secondary brain injury after intracerebral hemorrhage
    Article Snippet: .. Cholesterol metabolic pathway activation and microglia-specific upregulation of Soat1 are tightly associated with lipid droplet accumulation after ICH To define the core metabolic pathways and key regulators driving microglial LD accumulation after ICH, we analyzed the day 7 perihematomal tissue subset of a spatial transcriptomics dataset (STOmics DB, ID:STT0000047), with a focus on lipid metabolic cascades underlying LD biogenesis (Fig. 3A). ..

    Tissue:

    Article Title: Spi1-Soat1 Transcriptional axis drives microglial lipid droplet accumulation and secondary brain injury after intracerebral hemorrhage
    Article Snippet: .. Cholesterol metabolic pathway activation and microglia-specific upregulation of Soat1 are tightly associated with lipid droplet accumulation after ICH To define the core metabolic pathways and key regulators driving microglial LD accumulation after ICH, we analyzed the day 7 perihematomal tissue subset of a spatial transcriptomics dataset (STOmics DB, ID:STT0000047), with a focus on lipid metabolic cascades underlying LD biogenesis (Fig. 3A). ..

    H&E Stain:

    Article Title: Spatial transcriptomic profiling of porcine tissue microarray detecting subclinical circovirus infection
    Article Snippet: .. The first section was subjected to H&E staining for histological evaluation, while the second was mounted directly onto a Stereo-seq chip N Slide V1.0 (STOmics, Cat. No. 210CN114). .. Subsequent processing was performed according to the Stereo-seq Transcriptomics Set for FFPE User Manual (Document No. STUM-TT004) using the Stereo-seq Transcriptomics N Kit V1.0 (Cat. No. 211KN114) and Stereo-seq 16 Barcode Library Preparation Kit V1.0 (Cat. No. 111KL160).



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    Image Search Results


    Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) Permeabilization, in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions

    Journal: Genome Biology

    Article Title: ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq

    doi: 10.1186/s13059-025-03900-3

    Figure Lengend Snippet: Schematic workflow and bioinformatics analysis of the ST-FFPE-mIF whole solution. (1) FFPE tissue section was mounted on the chip and performed de-paraffinization (2) The section on the chip was subjected to antigen repair, blocking, antibody incubation, and mIF imaging. Before the 2nd round of mIF staining, antibodies from the 1 st round should be removal, and the epitope would be re-exposed. Then, the above mIF protocol should be repeated to generate another mIF image. Nine-colored mIF images were obtained accordingly (3) Permeabilization, in situ cDNA synthesis and collection were conducted after De-crosslink (4) cDNA amplification, library construction, and sequencing were performed according to manufacturer’s protocol to obtain Stereo-seq sequencing result (5) mIF images and spatially resolved gene expression was subjected to downstream spatial visualization and bioinformatics analyses including image processing and spatial multi-omics analysis to address scientific questions

    Article Snippet: Post-fixation, the Stereo-seq chip was air-dried, and the tissue section was incubated in permeabilization buffer (Cat# 211SN114, STOmics) supplemented with 3 μL of Tetramethylene sulfone (Cat#A610163, Sangon Biotech) for 25 min at 37 °C.

    Techniques: Blocking Assay, Incubation, Imaging, Staining, In Situ, cDNA Synthesis, Amplification, Sequencing, Gene Expression, Biomarker Discovery