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stereo seq transcriptomics set user manual  (Complete Genomics Inc)


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    Complete Genomics Inc stereo seq transcriptomics set user manual
    Stereo Seq Transcriptomics Set User Manual, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 99/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/stomics+stereo+seq+chips/Stereo-seq+Transcriptomics+Set/pmc10460394-283-7-12
    Average 99 stars, based on 36 article reviews
    stereo seq transcriptomics set user manual - by Bioz Stars, 2026-11
    99/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: Single-cell Stereo-seq reveals regulatory mechanisms driving regeneration of injured proximal tubules during AKI.
    Article Snippet: .. Stereo-seq spatial transcriptomics data (BGI) were normalized using SCTransform in Seurat Spots with <1,000 total UMIs were filtered. ..

    Article Title: Somatic structural variants drive upper tract urothelial carcinoma muscle invasiveness via activation of TPX2 transcription.
    Article Snippet: .. 6 www.thelancet.com Vol 125 ▪, 2026 Spatial transcriptomics data generation and analysis Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer’s protocols. ..

    Article Title: A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics
    Article Snippet: .. These include sequencing-based: Visium (probe-based and polyA-based) , Visium CytAssist , and VisiumHD (all Visium platforms are products of 10X Genomics), Spatial Transcriptomics (Spatial Transcriptomics AB), Stereo-seq (BGI), BMK S1000 (BMKGENE), and Open-ST , and image-based platforms: Xenium (10X Genomics) and CosMx (Nanostring). ..

    Article Title: Somatic structural variants drive upper tract urothelial carcinoma muscle invasiveness via activation of TPX2 transcription
    Article Snippet: .. Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer's protocols. .. Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer's protocols.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Somatic structural variants drive upper tract urothelial carcinoma muscle invasiveness via activation of TPX2 transcription.
    Article Snippet: .. 6 www.thelancet.com Vol 125 ▪, 2026 Spatial transcriptomics data generation and analysis Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer’s protocols. ..

    Article Title: Somatic structural variants drive upper tract urothelial carcinoma muscle invasiveness via activation of TPX2 transcription
    Article Snippet: .. Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer's protocols. .. Formalin-fixed paraffin-embedded (FFPE) urothelial carcinoma tissue sections were profiled using the Stereo-seq spatial transcriptomics platform (MGI, China) according to the manufacturer's protocols.

    Article Title: Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
    Article Snippet: across Countries with Varying Stomach Cancer Incidence Kie Kyon Huang1, Takeshi Hagihara1, Benedict Shi Xiang Lian1, Zhi Xuan Ong1, Shen Kiat Lim1, Roxanne Hui Heng Chong2, Supriya Srivastava2, Jason Xing Kang3, May Yin Lee4, Angie Lay-Keng Tan1, Minghui Lee1, Shamaine Wei Ting Ho4, Siti Aishah Binte Abdul Ghani1, Clara Shi Ya Ng1, Ruanyi Liang1, Lin Liu2, Su Ting Tay1, Xuewen Ong1, Feng Zhu2, Hui Chen5, Zhen Li5, Tiing Leong Ang6, Takuji Gotoda7,8, Robert J. Huang9, Christopher J.L.. Khor1,10, Hyun-Soo Kim11, Louis Ho Shing Lau12,13, Yi-Chia Lee14, Ayaka Takasu7,8, Ming Teh15, Mann Yie Thian16, Wai Leong Tam4,17,18,19, Xin Lu20, Sunny H. Wong3, Jimmy B.Y.. So21, Hyunsoo Chung22, Jonathan Lee2,23,24,25, Khay Guan Yeoh2,25, and Patrick Tan1,4,26,27,28; for the Singapore Gastric Cancer Consortium D ow nloaded from http://aacrjournals.org/cancerdiscovery/article-pdf/doi/10.1158/2159-8290.C D -25-0778/3726001/cd-25-0778.pdf by guest on 17 January 2026 AACRJournals.orgOF2 | CANCER DISCOVERY XXX 2026 intRoduction Gastric cancer is the fifth most common malignancy worldwide and the fourth leading cause of cancer death, accounting for 769,000 deaths globally in 2020 (1).

    Sequencing:

    Article Title: A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics
    Article Snippet: .. These include sequencing-based: Visium (probe-based and polyA-based) , Visium CytAssist , and VisiumHD (all Visium platforms are products of 10X Genomics), Spatial Transcriptomics (Spatial Transcriptomics AB), Stereo-seq (BGI), BMK S1000 (BMKGENE), and Open-ST , and image-based platforms: Xenium (10X Genomics) and CosMx (Nanostring). ..

    Article Title: Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
    Article Snippet: across Countries with Varying Stomach Cancer Incidence Kie Kyon Huang1, Takeshi Hagihara1, Benedict Shi Xiang Lian1, Zhi Xuan Ong1, Shen Kiat Lim1, Roxanne Hui Heng Chong2, Supriya Srivastava2, Jason Xing Kang3, May Yin Lee4, Angie Lay-Keng Tan1, Minghui Lee1, Shamaine Wei Ting Ho4, Siti Aishah Binte Abdul Ghani1, Clara Shi Ya Ng1, Ruanyi Liang1, Lin Liu2, Su Ting Tay1, Xuewen Ong1, Feng Zhu2, Hui Chen5, Zhen Li5, Tiing Leong Ang6, Takuji Gotoda7,8, Robert J. Huang9, Christopher J.L.. Khor1,10, Hyun-Soo Kim11, Louis Ho Shing Lau12,13, Yi-Chia Lee14, Ayaka Takasu7,8, Ming Teh15, Mann Yie Thian16, Wai Leong Tam4,17,18,19, Xin Lu20, Sunny H. Wong3, Jimmy B.Y.. So21, Hyunsoo Chung22, Jonathan Lee2,23,24,25, Khay Guan Yeoh2,25, and Patrick Tan1,4,26,27,28; for the Singapore Gastric Cancer Consortium D ow nloaded from http://aacrjournals.org/cancerdiscovery/article-pdf/doi/10.1158/2159-8290.C D -25-0778/3726001/cd-25-0778.pdf by guest on 17 January 2026 AACRJournals.orgOF2 | CANCER DISCOVERY XXX 2026 intRoduction Gastric cancer is the fifth most common malignancy worldwide and the fourth leading cause of cancer death, accounting for 769,000 deaths globally in 2020 (1).

    other:

    Article Title: Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
    Article Snippet: After hybridization, slides were washed in Tris-NaCl buffer (20 mmol/L Tris-HCl, pH 7.2 and 40 mmol/L NaCl) and treated with the ReadyProbes Tissue Autofluorescence Quenching Kit (cat. # R37630 , Invitrogen).

    Article Title: Single-cell spatiotemporal dissection of the human maternal-fetal interface.
    Article Snippet: Dissected tissues were sequentially washed to remove residual blood cells in DMEM/H-21 medium, supplemented with 12.5% FBS (Hyclone), 1% L-glutamine (Atlanta Biologicals), 1% penicillin/streptomycin and 0.1% gentamicin and cold 1× PBS (Gibco, Thermofisher).

    Transcriptomics:

    Article Title: Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
    Article Snippet: across Countries with Varying Stomach Cancer Incidence Kie Kyon Huang1, Takeshi Hagihara1, Benedict Shi Xiang Lian1, Zhi Xuan Ong1, Shen Kiat Lim1, Roxanne Hui Heng Chong2, Supriya Srivastava2, Jason Xing Kang3, May Yin Lee4, Angie Lay-Keng Tan1, Minghui Lee1, Shamaine Wei Ting Ho4, Siti Aishah Binte Abdul Ghani1, Clara Shi Ya Ng1, Ruanyi Liang1, Lin Liu2, Su Ting Tay1, Xuewen Ong1, Feng Zhu2, Hui Chen5, Zhen Li5, Tiing Leong Ang6, Takuji Gotoda7,8, Robert J. Huang9, Christopher J.L.. Khor1,10, Hyun-Soo Kim11, Louis Ho Shing Lau12,13, Yi-Chia Lee14, Ayaka Takasu7,8, Ming Teh15, Mann Yie Thian16, Wai Leong Tam4,17,18,19, Xin Lu20, Sunny H. Wong3, Jimmy B.Y.. So21, Hyunsoo Chung22, Jonathan Lee2,23,24,25, Khay Guan Yeoh2,25, and Patrick Tan1,4,26,27,28; for the Singapore Gastric Cancer Consortium D ow nloaded from http://aacrjournals.org/cancerdiscovery/article-pdf/doi/10.1158/2159-8290.C D -25-0778/3726001/cd-25-0778.pdf by guest on 17 January 2026 AACRJournals.orgOF2 | CANCER DISCOVERY XXX 2026 intRoduction Gastric cancer is the fifth most common malignancy worldwide and the fourth leading cause of cancer death, accounting for 769,000 deaths globally in 2020 (1).

    In Situ:

    Article Title: Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
    Article Snippet: across Countries with Varying Stomach Cancer Incidence Kie Kyon Huang1, Takeshi Hagihara1, Benedict Shi Xiang Lian1, Zhi Xuan Ong1, Shen Kiat Lim1, Roxanne Hui Heng Chong2, Supriya Srivastava2, Jason Xing Kang3, May Yin Lee4, Angie Lay-Keng Tan1, Minghui Lee1, Shamaine Wei Ting Ho4, Siti Aishah Binte Abdul Ghani1, Clara Shi Ya Ng1, Ruanyi Liang1, Lin Liu2, Su Ting Tay1, Xuewen Ong1, Feng Zhu2, Hui Chen5, Zhen Li5, Tiing Leong Ang6, Takuji Gotoda7,8, Robert J. Huang9, Christopher J.L.. Khor1,10, Hyun-Soo Kim11, Louis Ho Shing Lau12,13, Yi-Chia Lee14, Ayaka Takasu7,8, Ming Teh15, Mann Yie Thian16, Wai Leong Tam4,17,18,19, Xin Lu20, Sunny H. Wong3, Jimmy B.Y.. So21, Hyunsoo Chung22, Jonathan Lee2,23,24,25, Khay Guan Yeoh2,25, and Patrick Tan1,4,26,27,28; for the Singapore Gastric Cancer Consortium D ow nloaded from http://aacrjournals.org/cancerdiscovery/article-pdf/doi/10.1158/2159-8290.C D -25-0778/3726001/cd-25-0778.pdf by guest on 17 January 2026 AACRJournals.orgOF2 | CANCER DISCOVERY XXX 2026 intRoduction Gastric cancer is the fifth most common malignancy worldwide and the fourth leading cause of cancer death, accounting for 769,000 deaths globally in 2020 (1).



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    a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

    Journal: bioRxiv

    Article Title: YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

    doi: 10.64898/2026.02.01.702698

    Figure Lengend Snippet: a , Schematic of the spatial transcriptomics (SRT) workflow. Cryosections were obtained from the indicated anatomical region (highlighted in schematic). Adjacent sister sections were stained with H&E, and sections for SRT were processed with BGI Stereo-seq technology. b , Spatial feature plot showing spot-level transcriptomic clustering of WT and PY-TB zebrafish samples. Clusters were identified by Seurat using principal component analysis and graph-based clustering of transcriptomic neighbourhoods. c , Integrated UMAP of all spatial transcriptomic spots coloured by Seurat-defined cluster identity. Cluster annotation was guided by regionally enriched marker genes and tissue interpretation using Zebrahub. d , UMAP and spatial feature plots highlighting hepatocyte-enriched spots defined by expression of hepatocyte marker, fabp10a , above the 75th percentile. Cells are grouped by sample: WT hepatocytes (blue) and PY-TB hepatocytes (red). e , Volcano plot of differentially expressed genes (DEGs) between PY-TB hepatocytes and WT hepatocytes, both defined by fabp10a expression in the spatial data. f , Spatial projection of cholangiocyte marker, anxa4, expression, visualised over spatial coordinates of the tissue section. g-i , Gene set enrichment analysis (GSEA) plots of selected pathways enriched in PY-TB hepatocytes versus WT, derived from DEGs identified in the SRT dataset. j , H&E and immunofluorescence staining of liver sections of WT and PY-TB fish at 21 dpf. Nuclei are marked with DAPI (cyan), hepatocytes with GFP (green), and cholangiocytes with ANXA4 (magenta). White arrow represents GFP+/ANXA4+ bi-lineage cells. Scale bar, 100 μm.

    Article Snippet: Frozen tissue blocks were stored at −80 °C and cryosectioned at 10 μm onto STOmics Stereo-seq chips (V1.1; BGI Research).

    Techniques: Spatial Transcriptomics, Staining, Marker, Expressing, Derivative Assay, Immunofluorescence