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  • 1.  FFPE spatial transcriptomics

    Posted 05-20-2024 11:38

    Hi everyone,

    I hope some one in the community can help one of my users. 

    She would like to use FFPE tissue in a 10x Genomics CytAssist experiment looking at both the transcriptome as well as surface proteins. The tissue is human pancreatic, normal and tumor. 

    They have checked the quality of the RNA  from quite a few archived samples and the RNA is in bad shape, not useable.

    They would like to FFPE fix some fresh samples but are unsure how best to do this.  I told them I would put it out to the ABRF community for recommendations.

    Does anyone have a protocol for FFPE fixing tissue, preferably human pancreatic tissue, that has resulted in a  successful 10x Genomics CytAssist experiment that they are willing to share?

    Thanks in advance,

    Kathy



    ------------------------------
    Kathleen Brundage
    Director, WVU Flow Cytometry & Single Cell Core Facility
    West Virginia University
    Morgantown WV
    ------------------------------


  • 2.  RE: FFPE spatial transcriptomics

    Posted 05-21-2024 12:02

    Hey Kathy,

    Something to think about, was this a surgical resection or an autopsy obtained tissue sample? With those pancreases loaded with enzymes, if they are not dropped into a fixative *right* away, they might be suboptimal right out of the gate. 

    Kathy



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    Kathy Cormier
    Histology Core Leader
    Koch Institute MIT
    Cambridge MA
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    Original Message


  • 3.  RE: FFPE spatial transcriptomics

    Posted 05-21-2024 12:26
    Hi Kathleen,
    Following is the recommendation from my Biorepository and Histopathology CoRE. This is a general and not specifically for pancreatic tissue though

    fix fresh tissue immediately in 10% neutral buffered formalin for ~16-24 hours maximum. Then the tissue should be immediately transferred to 70% ethanol until standard machine tissue processing.

    Please let me know if you want to discuss their experience further with you.

    Shekhar Patil, PhD
    Senior Director, Shared Research Resources and Core Administration
    Icahn School of Medicine at Mount Sinai
    Email: Shekhar.Patil@mssm.edu
    Phone: (332) 243-0768


    Original Message


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