May 25, 2026

JAX-Sen: Placenta collection, processing, and shipment protocol for spatial transcriptomics

DOI
https://dx.doi.org/10.17504/protocols.io.dm6gp74dpgzp/v1
  • Alicia Warren1,
  • Vicki Ingalls1,
  • Susan Sheehan1
  • 1The Jackson Laboratory, Bar Harbor, ME, USA
  • Cellular Senescence Network (SenNet) Method Development Community
Harshpreet Chandok
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DOI: https://dx.doi.org/10.17504/protocols.io.dm6gp74dpgzp/v1
Protocol Citation: Alicia Warren, Vicki Ingalls, Susan Sheehan 2026. JAX-Sen: Placenta collection, processing, and shipment protocol for spatial transcriptomics. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp74dpgzp/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 20, 2026
Last Modified: May 25, 2026
Protocol  Integer ID: 317613
Keywords: JAX-Sen, shipment protocol for spatial transcriptomic, shipment for spatial transcriptomics sample, spatial transcriptomics sample, spatial transcriptomic, placenta collection, purpose of this sop, shipment protocol, details on specimen collection, downstream procedure, specimen collection
Funders Acknowledgements:
National Institute on Aging (NIA) JAX-Sen Senescence Tissue Mapping Center
Grant ID: U54 AG079753
Abstract
The purpose of this SOP is to provide details on specimen collection, downstream procedures, and shipment for Spatial Transcriptomics samples.
Reagents and Materials
  • 10% NBF fixative
  • x PBS
  • Paraffin
  • Tweezers
  • Appropriate container for fixing
Quality Key Points
The tissue specimen should be always kept at 4 degrees Celsius and RNase-free. It is crucial to not store the tissue specimen at RT to avoid any cell death, and tissue and/or RNA degradation. After embedding, protect from FFPE blocks from light when possible.
Procedure
Collection:
Euthanize mice via cervical dislocation
a. Record start time
Open the female's abdomen carefully as to not damage any fetuses.
a. Euthanize fetuses via decapitation if they are older than E15
Remove the hind left limb from one animal per litter.
Keep in 1x PBS until ready to take a image for limb staging
Separate individual yolk sac containing fetus and embryos
Remove any un-needed tissue (such as yolk sac and uterine wall) from placenta. There will be a layer of tissue on the side on the placenta connecting to the umbilical cord that will need to be removed. Similar looking layer of tissue on the other side is part of the placenta and should not be removed.
Take appropriate measurements in mm
a. Diameter of the placenta
b. Crown to rump length (CRL) of embryo
10% NBF: place placenta is scintillation vial filled with FFPE (10% NBF). Ensure that the placenta is completely submerged
Transfer to a shaker at room temperature to fix for 24 hours.
Take piece of the embryo (ideally tail) for genotyping and another piece as back-up. Place on wet ice.
Clean tools and proceed to next animal
Record time when the last sample was collected
Fixation, embedding, and sectioning:
After 24-hours of fixation in 10% NBF, transfer the sample into a labelled cassette
Place cassettes into 1x PBS. Keep cold at 4C and RNase-free
Embed samples in paraffin and trim to expose tissue.
a.     Place the placenta (disc-shaped) upright, and not flat. See picture below.
When sectioning, take 5um-thick slices.



Shipping:
Seal samples and ship to Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 on cold packs to keep samples at 4C