Protocol Citation: Emily Eisner 2024. Nuclei Preparation from Frozen Tissue for 10X Multiome using Dounce Homogenization, Iodixanol Gradient Centrifugation, and FANS (v1.2, Jan 2024). protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzx435gx1/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
This protocol describes isolation of nuclei from frozen tissue using dounce homogenization, iodixanol gradient centrifugation, and FANS. Nuclei are permeabilized, washed, and counted; single-nucleus suspensions of sufficient concentration and nuclei quality may then be processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338, Rev F) protocol from 10X Genomics.
Pre-chill a large, swing-bucket tabletop centrifuge to 4°C.
Retrieve a 1 mL dounce homogenizer with 2 pestles (“Loose” and “Tight”) for each sample. Place on ice and allow to chill.
Add 1 mL of NIM-DP-L buffer to each dounce homogenizer.
**If tissue mass is very small (< 50 mg), instead add 600 µL of NIM-DP-L.
Transfer each sample to a dounce homogenizer.
Using the loose pestle, gently homogenize the sample until most of the tissue has broken into small pieces (usually 5-10 strokes).
Switch to the tight pestle and homogenize until the solution is uniform with no obvious particles (usually 15-25 strokes). Be gentle and avoid introducing bubbles.
Transfer the full volume of homogenized sample to a 30 μm filter in a 1.5 mL Eppendorf Lobind tube.
Rinse each dounce with 1 mL of NIM-DP buffer and transfer the rinse to the filter.
Centrifuge for 10 mins at 1000 rcf, 4°C, and 3/3 acceleration/deceleration.
**If tissue mass is very small (< 50 mg),skip steps 10-11**
Discard the supernatant and resuspend the pellet in 1 mL of NIM-DP.
Centrifuge for 10 mins at 1000 rcf, 4°C, and 3/3 acceleration/deceleration.
Discard the supernatant and resuspend the pelleted nuclei in 2 mL of 20% iodixanol.
**If tissue mass is very small (< 50 mg), instead resuspend in 400 uL of 50% iodixanol (for a final iodixanol concentration of 20%).
Slowly pipette the suspension dropwise onto a 500 µL cushion of 25% iodixanol in a 5 mL Eppendorf Lobind tube. **Do not mix this solution oncetransferred.**
Centrifuge for 30 mins at 4000 rcf, 4C, and 3/1 acceleration/deceleration.
Discard the supernatant, leaving a small volume (< 20 µL) to avoid disturbing the pellet.
Resuspend the pellet in 500 µL of sort buffer and incubate on ice for 10 mins, protected from light.
Sort 120,000-130,000 nuclei into a 1.5 mL Eppendorf Lobind tube containing 90 μL of collection buffer using a Sony SH800 Cell Sorter.
Centrifuge the sorted nuclei for 5 mins at 500 rcf, 4°C, and 3/3 acceleration/deceleration.
Discard the supernatant.
Resuspend the pellet in 100 μL of NPB. Incubate on ice for 1 minute.
Add 900 μL of wash buffer.
Centrifuge for 5 mins at 500 rcf, 4°C, and 3/3 acceleration/deceleration.
Carefully remove the supernatant, leaving 10-15 μL to avoid disturbing the pellet.
Gently resuspend in 12 μL of 1X Nuclei Buffer (prepared from 10X Genomics Multiome protocol).
Stain an aliquot of nuclei with 0.4% Trypan Blue. Load 10 μL into one chamber of a hemocytometer.
Count nuclei in four quadrants. Average the count and determine the nuclei concentration (nuclei/μL).
Capture images from the microscope field at 10X and 20X magnification. Assess nuclei quality.
Follow the 10X Genomics protocol “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression” (CG000338, Rev F) for the remainder of the experiment. Input 18,000 nuclei for each tagmentation reaction for a targeted recovery of ~10,000 nuclei.