Jul 30, 2024
Human Fixed Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics)
- Satoshi Ishishita1,
- Katherin Gabriel2,
- Seph Palomino1,
- Allan-Hermann Pool1
- 1University of Texas Southwestern Medical Center;
- 2University of Texas at Dallas
Protocol Citation: Satoshi Ishishita, Katherin Gabriel, Seph Palomino, Allan-Hermann Pool 2024. Human Fixed Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics). protocols.io https://dx.doi.org/10.17504/protocols.io.261ge5xqyg47/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: July 19, 2024
Last Modified: July 30, 2024
Protocol Integer ID: 103678
Keywords: single-nucleus RNA-seq, neuronal nucleus suspension, human tissue, spinal cord, human fixed nucleus isolation for single, nucleus transcriptomic, human fixed nucleus isolation, nucleus transcriptomic profiling, fixed human nuclei, human nuclei, 10x genomic, nuclei
Funders Acknowledgements:
Allan-Hermann Pool
Grant ID: UTSW Endowed Scholars Program
Abstract
Protocol for generating suspensions of fixed human nuclei for single-nucleus transcriptomics.
Equipment and Reagents
Equipment
- Kimble Dounce Kontes tissue-grinder set (DWK 885300-0000)
- 50 ml Oakridge tubes (#0556214D) // can replace with 50 mL Falcon Tubes
- 15 mL Falcon tubes (Fisher #352097)
- 50 mL Falcon tubes (Fisher #352070)
- 1.5mL LoBind Eppendorf Tubes
- 70-micron Corning Cell Strainer (#431751)
- Fire polished glass Pasteur pipettes (VWR #14672-380, polished in an open gas flame down to ~600 micron, 300 micron and 150 micron tip opening sizes) // alternatively can replace with regular pipetting
Reagents
- Roche Protector RNase Inhibitor (Millipore Sigma RNAINH-RO)
- 1M DTT (dithiothreitol, prepare fresh every couple of months and store at -20°C)
- Ultrapure RNA-se free/ DNA-se free water
Protocol Outline
Figure 1: Protocol outline with spinal cord as sample central nervous system tissue.
Solutions
NMDG-Hepes-ACSF
- NMDG (93 mM)
- KCl (2.5 mM)
- NaH2PO4 (1.2 mM)
- NaHCO3 (30 mM)
- HEPES (20 mM)
- Glucose (25 mM)
Bring pH to between 7.3 - 7.4 with 10N HCl and filter sterilize (good for 2 weeks at 4°C).
On the morning of tissue preparation add the following components (final concentration):
- Na-Ascorbate (5 mM)
- Thiourea (2 mM)
- Na-pyruvate (3 mM)
- MgSO4 (10 mM, prepare 2M stock that is good for 6-months at 4°C)
- CaCl2 (1 mM, prepare 2M stock that is good for 6-months at 4°C)
- Kynurenic acid Na-salt (1 mM)
Nuclear Buffer
- Sucrose (320 mM)
- Tris-HCl (pH=7.4) (10 mM)
- MgCl2 (3 mM)
- NaCl (10 mM)
- BSA (RNAse free) (0.50%)
- Kollidon VA64 (1 %)
- Ultrapure water, fill to 50 mL and 0.22 micron filter sterilize.
Morning of run:
- DTT (dithiothreitol, 1 mM)
- Roche Protector RNAse Inhibitor (0.1 U/uL)
Lysis Buffer
- Nuclear buffer
- Triton-X100 (0.1%)
1.8M Sucrose Cushion
Sucrose (1.8 M)
Tris-HCl (pH=7.4) (10 mM)
MgCl2 (3 mM)
NaCl (10 mM)
BSA (nuclease free) (0.50%)
Kollidon VA64 (1%)
Water (ultrapure) Fill to 50 mL
Do NOT Filter sterilize!
Protocol
1. Prepare solutions and equipment
- Prepare 50 mL of NMDG-HEPES-ACSF from pre-prepared stock by adding (Na-Ascorbate, Thiourea, Na-pyruvate, MgSO4, CaCl2 and Kynurenic acid Na-salt) and place on ice.
- Prepare Nuclear Buffer (add DTT and RNA-se inhibitor to preprepared solution) and place on ice.
- Prepare Lysis Buffer from Nuclear Buffer (add Triton-X100 to 0.1% of final volume) and pipette 0.75 mL into a Kontes tissue grinder.
- Prepare 1M sucrose cushion (add DTT and RNA-se inhibitor to preprepared solution) and place on ice.
- Pre-cool centrifuge to 4°C.
- Place 100 mm dissection dish into a 150 mm dish with dry ice.
2. Dissect out tissue
Place snap frozen brain tissue into 100 mm tissue culture dissection dish on a layer of dry ice in a larger 150 mm dish. Microdissect out desired tissue parts and cut into small 1.5 mm3 cubicles. Drop the latter into ice-cold NMDG-Hepes-ACSF in 1.5 mL collection tubes on ice.
3. Generate nuclear suspension
- Transfer tissue pieces into the Lysis Buffer in the Kontes tissue grinder.
- Apply 5 strokes with the loose pestle followed by 15 strokes with the tight pestle.
- Place a 70-micron cell strainer on a 50 mL Falcon tube and pre-wet with 500 μL of Nuclear Buffer.
- Add 250 μL of Nuclear Buffer to the tissue grinder.
- Mix nuclear suspension in tissue grinder twice with a 600-micron fire polished glass capillary and transfer through the cell strainer.
- Wash tissue grinder with 750 μL Nuclear Buffer and transfer again through the cell strainer.
- Wash cell strainer with final 750 μL Nuclear Buffer.
4. Spin nuclei down and resuspend in fresh Nuclear Buffer
- Spin nuclei down for 5 min at 500g at 4°C in a spin-out rotor.
- Remove supernatant and resuspend in fresh 3 mL Nuclear Buffer.
5. Purify nuclei with a sucrose cushion centrifugation
- Transfer 12 mL of Sucrose Cushion into a 50 mL Oakridge tube.
- Gently layer the nuclear suspension from the previous step on the sucrose cushion (avoid mixing of the layers).
- Centrifuge the tubes at 3200g at 4°C for 20 minutes.
- After centrifugation, pour out the supernatant by decanting in one smooth motion and drying out the neck of the Oakridge tube with a Kimwipe.
- Resuspend the nuclear pellet in 100 μL of ice-cold Nuclear Buffer and mix gently with a 300 micron fire polished Pasteur pipette.
- Transfer purified nuclear suspension to a new 15 mL tube on ice.
6. Evaluate debris
- Pipette 3 μL of the nuclear suspension on a glass slide and evaluate debris under a brightfield microscope
- If there is a lot of debris, add 2ml of Nuclear Buffer to the nuclear suspension and spin nuclei down at
500g for 5 min at 4C in a spin-out-rotor.
7. Fix nuclei and proceed with profiling
- Remove supernatant and resuspend nuclei in 1mL of Fixation buffer from the 10X fixation
of cells & nuclei for Chromium fixed RNA profiling (CG000478) and transfer resuspension to a microcentrifuge tube and incubate for 18hr at 4°C.
- Continue with 10x fixation protocol.