Jul 22, 2024
Version 1
Human Neuronal Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics) V.1
- 1University of Texas Southwestern Medical Center
Protocol Citation: Satoshi Ishishita, Allan-Hermann Pool 2024. Human Neuronal Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics). protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l2q3p4l1y/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 16, 2024
Last Modified: July 22, 2024
Protocol Integer ID: 103467
Keywords: single-nucleus RNA-seq, neuronal nucleus suspension, human tissue, spinal cord, human neuronal nucleus isolation for single, human neuronal nucleus isolation, nucleus transcriptomic, nucleus transcriptomic profiling, protocol generating suspensions of neuronal nuclei, neuronal nuclei, human central nervous system tissue, nuclei, 10x genomic
Abstract
Protocol generating suspensions of neuronal nuclei (NeuN+) from human central nervous system tissue for single-nucleus transcriptomics.
Equipment and Reagents
Equipment
- Kimble Dounce Kontes tissue-grinder set (DWK 885300-0000)
- 50 ml Oakridge tubes (#0556214D)
- 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)
Reagents
- Roche Protector RNase Inhibitor (Millipore Sigma RNAINH-RO)
- BioLegend anti-NeuN antibody (#608452, for labeling neuronal nuclei)
- Alexa Fluor 647 Microscale Protein Labeling Kit (ThermoFisher #A30009)
- 1 mg/ml 7-AAD (nuclear labeling)
- 1M DTT (dithiothreitol, prepare fresh every couple of months and store at -20°C)
- Ultrapure RNA-se free/ DNA-se free water
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%)
1M Sucrose Cushion
Sucrose (1 M)
Tris-HCl (pH=7.4) (10 mM)
MgCl2 (3 mM)
NaCl (10 mM)
BSA (nuclease free) (0.50%)
Kollidon VA64 (1%)
Water (molecular biology grade) Fill to 50 mL
Do NOT Filter sterilize!
Resuspension Buffer
- Sucrose (320 mM)
- Tris-HCl (pH=7.4) (10 mM)
- MgCl2 (1 mM)
- NaCl (10 mM)
- BSA (RNAse free) (0.50%)
- 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)
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 in a spin-out rotor.
- 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 300 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. Stain nuclei for FACS sorting
- Add 3 μL of anti-NeuN-Alexa-647 Ab and 3 μL of 7-AAD to the nuclear suspension.
- Incubate the nuclear suspension at 4°C (not on ice!; keep dark as 7-AAD is light sensitive).
- Bring nuclear suspension volume to 3 mL with Nuclear Buffer.
- Spin nuclei down at 500g for 5 min at 4°C in a spin-out rotor.
- Remove most of supernatant and resuspend nuclei in 3 mL of Nuclear Buffer.
- Place suspension at 4°C for 5 min.
- Spin nuclei down at 500g for 5 min at 4°C.
- Remove supernatant and resuspend nuclei in 0.5 mL of Nuclear Buffer.
- Gently triturate with 150 micron glass Pasteur pipette to declump any nuclei.
- Add 1 mL of Nuclear Buffer and take to FACS sorting.
7. FACS sorting
- Sort at low pressures (4 or 5 PSI on BD sorters).
- Select for 7-AAD and Alexa 647 double-positive nuclei (note - perform compensation with single-stains of dyes before the actual profiling run to get clear separation between double-positive neuronal nuclei and single-positive non-neuronal nuclei).
Sorting gates for isolating neuronal nuclei (double positive for 7-AAD and Alexa-647)
8. Concentrate nuclei
- Spin FACS sorted nuclei down at 500g for 5 min at 4°C in a spin-out rotor and gently resuspend in desired buffer for 10x profiling (e.g. Resuspension Buffer above). Note 1 - post-FACS centrifugation is ok with human neuronal nuclei but not recommended with post-FACS mouse nuclei.
- During optimization stage, visualize nuclei with a 40x objective in brightfield and make sure resulting nuclei have predominantly (~85%+) round intact nuclear membranes.
- Optional: gently pipette the suspension with 150 micron fire polished Pasteur pipette to get rid of any remaining nuclear clumps.
- Proceed to 10x Genomics or other profiling.