Feb 01, 2023
Version 2
Nuclei isolation from frozen human brain samples for snRNA-seq V.2
- 1[Department of Neurological Surgery/ Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco]
Protocol Citation: Marcos Nascimento 2023. Nuclei isolation from frozen human brain samples for snRNA-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlkk9ydl5r/v2Version created by Marcos Nascimento
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: February 01, 2023
Last Modified: February 01, 2023
Protocol Integer ID: 76247
Funders Acknowledgement:
National Institute of Neurological Disorders and Stroke (NINDS)
Grant ID: R01NS028478
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Abstract
Protocol to isolate nuclei from snap-frozen human brain samples for sn-RNAseq
Materials
Sectioned or finely chopped frozen human tissue (10-30 mg).
- Lysis Buffer (LB, 4ml/sample)
- Wash and Resuspension Buffer (WRB, 7ml/sample)
- Sucrose Buffer (11ml/sample)
2000U of RNAse inhibitor/sample
Preparation
Preparation
10m
Check if the Rotor SW32Ti rotor is at 4°C
Clean your work area (bench and pipettes) with RNAse Zap.
1m
Add RNAse inhibitor (Sigma cat.# 3335402001) to lysis buffer (LB) and wash and resuspension buffer (WRB) to a final concentration of 0.2U/ul.
Put LB and sucrose solutions on ice; also label the glass dounce homogenizer (Thomas Scientific; Catalog # 3431D76; size A) and the centrifuge tubes (Beckman Coulter cat.# 355631) and put them on ice.
Nuclei Isolation
Nuclei Isolation
4h
Cut the tip of a p1000 pipette tip. Use it to add 1ml of LB in the sample eppendorf, pipette-mixing the LB-sample mix thoroughly.
Transfer the LB-sample mix to a labelled glass dounce homogenizer . Add 2ml of LB, bringing the total volume in the douncer to 3mL.On ice
You can add 1ml of LB to the sample eppendorf to collect any remaining tissue.
Dounce tissue on ice with 10-15 strokes or until no chunks of tissue are visible.On ice
Transfer homogenized tissue in LB into a labeled thick wall ultracentrifuge tube on ice (Beckman Coulter; 355631).On ice
Carefully pipette 9 mL of Sucrose solution to the bottom of the tube containing LB.
Be careful not to introduce bubbles: Aspirate 10ml with a serological pipette and dispense 9ml.
You should see two clearly separated phases: sucrose on the bottom and a cloudy homogenate on top.On ice
When you are done with all samples weigh them and bring to the same weight by adding LB.
Load the samples to SW32Ti rotor (needs to be swing bucket). If using less than 6 samples still balance with empty buckets.107163 rcf, 4°C, 02:30:00 , 24400 RPM on SW32Ti Rotor
2h 30m
After the spin, transfer samples on ice and carefully remove the supernatant using a P200 tip cut at an angle and vacuum. Make sure not to touch the bottom (stick to the wall and tilt the tube), but remove all the liquid. Carefully pipette 200uL of WRB on the bottom. Wait 20 min on ice.
20m
Meanwhile, transfer materials to the tissue culture room. Prepare eppendorf tubes with 10ul of DAPI for each sample.
Add 800ul of WRB (for a total of 1ml of WRB)and resuspend cells.On ice
Pipette mix thoroughly the nuclei suspension for 2 minutes using a P200
Filter twice using Miltenyi Pre-separation filters (30um). (130-041-407)
Add 10ul of each filtered sample to 10ul of DAPI. Count nuclei in each sample using a hemocytometer.
You should have at least 30,000 nuclei/sample
Expected result
1mg of human cortex typically yields ~104 nuclei
Centrifuge nuclei using a swing bucket rotor 500 rcf, 4°C, 00:10:00
10m
Resuspend nuclei at 1,000 nuclei/ul.
Pipette mix thoroughly the nuclei suspension for 2 minutes using a P200. Confirm the cell concentration in the hemocytometer. If clumps of nuclei are still observed, pipette mix for one more minute.
Load 16,500 nuclei/10x well to aim for a 10k nuclei recovery