Adult human lung cell dissociation (on ice)
Andrew Potter
Abstract
This protocol was used to generate a single cell suspension from transbronchial biopsies from human lung. The procedure is carried out on ice, reducing artifact gene expression changes. Cell yield / mg is >5000 cells/mg with 80-90% viability (trypan blue dye exclusion). 10X scRNA-seq data is high quality (3'v3.1 and 5' v1.1) with >74% of cells retained after initial QC filtering (<20% mitochondrial gene reads, >500 genes/cell and >800 RNA molecules/cell). Expression of IER genes FOS and JUN is low in integrated, QC filtered dataset (normalized avg gene expression <3). Cell populations identified in single cell data include:
-CD8+ T
-CD4+ T
-γδ+ T
-NK
-Mast
-mDC/pDC
-B / plasma
-Monocyte
-Macrophage
-AT1 / AT2
-Ciliated
-Goblet
-Pericyte
-SMC
-Endothelial (several populations)
-Fibroblast
-Basal
If you have any questions regarding the single cell analysis thus far, please contact Andrew Potter.
Before start
Just prior to starting
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Prepare enzyme mixes and leave on ice.
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Cool centrifuges to 4 °C. Enzyme Mixtures
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Collagenase, elastase and dispase enzyme stock mixes are prepared ahead of time by diluting in PBS, and frozen in 500 µL aliquots at -80 C.
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StemCell DNAse (#07469) has an activity of 2,000 U / mg. We weigh out the powder, dilute in PBS to 125 U per 5 µL, make single-use aliquots to 20-40 µL (depending on samples run at a time), and freeze at -80 C. For 10 mg of weighed powder (20,000 U of activity total), we add 800 µL PBS, mix gently, make aliquots and freeze.
10% FBS/PBS is made up with heat-inactivated, sterile filtered FBS (MLS) with Ca/Mg-free PBS.
Equipment
- Centrifuge for 1.5 mL, 15 mL conicals (preferably swinging bucket)
- Pipettes and pipet tips.
- 15 mL conicals (MLS)
- 1.5 mL tubes (MLS)
- 30 µM filters (Miltenyi, 130-098-458)
- Petri dish (MLS)
- Razor blades (MLS)
- Ice bucket w/ice
- Hemocytometer - InCyto Neubauer Improved (DHC-N01-5)
Steps
Isolate and mince tissue
Transport tissue in ice-cold PBS.
Transfer 13 mg tissue to petri dish on ice with 100 µL enzyme mix; using razor blade mince thoroughly for 2 min until large chunks are broken up finely.
0h 2m 0s
Layer 1
Add 13 mg minced tissue to 900 µL enzyme mix (1 mL total) in 1.5 mL tube using cut p200 pipet to transfer.
13
Incubate on ice. Triturate 10x using 1 mL pipet set to 700 µL every 3 min (w/tip cut). Shake 3-5X to re-suspend every 2 min.
0h 3m 0s
0h 2m 0s
After 30 minutes of incubation let settle on ice 1 min.
0h 30m 0s
0h 1m 0s
Pipet and save 80% of the supernatant (consisting of released cells), leaving undigested tissue chunks on the bottom of the tube. Add released cells (supernatant) to sterile 30 µM filter on 15 mL conical. Rinse filter w/12 mL ice-cold 10% FBS/PBS. Tap filter to ensure passage of cells.
12mL
Remove filter from 15 mL conical. Spin the 15 mL conical with released cells 300 g for 5 min at 4 °C.
0h 5m 0s
4
Remove supernatant for the 15 mL conical with pelleted supernatant. Re-suspend the pellet in 14 mL ice-cold 10% FBS/PBS and leave on ice while performing next steps.
14
Layer 2
Add additional 1 mL enzyme mix to residual tissue chunks from Layer 1.
1
Continue incubating on ice for 40 additional minutes (1 hr. 10 min. total). Triturate 10x using 1 mL pipet set to 700 µL every 3 min (w/tip cut if necessary). Shake 3-5X to re-suspend every 2 min.
0h 40m 0s
0h 3m 0s
0h 2m 0s
After 1 hr. 10 min total incubation time triturate digest mix 10X and add total digest mix (including any chunks) to a new sterile 30 µM filter on 15 mL conical.
Rinse filter w/12 mL ice-cold 10% FBS/PBS.
12
Remove filter. Spin the 15 mL conicals from the first and second layer, 300 g for 5 min at 4 ºC.
0h 5m 0s
4°C
RBC Lysis
Remove supernatant for all tubes. Re-suspend combined volume in 5 mL RBC lysis buffer. Pipet 20x to mix. Incubate on ice 5 min.
5
0h 5m 0s
Add 9 mL ice-cold 10% FBS/PBS to 5 mL RBC lysis buffer. Triturate and apply to sterile 30 µM filter on 15 mL conical.
9
Separate flow-through to two 15 mL conicals. Bring volume for each to 14 mL with ice-cold 10% FBS/PBS.
14
Re-suspend and prepare for scSeq
Spin 300 g for 5 min at 4 °C. Remove supernatant.
0h 5m 0s
4°C
Re-suspend cells in 100 µL ice-cold 10% FBS/PBS. Analyze viability and cell yield using a hemocytometer with trypan blue.
100
Adjust cell concentration to 700-1200 cells / µL for 10x chromium.
