This protocol presents an accessible guide for collecting, storing, and thawing peripheral blood mononuclear cells suitable for downstream analyses and workflows like flow cytometry and RNA sequencing. Plasma and buffy coat collections are also demonstrated.
Peripheral blood mononuclear cells (PBMCs) are commonly used in biomedical research on the immune system and its response to disease and pathogens. This detailed protocol describes the equipment, supplies, and steps for isolating, cryopreserving, and thawing high-quality and highly viable PBMCs from whole blood cells suitable for downstream applications such as flow cytometry and RNA-sequencing. Protocols for processing plasma and buffy coat from the whole blood in parallel and concurrently with PBMCs are also described. This easy-to-follow step-by-step protocol, which utilizes density gradient centrifugation to isolate PBMCs, is accompanied by a checklist of supplies, equipment, and preparation steps. This protocol is suitable for individuals with any prior experience with laboratory techniques and can be implemented in clinical or research laboratories. High-quality cell viability and RNA sequencing resulted from PBMCs collected by operators with no prior laboratory experience using this protocol.
This protocol demonstrates an accessible method and workflow for the isolation of peripheral blood mononuclear cells (PBMCs) from whole blood. This protocol is especially targeted towards novice research technicians, students, and clinical lab staff with the objective of facilitating the collection and cryopreservation of PBMCs without assuming prior training in laboratory techniques.
This protocol utilizes centrifugation to separate the components of whole blood by density. Whole blood consists of four main components listed in order of decreasing density: red blood cells/erythrocytes (~45% of volume), white blood cells (<1% of volume), platelets (<1% of volume), and plasma (~55% of volume)1,2,3,4,5,6. White blood cells can be subdivided into two categories based on their nuclei characteristics: round or multi-nucleated6. PBMCs are defined as white blood cells with round nuclei and consist of the following cell types: lymphocytes (T cells, B cells, NK cells), dendritic cells, and monocytes6. Multi-nucleated white blood cells include granulocytes, which consist of the following cell types: neutrophils, basophils, and eosinophils6. Multi-nucleated white blood cells are denser than PBMCs6. The densities of each component of whole blood are detailed in Table 1.
In this protocol, whole blood is collected in density gradient centrifugation tubes. These tubes contain a pre-packed density gradient medium that has a density of 1.077 g/mL. Following centrifugation, denser cells, including multi-nucleated white blood cells and erythrocytes, are separated from PBMCs and platelets by the density gradient medium (Figure 1A)6,7. The PBMC and platelet fraction is then collected, washed, and centrifuged to remove platelets. The resulting purified PBMCs are collected and stored at -80 °C or in liquid nitrogen. Cryopreserved PBMCs may be viably thawed and directly used in downstream analyses or additionally processed to isolate specific component cell types.
This protocol has been optimized for high-quality RNA sequencing from highly viable PBMCs. In this article, PBMCs were isolated and cryopreserved from patients in an outpatient clinic. Subsequently, monocytes were isolated from PBMCs by FACS and analyzed via RNA-sequencing. However, the protocol can be widely adapted to other experimental needs such as cell culture, gene editing, ex-vivo functional studies, single-cell analyses, phenotyping by flow cytometry or cytometry by time of flight, isolation of DNA/RNA or proteins, slides for immunohistochemistry, amongst others8,9,10,11,12,13,14,15,16,17,18.
In addition to PBMC collection from density gradient centrifugation tubes, this protocol reviews how to collect plasma and buffy coat via centrifugation using an EDTA tube. After centrifugation, whole blood is separated into plasma, erythrocytes, and a thin interface layer termed buffy coat containing leukocytes (Figure 1B)6. The buffy coat is commonly used for DNA extraction and subsequent genomic analyses19,20. The plasma layer contains the cell-free components of whole blood and can be used for biomarker assays21,22.
The study protocol was approved by the UCSD and KUMC Human Protections Program and conforms to the Declaration of Helsinki. All individuals provided informed consent for participation and blood collection.
1. Processing and cryopreservation of PBMCs
2. Processing of plasma and buffy coat from EDTA tubes
3. Thawing PBMCs
4. Cell counting and viability
Following PBMC collection and cryopreservation, viability of thawed PBMCs, monocytes, and lymphocytes from 56 unique samples was assessed by flow cytometry using reagents listed in Table 4 following manufacturers' instructions (Figure 2A-F). A mean ± SD viability of PBMCs, monocytes, and lymphocytes of 94 ± 4.0%, 98 ± 1.1%, and 93 ± 5.6%, respectively, was achieved (Figure 2G). Viability measurement by Trypan Blue exclusion yielded a mean viability of 88 ± 7.5% and a cell count of 2.3 x 106 ± 1.9 x 106. Flow cytometry analysis also demonstrated that live monocytes comprised 17 ± 5.9% and lymphocytes made up of 53 ± 13.0% of total PBMCs.
Subsequently, monocytes were sorted from thawed PBMCs from 59 unique samples by flow cytometry and submitted for library preparation and RNA-sequencing as described elsewhere24. A mean ± SD total sequence count of 18.0 ± 16.3 million was achieved with a 93 ± 6.3% read alignment and 49.6 ± 1.4% GC content (Figure 3A-B). A mean ± SD uniquely mapped reads percentage of 88 ± 3.6% was found with a subset of 56 unique samples. These parameters demonstrate that highly viable PBMCs suitable for downstream applications, including high-quality RNA sequencing, can be obtained by operators with any level of laboratory training using this protocol.
Component | Density | Citation |
Plasma | 1.022 g/mL to 1.026 g/mL | 1 |
Platelets | <1.061 g/mL to >1.070 g/mL | 2 |
PBMCs | <1.077 g/mL | 6 |
Low density neutrophils* | <1.077 g/mL | 3 |
Granulocytes (neutrophils*, basophils, and eosinophils) | >1.077 g/mL | 6 |
Erythrocytes | 1.11 g/mL | 4 |
Table 1: Components of whole blood listed by order of decreasing density.
Reagant/Material | Amount (per 6 CPT tubes and 1 EDTA tube) | Tip | Caution Statements | ||||||
CPT Tubes | 6 | Label according to patient or sample ID. | |||||||
EDTA Tube | 1 | Label according to patient or sample ID. | |||||||
50 mL conical tube | 2 | In addition to patient or sample ID, label 1 tube for PBMCs and 1 for waste. | |||||||
Cryovials | 39 | Label 30 for PBMCs, 8 for EDTA plasma, and 1 for buffy coat. Not all cryovials may be used. | |||||||
Mr. Frosty | 2 | Fill up to the halfway mark with isopropanol and pre-chill overnight at -20°C. | Isopropanol is a flammable irritant. Keep away from sparks/flames. Avoid inhaling and handle with gloves and care. | ||||||
Flavopiridol | 100 µL of 1000X stock | To prepare 1000X flavopiridol stock, suspend 5 mg flavopiridol in 1.14 mL of DMSO for a concentration of 10 mM. Aliquot 200 µL into individual containers then freeze. To use, thaw individual aliquots and dilute 1:10 in DNase/RNase-free distilled water, and then use as a 1000X solution. | Flavopiridol is an irritant. Handle with gloves and care. | ||||||
Solution 1 | 50 mL | RPMI Medium. To make 50 mL of stock solution, use 50 mL of RPMI Medium. |
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Solution 2 | 15 mL | RPMI Medium + 12.5% Human Serum Albumin + 1 µM Flavopiridol. To make 50 mL of stock solution, use 25 mL RPMI medium + 25 mL Human Serum Albumin + 50 µL 1000X Flavopiridol. |
Flavopiridol is an irritant. Handle with gloves and care. | ||||||
Solution 3 | 15 mL | RPMI Medium + 11.25% Human Serum Albumin + 1 µM Flavopiridol + 10% DMSO. To make 50 mL of stock solution, use 22.5 mL RPMI medium + 22.5 mL HSA + 5 mL DMSO + 50 µL 1000X Flavopiridol. |
Flavopiridol is an irritant and DMSO is toxic and is readily absorbed through skin. Handle with gloves and care. |
Table 2: Checklist of reagents and materials to prepare and label for collecting and cryopreserving PBMCs.
Reagant/Material | Amount (per 1 mL aliquot of frozen PBMCs) | Tip | Caution Statements | |
Solution 4 | 10 mL | PBS + 2 mM EDTA To make 50 mLs of stock solution, use 5 mL 10X PBS + 200 µL 0.5M EDTA + 44.8 mL DNase/RNase-free distilled water |
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50 mL conical tube | 3 | In addition to patient or sample ID, label 1 tube for pre-strained PBMCs, 1 for post-strained PBMCs, and 1 for waste. Fill the tube labelled for pre-stained PBMCs with 9 mLs of solution 4 per mL of frozen PBMCs | ||
1.5 mL tube | 1 | For cell counting; label with patient or Sample ID | ||
0.4% Trypan Blue Solution | 20 µL | For cell counting; can be added to the 1.5 mL tube ahead of time the day before. | Trypan Blue is a carcinogen. Handle with gloves and care. |
Table 3: Checklist of reagents and materials to prepare and label for thawing and counting PBMCs.
Reagent/Material | Amount (per million cells) |
Live-Dead Stain | 5 μL |
Human Trustain FcX | 5 μL |
CD3 Antibody | 5 μL |
CD19 Antibody | 5 μL |
CD56 Antibody | 5 μL |
CD66b Antibody | 5 μL |
HLA-DR Antibody | 5 μL |
CD14 Antibody | 5 μL |
CD16 Antibody | 2.5 μL |
RNAsin | 100 Units |
Table 4: Table of reagents for isolation of monocytes from PBMCs by flow cytometry.
Figure 1: Whole blood components as separated by centrifugation in density gradient centrifugation or EDTA tubes. (A) Centrifugation of whole blood in density gradient centrifugation tubes results in the separation of plasma, platelets, and PBMCs above the density gradient medium with multi-nucleated and erythrocytes below the density gradient medium. (B) Centrifugation of whole blood in EDTA tubes results in the separation of plasma in the topmost layer, erythrocytes in the bottom layer, and the buffy coat in the interface. Created with Biorender.com. Please click here to view a larger version of this figure.
Figure 2: The viability of thawed cryopreserved PBMCs was assessed by live/dead flow staining and flow cytometry. (A) Debris, denoted by an asterisk *, is excluded from PBMCs by forward and side scatter gating. (B) Representative live/dead analysis of whole PBMCs (C) Pan-monocytes are gated as HLA-DR positive and negative for the following FITC-labeled surface antigens: CD3, CD19, CD56, and CD66b. (D) Representative live/dead analysis of monocytes. (E) Lymphocytes gated by the following FITC labeled surface antigens: CD3, CD19, CD56, and CD 66b. (F) Representative live/dead analysis of lymphocytes. (G) Percent viability of each cell type quantified from 56 samples. Please click here to view a larger version of this figure.
Figure 3: RNA-sequencing quality of monocytes sorted from cryopreserved PBMCs. 56 unique samples were sequenced and a mean ± SD 18.0 ± 16.3 million total sequences were generated. (A) Alignment was high, with 92.5% ± 6.3% of the sequences aligning with the reference genome. (B) The GC content of these sequences was 49.6 ± 1.4%. Created with FastQC25. Please click here to view a larger version of this figure.
Supplementary Video 1: Demonstration of how to use the centrifuge Please click here to download this File.
Supplementary Video 2: Demonstration of how to operate a multi-dispenser pipette. Please click here to download this File.
This protocol for PBMC collection and cryopreservation has been successfully implemented by individuals with and without prior research laboratory training. In our application, FACS and RNA-sequencing of highly viable monocytes purified from stored PBMCs resulted in high-quality sequences.
A major strength of this protocol is its accessibility. The technique presented in the protocol utilizes tubes pre-packed with a solid-density gradient medium. As a result, whole blood can be collected directly into the tube and then immediately processed to isolate PBMCs. A relatively small number of premade solutions and specialized equipment is needed, facilitating collaboration between the research laboratory, where reagents may be prepared, and the clinical laboratory, where samples are collected and processed. The written and video protocols are geared towards operators at any level of training.
While this protocol utilizes fresh whole blood to isolate PBMCs and, therefore, has a relatively high expected yield and purity of >90%, it may not be suitable for applications necessitating exceptionally high purities of >98%26,27. Moreover, density gradient centrifugation tubes can be costly to obtain, especially if a large number of samples need to be collected.
Alternative methods of PBMC collection include the use of a liquid density gradient medium or immunomagnetic depletion28,29. Briefly, the former involves layering a pre-made density gradient medium under heparinized whole blood followed by centrifugation. The latter utilizes magnetically tagged antibodies to label non-PBMCs, which are then retained in a magnetic column while unlabeled PBMCs pass through unaffected.
Relative to the presented protocol, the use of a liquid density gradient medium is both less costly and necessitates much less material due to the lack of density gradient centrifugation tubes; PBMC isolation can be performed in a standard 50 mL tube8. However, this technique is more elaborate, has a longer processing time, and may be subject to a higher risk of user error. Heparin must be precisely added to avoid over-dilution and the density gradient medium must be layered carefully in the correct amounts to ensure good PBMC separation26.
Relative to the presented protocol, the use of immunomagnetic depletion offers higher yield and purity, reduced handling due to lack of centrifugation, a faster processing time, and necessitates much less material30,31,32. However, the main downside is that this method is the costliest of the three methods described, especially at scale.
While this protocol is robust, certain critical steps may require additional attention. Throughout the protocol, ensure that samples are not mixed and are placed into the appropriately labelled tubes, especially when working with multiple patients or conditions simultaneously. For step 1.4, ensure that no PBMCs are discarded; excess plasma will only decrease the concentration of PBMCs, which is less critical in maintaining sample viability and quality. Separately, the presence of precipitates in collected PBMCs suggests that pieces of the density gradient medium were dislodged. Pipette more gently in step 1.5 to prevent this issue. In steps 1.10 and 3.6, ensure that the centrifuged cell pellet is not discarded. Working expeditiously is critical for step 1.12 and 3.3 as Solution 3 contains DMSO, which is toxic to cells at room temperature33. It is also important to note that storage of PBMCs in liquid nitrogen is recommended over storage at -80°C. Long-term storage at -80°C has been associated with decreased cell viability and altered gene expression34,35.
This protocol may be adapted according to experimental needs. The addition of flavopiridol, an inhibitor of RNA polymerase and mRNA synthesis, in Solutions 2 and 3 is intended to prevent any handling and stress induced artifact with RNA-sequencing36. However, flavopiridol may be omitted if functional or ex vivo studies utilizing PBMCs are desired.
Plasma collected from EDTA tubes will become contaminated with EDTA, a chelating agent. As a result, EDTA plasma is unsuitable for assays involving coagulation or calcium ions37,38. If desired, the plasma layer in the density gradient medium tubes post-centrifugation can instead be collected in step 1.4. These tubes contain sodium heparin as an anticoagulant which can be removed with the addition of heparinase39. Notably, heparin inhibits reverse transcriptase and PCR amplification, making the collected plasma unsuitable for PCR experiments without the addition of a heparin-blocking agent40.
The collected buffy coat from EDTA tubes is not stored in a solution containing DMSO or flavopiridol. DMSO is important in reducing ice crystal formation and cell death41. Flavopiridol is important for the inhibition of RNA synthesis36. Thus, the buffy coat is unsuitable for ex vivo and transcriptomic analyses. If desired, steps 1.6 to 1.15 can be performed using collected buffy coat in order to maximize cell viability and inhibit RNA synthesis.
While this protocol was designed for RNA-sequencing, additional potential applications of PBMCs collected and cryopreserved using this protocol include cell culture, gene editing, ex-vivo functional studies, single cell analyses, phenotyping by flow cytometry or cytometry by time of flight, isolation of DNA/RNA or proteins, slides for immunohistochemistry, amongst others.
The authors have nothing to disclose.
We'd like to thank the patients who volunteered their consent, time, and donation of blood samples. We also acknowledge Dr. Patrick Moriarty, Julie-Ann Dutton, and Mark McClellen at the Kansas University Medical Center for their collaboration and for implementing this protocol at a remote site. CY has received research support from NIH grant 1K08HL150271.
1000 µL Tips | Gilson | F174501 | Approximately 3 tips needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
15 mL tube | Biopioneeer | CNT-15 | To hold Solutions 2/3 2 needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
2 mL Cryovials | Globe Scientific | 3012 | Approximately 40 cryovials needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
20 µL Tips | Gilson | F174201 | For use in cell counting; volume needed is dependent on method of cell counting used. 1 tip is needed per 1 mL of unpooled frozen PBMCs to be defrosted |
50 mL Conical Tube | CEM Corporation | 50-187-7683 | 2 needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection 3 needed per 1 mL of unpooled frozen PBMCs to be defrosted |
CD14 Antibody | Biolegend | 325621 | |
CD16 Antibody | Biolegend | 360723 | |
CD19 Antibody | Biolegend | 363007 | |
CD3 Antibody | Biolegend | 300405 | |
CD56 Antibody | Biolegend | 318303 | |
CD66b Antibody | Biolegend | 305103 | |
Cell Strainer | Biopioneeer | DGN258367 | 1 needed per 1 mL of unpooled frozen PBMCs to be defrosted |
CPT Mononuclear Cell Preparation Tube | BD Biosciences | 362753 | 6 tubes needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
Cryo Freezer Box | Southern Labware | SB2CC-81 | Holds 81 tubes 1 needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
Cryotube Rack | Fisherbrand | 05-669-45 | Holds up to 50 cryovials |
DMSO | Invitrogen | 15575020 | Approximately 2.5 mL needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
DNase/RNase-Free Distilled Water | Invitrogen | 10977015 | Approximately 2 mL needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection Approximately 9 mL needed per 1 mL of frozen PBMCs to be defrosted |
EDTA Tubes | BD Biosciences | 366643 | 1 tube needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
Flavopiridol | Sigma-Aldrich | F3055-5MG | |
HLA-DR Antibody | Biolegend | 307609 | |
Human Serum Albumin | GeminiBio | 800-120 | Approximately 25 mL needed per patient or treatment condition for PBMC/Plasma/Buffy Coat Collection |
Human Trustain FcX | Biolegend | 422301 | |
Isopropanol | Sigma-Aldrich | W292912-1KG-K | For use in Mr. Frosty |
Label Printer | Phomemo | M110-WH | |
Live-Dead Stain | Biolegend | 423105 | |
Mr. Frosty | Thermo Scientific | 5100-0001 | Holds up to 18 tubes. 2 Mr. Frostys needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
Multidispense Pipette | Brandtech | 705110 | |
Multidispense Pipette Tips | Brandtech | 705744 | Approximately 3 tips needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
P1000 Pipette | Gilson | F144059M | |
P20 Pipette | Gilson | F144056M | For use in cell counting; volume needed is dependent on method of cell counting used. |
Printer Labels | Phomemo | PM-M110-3020 | Approximately 45 labels needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection Approximately 5 labels needed per 1 mL of unpooled frozen PBMCs to be defrosted |
RNase-Free EDTA (0.5 M) | Invitrogen | AM9260G | Approximately 40 µL needed per 1 mL of frozen PBMCs to be defrosted |
RNase-Free PBS (10X) | Invitrogen | AM9625 | Approximately 1 mL needed per 1 mL of frozen PBMCs to be defrosted |
RNasin | Promega | N2111 | |
RPMI | Corning | 10-040-CV | Approximately 80 mL needed per patient or treatment condition for PBMC/Plasma/Buffy Coat Collection |
Transfer Pipettes | Fisherbrand | 13-711-7M | Approximately 5 needed per patient/treatment condition for PBMC/Plasma/Buffy Coat Collection |
Tube Holder | Endicott-Seymour | 14-781-15 | Holds up to 80 CPT/EDTA Tubes |