1k Human PBMCs (unstimulated and PHA stimulated), proxiome-immuno-155 panel
PBMC isolation and fixation
Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coat using Ficoll-Paque density gradient centrifugation. Following isolation, the PBMCs underwent red blood cell lysis and cells were centrifuged three times at 300 x g for 8 minutes to minimize platelet contamination. Subsequently, the cells were fixed with 1% paraformaldehyde for 15 minutes at room temperature.
For phytohemagglutinin (PHA) stimulation, PBMCs were seeded at 1M cells/mL in RPMI media. Cells were stimulated with PHA (Thermofisher, Cat. no: 00-4977-03) at a 1:1000 dilution for 72 hours, then fixed and blocked as described above.
Cells were then fixed with 1% PFA for 15 minutes at room temperature as described in UM001: User Manual Proxiome kit Cell Surface v.100.
PNA workflow
Fixed cells were processed as described in UM001: User Manual Proxiome kit Cell Surface v.100, and sequenced on an Illumina NextSeq2000 sequencing system using 44 cycles for read1 and 78 cycles for read2.
Data processing
The generated sequencing data was processed by Pixelator 0.21.2 (using nf-core/pixelator revision 6029df575bd21bfa369a3d641d3b2c038bf10f85) with default parameters.
File Download
In order to process the dataset FASTQ files, you need to have the required infrastructure by nf-core/pixelator.
- Download in browser
- Batch download
| Panel file | Size | Checksum (MD5) |
|---|---|---|
| Proximome Immuno 155 Panel | 6.77 KiB | 337eb9c782a6de052f242e51e73e51a9 |
| Samplesheet | Size | Checksum (MD5) |
|---|---|---|
| 1k Human PBMCs sampesheet CSV | 365 B | b6c88d06ab42b26e5eabd913436c86b4 |
| Input files | Size | Checksum (MD5) |
|---|---|---|
| PHA Stimulated Human PBMCs S04_R1 FASTQ | 10.16 GiB | 8daafbe69437d2ba80fdcca45b6040ec |
| PHA Stimulated Human PBMCs S04_R2 FASTQ | 17.61 GiB | b0cba534115a81a442b15070c0f35f06 |
| Unstimulated Human PBMCs S02_R1 FASTQ | 10.62 GiB | a01b88348606680d417b8a83aa8d9fb2 |
| Unstimulated Human PBMCs S02_R2 FASTQ | 18.32 GiB | 5591a56624f0dc174fbf91ab7895c616 |
| Output files | Size | Checksum (MD5) |
|---|---|---|
| PHA Stimulated Human PBMCs S04 PXL | 4.96 GiB | adbc4d5641597e09d0c379b7a347e36f |
| Unstimulated Human PBMCs S02 PXL | 3.63 GiB | 51dab82dc70e471b0af578dcba1bd632 |
| Report files | Size | Checksum (MD5) |
|---|---|---|
| PHA Stimulated Human PBMCs S04 HTML | 5.41 MiB | ecd99f243fbf5ef4bf35ea540b0905f7 |
| Unstimulated Human PBMCs S02 HTML | 5.38 MiB | 5858015dcc82e1efc8df87f02701777c |
# Panel file
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/proxiome-immuno-155.csv
# Samplesheet
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/samplesheet.1k-human-pbmc.csv
# Input files
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/fastqs/PNA062_PHA_PBMCs_1000cells_S04_S4_R1_001.fastq.gz
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/fastqs/PNA062_PHA_PBMCs_1000cells_S04_S4_R2_001.fastq.gz
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/fastqs/PNA062_unstim_PBMCs_1000cells_S02_S2_R1_001.fastq.gz
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/fastqs/PNA062_unstim_PBMCs_1000cells_S02_S2_R2_001.fastq.gz
# Output files
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/sha-079762b-2025-07-02-74062c09/pixelator/PNA062_PHA_PBMCs_1000cells_S04_S4.layout.pxl
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/sha-079762b-2025-07-02-74062c09/pixelator/PNA062_unstim_PBMCs_1000cells_S02_S2.layout.pxl
# Report files
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/sha-079762b-2025-07-02-74062c09/pixelator/report/PNA062_PHA_PBMCs_1000cells_S04_S4.qc-report.html
curl -O https://pixelgen-technologies-datasets.s3.eu-north-1.amazonaws.com/pna-datasets/v2/sha-079762b-2025-07-02-74062c09/pixelator/report/PNA062_unstim_PBMCs_1000cells_S02_S2.qc-report.html
License
Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
How to Cite
If you are using this data in your research, please cite the Proximity Network Assay pre-print as follows:
Single-Cell Protein Interactomes by the Proximity Network Assay. Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, Maud Schweitzer, Ludvig Larsson, Vincent van Hoef, Pouria Tajvar, Johan Dahlberg, Florian De Temmerman, Louise Leijonancker, Sylvain Geny, Rikard Forlin, Erika Negrini, Stefan Petkov, Lovisa Franzén, Jessica Bunz, Christine Moge, Henrik Everberg, Petter Brodin, Alvaro Martinez Barrio, Simon Fredriksson bioRxiv 2025.06.19.660329; doi: https://doi.org/10.1101/2025.06.19.660329