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| Status |
Public on Jan 30, 2020 |
| Title |
CITEseq of human PBMC from healthy adult blood |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes. Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.
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| Overall design |
peripheral blood mononuclear cells (PBMCs) were isolated by sedimentation on Lymphopure TM (BioLegend) and labelled with 5 TotalSeq TM -A antibody mixes (to CD14, CD16, CD19, CD3, CD4, CD45, CD45RA, CD62L, CD8 and isotype controls) . For each antibody mix, a different TotalSeq TM -A hashtag (0.5 μ g/test) was used to allow for sample multiplexing.
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| Contributor(s) |
Fournié J, Pont F, Tosolini M, Gao Q, Huang TS, Nazor K |
| Citation |
Frédéric Pont, Marie Tosolini, Qing Gao, Marion Perrier, Miguel Madrid-Mencía, Tse Shun Huang, Pierre Neuvial, Maha Ayyoub, Kristopher Nazor, and Jean-Jacques Fournié. Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa025, doi:10.1093/nargab/lqaa025
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| Submission date |
Jan 29, 2020 |
| Last update date |
Apr 30, 2020 |
| Contact name |
Jean Jacques FOURNIE |
| E-mail(s) |
jean-jacques.fournie@inserm.fr
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| Phone |
+33619900602
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| Organization name |
INSERM
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| Department |
oncology
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| Lab |
Cancer Research Center of Toulouse
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| Street address |
2 av Hubert Curien
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| City |
Toulouse |
| ZIP/Postal code |
31037 |
| Country |
France |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA603655 |
| SRA |
SRP245801 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144434_RAW.tar |
15.0 Mb |
(http)(custom) |
TAR (of CSV, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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