Daniel CaronJan 9, 2024

Excited to share a new #preprint! This represents a truly gargantuan effort to profile #ImmuneCells across the human body as part of the #HumanCellAtlas network. Using multimodal profiling of single cells, we uncover tissue-directed and age-associated gene and protein signatures, which will help us understand features of healthy immune cell heterogenity across life!

https://www.biorxiv.org/content/10.1101/2024.01.03.573877v2.full

#scRNAseq #CITEseq #Multiomics #Immunology #TissueImmunity #Research

🧵1/7

Daniel CaronJul 17, 2023

Cool computational method for separating γδ #Tcells by #rna #sequencing
Rather than relying on paired #TCRseq or #CITEseq, they calculate module scores of TCR constant and variable region gene expression

https://doi.org/10.1093/jleuko/qiad069

Human γδ T cell Identification from Single-cell RNA Sequencing Datasets by Modular TCR Expression

Analysis method, based on TCR gene module scores, to identify γδ T cells from 5'-end scRNA-seq datasets.

OUP Academic
Daniel CaronJul 7, 2023

So excited to share MMoCHi: a tool I've built for multi-modal cell type classification for CITE-seq data
The pre-print can be found here:
https://www.biorxiv.org/content/10.1101/2023.07.06.547944v1

And we've put it out on #GitHub so that you can try it out on your own data:
https://mmochi.readthedocs.io
#scRNAseq #scRNA #CITEseq #sequencing #analysis #ColumbiaUniversity #immunology

Haojia WuJan 26, 2023
A new multiomics study from Satija Rahul's lab identified a unique population of CD8+ T cells after COVID-19 vaccination. These cells are the SARS-CoV-2 antigen specific and capable of rapid clonal expansion. The relative frequency and differentiation of these cells can predict clinical outcomes for COVID-19 patients. #covid #multiomics #scRNAseq #scATACseq #CITEseq #ASAPseq #TCR
https://www.biorxiv.org/content/10.1101/2023.01.24.525203v1
Haojia WuDec 1, 2022
Prox-seq for simultaneous measurement of proteins, protein complexes and mRNAs in thousands of single cells! With this multi-modal profiling technique, the authors were able to directly measure the protein complexes on naïve CD8+ T cells and protein interactions during TLR4 activation in macrophages. #singlecell #multimodal #newtech #CITEseq #REAPseq
https://www.nature.com/articles/s41592-022-01684-z
Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing - Nature Methods

This work presents Prox-seq that couples sequencing and proximity ligation assay to simultaneously measure extracellular proteins, protein–protein interactions and mRNA in single cells.

Nature