Discover and read the best of Twitter Threads about #citeseq
Most recents (5)
New @medrxivpreprint from work over 5 years with @tsanglab!
Our framework for integrating human population & single cell variations identified a "naturally adjuvanted" baseline immune system setpoint linked to more robust & immunogenic vaccine responses.
medrxiv.org/content/10.110…
Our framework for integrating human population & single cell variations identified a "naturally adjuvanted" baseline immune system setpoint linked to more robust & immunogenic vaccine responses.
medrxiv.org/content/10.110…
We used mixed effects models to decompose variation in every gene attributable to cell type (defined by surface protein), individual, age, sex, and vaccination effects. Individual differences often explain substantial variation, highlighting the need for hierarchical models. 
After accounting for human population variation, we defined vaccine-induced transcriptome perturbations in each cell type, then integrated these statistical model results with "bottom up" computational reconstructions of transcriptional dynamics.
Thrilled to share my research from Dan Littman's lab at @nyulangone, online today in @Nature. If you are interested in the differentiation of CD4 T cell programs and the mucosal iTreg response, this is for you. #Treg, #ILC3, #Tolerance, go.nature.com/3RCXHkw, A 🧵 /1
CD4 T cell programs govern immune responses, directing inflammation or tolerance. It is widely accepted that classical DCs (cDC) present microbial peptides on MHCII to activate and direct the differentiation of all CD4 T cell programs. Our results challenge this dogma. /2
We show that both the tolerogenic iTreg and the inflammatory Th17 responses to gut microbes are initiated by two distinct antigen-presenting cell (APC) subsets, other than cDC. And what about cDC? Our data suggest that they initiate the T follicular helper (Tfh) response. /3
Excited to share our latest single cell multimodal assay. ASAP-seq pairs surface and intracellular protein detection with high quality chromatin accessibility on the @10xGenomics #scATACseq platform.
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
By employing a bridge oligo approach, #ASAPseq allows protein detection with existing @bioLegend TotalSeq family conjugates and is compatible with hashing. If you are doing #CITEseq now, buying a bridge oligo (~$40) is all it takes to start doing ASAP-seq.
ASAP-seq takes advantage of the recent mtscATAC-seq work that demonstrated that whole fixed cells can give high quality scATAC-seq libraries, with mtDNA clonal architecture as an optional added bonus.
nature.com/articles/s4158…
nature.com/articles/s4158…
1/n Our Collaborative "Single-Cell Omics Reveals Dyssynchrony of the Innate & Adaptive Immune System in Progressive #COVID19" paper is now on @medrxivpreprint. We provide @10xGenomics #scRNAseq, #Cite, #TCRseq & #BCRseq: my nonimmunologist's tweets follow medrxiv.org/content/10.110…
2/n As expected, type-1 IFN signature dominates all cell types (with a uniquely IFN-activated CD8 T cell cluster). The signature correlates strongly with initial viral load and in repeated samples with time #COVID19 #Covid19CellAtlas medrxiv.org/content/10.110…
3/n A skewed immunopralysis like anti-inflammatory signature is found in monocytes of #COVID19 progressive patients, connectome analysis suggested disrupted connectivity between LAG3 and MHC signalling medrxiv.org/content/10.110…
Running (EC)CITE-seq? #scRNAseq
Can I use FACS staining protocol? Should #CITEseq Abs be used at saturating conc? Can I reduce staining volume? Does cell# at staining matter? How can I minimize Background?
Tweetorial of biorxiv.org/content/10.110…
@SBKoralov @skinUCPH @NYGCtech
Can I use FACS staining protocol? Should #CITEseq Abs be used at saturating conc? Can I reduce staining volume? Does cell# at staining matter? How can I minimize Background?
Tweetorial of biorxiv.org/content/10.110…
@SBKoralov @skinUCPH @NYGCtech
When setting up #ECCITEseq we encountered many questions that we could not find answers to. Figuring we were not alone, we tested several conditions (tissue/conc./volume/cell #) and compiled the results into a manuscript that we hope will assist others!
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
We find that staining with high antibody conc. can cause unnecessarily high background signal and that concentrations of most antibodies can be reduced beyond general recommendations. Titration is best, but 0.6-1 µg/mL range appears to be a good starting point for most Abs tested
