Test dataset for countASAP package: a lightweight easy to use Python package for processing ASAPseq data
Test dataset for countASAP package: a lightweight easy to use Python package for processing ASAPseq data
Experimental protocols for ASAPseq data acquisition followed the following design: dissociated single cell suspensions from each mouse were dispensed into two sets of 96-well plates, with each well containing approximately 150,000 cells. Then cells were blocked with an anti-mouse CD16/32 antibody (Trustain FcX Plus: BioLegend) to prevent non-specific binding via the Fc receptor. After blocking, the cells were stained with Total Seq-B anti-mouse hashtag antibody (BioLegend). Hash-tagged cells were then pooled together (approx. 2 million cells) and stained with a mixture of sixty-two TotalSeq-B anti-mouse surface protein panel antibodies at concentrations ranging from 12.5ng to 100ng per pooled sample. Stained cells were washed with Cell Staining Buffer (BioLegend). Cell numbers were counted, along with viability. 5-week-old C57BL/6J mice were pre-exposed sequentially to Influenza A/Puerto Rico/8/34 (PR8) virus and Plasmodium yoelii strain 17XNL. Four doses of 1mg chloroquine were administered intraperitoneally over the course of 3 weeks to clear the malaria infection. Pre-exposed mice (now 12-15 weeks old) were injected intraperitoneally with 3mg anti-mouse IFNAR-1 to prevent rapid clearance of the vaccineâ€™s virus by Type I interferon responses. One day later, mice were vaccinated subcutaneously in one caudal thigh muscle with live-attenuated virus yellow fever vaccine YF17D (Sanofi Pasteur) or the same vaccine inactivated with formalin.  Serum was removed from whole blood, after which red blood cells were lysed with Ack lysing buffer. Lymphocytes were isolated from all tissues using density gradient centrifugation. Cells were stained with CITE-seq antibodies (HTOs and ADTs), after which single cells were encapsulated in gel-beads-in-emulsion. 10x Genomics ATAC protocol (CG000496 Rev B).