Extended Data Fig. 4: Quality control checks for scRNA-seq assessment of memory PbTII cell differentiation.
From: Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory
a, FACS gating strategy for isolation of naive (CD62L+ CD44-) donor PbTII cells for transfer into recipients, 24 hours prior to infection. A subset of these cells was also used for scRNA-seq assessment for PbTII responses at D0 p.i. Cells were then either sorted as single-cells onto 384-well plates for Smart-seq2 assessment or sorted as single-cells using the 10X Genomics platform. b, FACS gating strategy for isolation of PbTII cells from D7 p.i. onwards for scRNA-seq assessment for either Smart-seq2 or 10X Genomics assessment. c, Distribution of PbTII cells from the Smart-Seq2 dataset after filtering for number of genes (1000<nGene< 5000), mapped counts (> 100,000) and percentage of mitochondrial content (<0.35). d, The current Smart-seq2 (384) PbTII dataset of D0, D7, D10*, D14*, D17*, D21* and D28* p.i. cells were combined with our previous datasets18 containing PbTII cells isolated from D0 to D7 p.i. (SMARTer batch: D0, D2, D3, D4, D7 p.i.; Smart-seq2 (96) batch: D0, D4, D7 p.i.) PCA plots showing the entire time series, with shapes denoting the different experimental batches, (left) before and (right) after batch effect correction as described in methods. (*) = samples were isolated either from saline or IAT groups.
