Extended Data Fig. 5: Benchmarking FIND-seq as a technology.
From: Identification of astrocyte regulators by nucleic acid cytometry
(a) Quantification of percent aquaporin-4-expressing cells in naïve mice by antibody-based flow cytometry (n = 4); FIND-seq (n = 3), or scRNA-seq reanalyzed from ref. 22. (b) Validation of FIND-seq specificity and sensitivity through the analysis of AQP4+ and AQP4- cells isolated by flow cytometry and subjected to FIND-seq. Percentages show number of cells expressing Aqp4 in each population based on 70% bead loading. (c) PCA plot of bulk FIND-seq analysis of Aqp4+Edem1- cells. (d) Comparison of FIND-seq detection sensitivity with comparable technologies. (e) Correlation of raw expression counts per gene between bulk FIND-seq-sorted Aqp4+Edem1+ cells and Edem1+ astrocytes extracted from droplet-based scRNA-seq data that we previously reported in22. (f) Quantification of fraction of duplicate reads across bulk RNA-seq platforms. (g) Quantification of Ern1 in bulk FIND-seq data as a function of EAE and Edem1 expression. (h) Calculation of a signature score for transcripts enriched in astrocyte endfeet as reported by ref. 51, analyzed in astrocytes from ref. 22 and bulk FIND-seq.
