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. 2022 May 16;11:e69571. doi: 10.7554/eLife.69571

Figure 2. Two sequence candidates selectively activate adeno-associated virus (AAV) expression in parvalbumin-expressing (PV+) neurons.

Figure 2.

(a) Genome browser visualization of PV+-specific ATAC-seq signal at sequence candidates SC1 and SC2. * cSNAIL data, † INTACT data from Mo et al., 2015, ‡ snATAC-seq from Li et al., 2021. (b) Percentile rank of support vector machine (SVM) scores among 1755 true PV+-specific enhancer sequence candidates that scored positively across all models. Linear population-derived models are denoted with ‘pop,’ nonlinear population-derived models are denoted with ‘pop, rbf,’ and linear single-nucleus-derived models are denoted with ‘sn.’ (c) Example images of AAV Sun1GFP expression against parvalbumin (Pvalb) antibody staining. (d, e) Quantification of AAV Sun1GFP or Pvalb-2A-Cre/Ai14 reporter overlap with Pvalb+ cells. Bar heights represent the mean among images, and the error of the mean is shown. N cells = 1322 (SC1), 2570 (SC2), 1340 (Ai14), 2013 (Ef1a), and 504 (N.C.). N.C., negative control.

Figure 2—source data 1. Detailed information for 1755 experimental parvalbumin (PV)-enriched open chromatin regions (OCRs) with positive parvalbumin-expressing (PV+) model scores.
Genomic coordinates, peak log2 fold difference, adjusted p-value, support vector machine (SVM) scores, convolutional neural network (CNN) scores, snATAC-seq overlap, species conservation, and subcortical SVM scores are provided.
elife-69571-fig2-data1.xlsx (640.6KB, xlsx)
Figure 2—source data 2. Image quantification for Specific Nuclear-Anchored Independent Labeling (SNAIL) viruses or the Pvalb-2A-Cre mouse strain reporter with Pvalb immunohistochemistry.