Extended Data Fig. 7: In vivo screening of FIND-seq-identified candidate regulators of XBP1+ astrocytes.
From: Identification of astrocyte regulators by nucleic acid cytometry
(a) Predicted upstream regulator analysis showing Nr3c2 and Xbp1 from bulk FIND-seq data using Qiagen IPA. Differentially expressed genes were used as input and the overlap with the regulon controlled by each molecule was computed. Fisher’s exact test. (b) Left: Prediction of Nr3c2 as an upstream regulator in Aqp4+Edem1+ cells analyzed by FIND-seq during EAE using Qiagen IPA as in (a). Fisher’s exact test. Right: Identification of an NR3C2 motif by SeqPos in genes downregulated in Aqp4+Edem1+ versus Aqp4+Edem1- cells in EAE. (c) UMAP plot of Aqp4+Edem1+ cells from EAE mice analyzed by scFIND-seq. (d–e) Prediction of upstream regulators (d) and pathway analysis (e) based on Qiagen IPA in Cluster 1 astrocytes analyzed from Aqp4+Edem1+ cells in EAE mice shown in (c). Fisher’s exact test. (f) Schematic of lentiviral vector containing a sgRNA targeting candidate genes and spCas9 under the control of a Gfap promoter. EAE disease progression in mice transduced with sgScrmbl and candidate sgRNA lentiviruses. n = 4–5 mice per condition.
