Fig. 5

The transcriptome characteristics of CCDC144NL-AS1-knockdown hPSCs. a Unsupervised hierarchical clustering of RNA-seq data from CCDC144NL-AS1-KD-H9, CCDC144NL-AS1-KD-H14, CCDC144NL-AS1-KD-HDF-iPS, and their corresponding negative control cells. CCDC144NL-AS1-KD hPSC sample names are indicated in red, and all control sample names are indicated in black. b Three sample-specific modules identified by WGCNA. Two figures of each square respectively represent the correlation between a module and a corresponding sample, and p value of the correlation value. Colors of squares correspond to different correlation types: positive correlation (red), negative correlation (green), no correlation (white). c Gene Ontology (GO) analyses of MEbrown (upper panel) and MEturquoise (lower panel) module genes. d Unsupervised hierarchical clustering of RNA-seq data from CCDC144NL-AS1-KD hPSC, negative control hPSC, and samples of three other studies Chan et al. [18], Takashima et al. [15], and Guo et al. [19]. Sample names from different experiments are indicated in different colors, and all control sample names are indicated in black. e The expression data of CCDC144NL-AS1 in naïve hPSCs from Chan et al. [18], Takashima et al. [15], and Guo et al. [19] and in control hPSCs. Displayed are log₂ RPKM values. f Expression of genes identified by others as associating with the human naïve and primed states in CCDC144NL-AS1-KD hPSCs and control cells. The expression levels are determined by RNA-seq data.