Fig. 4

Localization of the potential cis-acting SE-lncRNAs. a Immunoblot of Cell Fractionation of Whole Cell Lysate, Cytoplasmic Fraction, and Nuclear Fraction in MCF10A and CA1 cells. GAPDH was used as control for Cytoplasmic fraction, while Tri-methyl Histone was used as control for Nuclear Fraction. b, c Localization of 14 SE-lncRNAs (11 up-regulated and 3 down-regulated) from our list of 27 potentially cis-acting SE-lncRNAs and 4 highest differentiated that are primarily localized within the nucleus. d Expression level of SE-lncRNA, RP11-379F4.1, and its neighboring mRNA, RARRES1, in MFC10A progression series, n = 3, * = P < 0.05,, one-way ANOVA with Tukey comparison, error bars represent standard deviation. Expression levels of SE-lncRNA RP11-379F4.1 in 24 DCIS and 24 IDC patients (* = P < 0.05), unpaired t test. e Expression level of the highest differentiated SE-lncRNA, RP11-465B22.8, in MCF10A progression series, n = 3, * = P < 0.05, one-way ANOVA with Tukey comparison, error bars represent standard deviation. Expression levels of SE-lncRNA RP11-465B22.8 in 16 DCIS and IDC patients (** = P < 0.005), unpaired t test. f Knockdown of the two target SE-lncRNAs was performed and expression of the SE-lncRNAs and their neighboring mRNAs was determined 48 h post-transfection in DCIS and CA1 cells, n = 3, * = P < 0.05, paired t-test, error bars represent standard deviation