Expression data from the control and Jmjd1c KD ESCs

The roles of histone demethylases (HDMs) for the establishment and maintenance of the pluripotent state are incompletely defined. Here, we show that JmjC domain-containing protein 1c (Jmjd1c), a putative histone H3 Lys 9 (H3K9) demethylase, is required for mouse embryonic stem cell (ESC) self-renewal. To understand how Jmjd1c knockdown (KD) and resultant changes in the H3K9 methylations would affect ESCs at a global gene expression level, we compared the whole genome transcriptomes between the control and Jmjd1c KD ESCs (6 samples, including 2 shNT control samples and 4 shJmjd1c samples, 2 from #3 and 2 from #4 shRNA, respectively) using affymetrix microarray. We used microarrays to identify genes affected by Jmjd1c knockdown in mouse ESCs. J1 ESCs were infected with lentiviral supernatants of shNT-pLKO.1, shJmjd1c#3-pLKO.1 or shJmjd1c#4-pLKO.1. One day post-infection, ESCs were selected with puromycin at the final concentration of 1.5ug/ml for 2 days. Subsequently, the puromycin-resistent ESCs were re-plated onto dishes, cultured for 4 days, and collected for RNA isolation. In total, six RNA samples were prepared from the two independent biological duplicates. Microarray analysis was performed with the Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. The procedures including RNA extraction, cDNA synthesis, labeling, hybridization, washing, and scanning were carried out according to the standard Affymetrix protocol by the Shanghai Biotechnology Corporation.