Project description:To verify Znf417 and Znf587 knock out whether leads to HERV-K element reactivation, we performed RNA-seq on Znf417/Znf587 double knock out (DKO) 293T cell lines. We did not find any significant changes in HERVK expression.
Project description:To verify ZNF417 and ZNF587 knock out whether leads to HERV-K element reactivation, we performed RNA-seq on ZNF417/ZNF587 double knock out (DKO) K562 cell lines. We observed a dozen of genes were upregulated in KO cells, and some of them possessed PBS-Lys sites near their promoters that can be directly targeted by ZNF417 and ZNF587, such as MS4A clusters. We also measured the expression levels of repetitive elements in ZNF417 ZNF587 dKO cells, which exhibited only some ERVs reactivation indirectly.
Project description:The ChIP-seq experiments using GFP antibody on ZNF417/ZNF587-GFP overexpressing 293T cells revealed that ZNF417/ZNF587 preferred to bind a PBS-Lys-containing HERVs. Further motif calling analysis showed that both ZNF417 and ZNF587 bind to HERVK PBS-resembled motif.
Project description:We infected ZNF417 ZNF587 dKO 293T or control 293T with NL4.3 virus for 48 hours. Then genomic DNA was purified from cell lysis with by phenol chloroform. DNA was sheared into 300 bp-500 bp random fragments using Covaris Adaptive Focused Acoustics (Covaris, Woburn, MA). Sheared DNA was ligated with a linker and PCR with primers targeting HIV LTR and linker. PCR products were performed second PCR with Illumina adaptor primers. Libraries were so constructed and sequenced on Novaseq 6000.
Project description:We conducted ribosome profiling and mRNA-seq using mouse skeletal muscle tissues and 293T cells (NTC control and DROSHA KO) with Hiseq 2500
Project description:RNAseq was performed by to compare gene expression between wildtype and Smchd1 KO ES cells, the gene expression pattern in Dux KO mutants , Double KO mutant Tet-TKO mutants and Tet TKO plus SMCKHD1 KO mutants were analyzed by RNAseq.
