GSE112729
SALL4 Crud ChIP sequencing-WT and RNA-seq of SNU398 cells treated with therapeutic SALL4 peptides
SALL4 is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in HCC, a malignancy with no effective treatment. In cancer cells, SALL4 associates with NuRD to silence tumor suppressor genes such as PTEN. Here, we design a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. To understand the pathways affected by the peptide treatment, we performed RNA sequencing on cells treated with different peptides. Furthermore,  to identify SALL4 DNA binding targets, we have performed CRUD-ChIP sequencing with SALL4 and H2K27Ac antibodies on HCC cell line SNU398. Overall design: For RNA sequencing, SNU398 were treated with 30µM of PEN, PEN-MUT, PEN-WT, or PEN-FFW for 8hrs and paired-end RNA-seq was performed for the treated samples. RNA-seq reads of each sample were mapped to hg19 using the STAR aligner.For Chip-sequencing, SNU398 cells were SNU398 cells were harvested and fixed. Only insoluble chromatin fractions were used for perfoming ChIP protocol, we renamed the protocol as CRUD-ChIP.