Project description:Cas9 expressing eHAP cells were transfected with sgRNA against TFDP1. 5 days after the transfection, polyA RNA was analyzed by RNA-seq
Project description:A genome-wide screening identified effector genes of chromatin accessibility. To investigate the functional consequences of the loss of each effector gene, we conducted Mnase-seq with eHAP cells knocked out for TFDP1.
Project description:A genome-wide screening identified effector genes of chromatin accessibility. To investigate the functional consequences of the loss of each effector gene, we conducted ATAC-seq analysis with eHAP cells knocked out for each effector gene.
Project description:eHap CRISPR-Cas9 mutagenized cells with no selection serves as a control. RPS6p antibody staining on the mutagenized eHap cells was used in a flow-sorting approach to isolate RPS6p high and low populations respectively. The genomic DNA from these different samples was isolated, subjected to PCR to amplify the genomically-encoded guide RNA sequences, the product(s) of which was then sequenced on a Hi-Seq X Ten instrument by Novogene.
Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.
