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.

2019-03-21 | PXD012930 | Pride

Identifying Novel Therapeutic Targets by Combining Transcriptional Data with Ordinal Clinical Measurements

Project description:Identifying Novel Therapeutic Targets by Combining Transcriptional Data with Ordinal Clinical Measurements

| PRJNA386152 | ENA

Identifying transcriptional targets of ONECUT3 by ChIP-seq

Project description:We report the direct target genes of the aberrant expression of ONECUT3 through next generation sequencing. We combine RNA-seq and ChIP-seq to identify target genes of ONECUT3 overexpression. RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) assays were performed on TP53-KO mouse embryonic fibroblast MEF with or without Doxycycline (100 ng/ml) to identify target genes both bound and regulated by ONECUT3. We found that genes related with sister chromosome exchange separation, mitotic nuclear division, and chromosome segregation were significantly upregulated by high level of ONECUT3. The top 10 directly activated target genes predicted by Binding and Expression Target Analysis (BETA) include Incenp and Cdca8, which are the critical components of Chromosomal Passenger Complex (CPC). Through this observation, we conclude that main role of ONECUT3 as transcription factors is to upregulate mRNA transcription of mitotic process. This sutdy provide new insight of genetic network of how dysfunctional ONECUT3 underlies mitotic defects and Chromosomal instability.

2024-03-01 | GSE202680 | GEO

Identifying miR-139 targets in motor neurons

Project description:Identifying miR-139 targets in motor neurons

| PRJNA838955 | ENA

Identifying the transcriptional targets of the Drosophila transcription factor Ets21c via Targeted DamID

Project description:Identifying the transcriptional targets of the Drosophila transcription factor Ets21c via Targeted DamID

| PRJNA503866 | ENA

ZFP541 ChIP-seq targets during male meiotic prophase

Project description:ZFP541 ChIP-seq targets during male meiotic prophase

| PRJNA688209 | ENA