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

iMEF SDHC-loss stable line ATAC-seq

Project description:iMEF SDHC-loss stable line ATAC-seq

| PRJNA533325 | ENA

Differential ATAC-seq and ChIP-seq peak detection using ROTS.

Project description: Not available

| S-EPMC8253552 | biostudies-literature

ATAC-seq of HEK293T cell line

Project description:An enhancer of chr8 (chr8:579137-581436) was deleted using CRISPR and the effects of its deletion were assessed using ATAC-seq

2017-08-01 | E-MTAB-5702 | biostudies-arrayexpress

ATAC-seq of Kasumi-7 acute lymphoblastic leukemia cell line harboring MEF2D-HNRNPUL1 fusion gene

Project description:ATAC-seq. was performed to examine open chromatin regions in an acute lymphoblastic leukemia cell line, Kasumi-7

2020-06-30 | E-MTAB-8491 | biostudies-arrayexpress

RNA-seq, ChIP-seq, and ATAC-seq analyses of mTECs

Project description:RNA-seq, ChIP-seq, and ATAC-seq analyses of mTECs

| PRJNA605193 | ENA