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ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression

ABSTRACT: ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression

PROVIDER: PRJNA269024 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1687310.fastq.gz	Fastqsanger.gz
	SRR1687311.fastq.gz	Fastqsanger.gz
	SRR1687351_1.fastq.gz	Fastqsanger.gz
	SRR1687351_2.fastq.gz	Fastqsanger.gz
	SRR1687312.fastq.gz	Fastqsanger.gz

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TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (ChIP-Seq)

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Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha

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.

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TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (ChIP-Seq)

Project description:Dysregulation of the canonical Wnt/β-catenin signaling pathway is a hallmark of colorectal cancer (CRC). The T-cell factor/lymphoid enhancer factor (TCF/LEF; hereafter, TCF) family of transcription factors are critical regulators of canonical Wnt/β-catenin target gene expression. Despite similarity across DNA-binding and protein-binding domains, TCF family members differentially regulate target gene expression in CRC. Of the four TCF family members, TCF7L1 predominantly functions as a transcriptional repressor and it has an oncogenic role in CRC. Despite this role, few target genes regulated by TCF7L1 in CRC have been identified. Through RNA-sequencing of transcripts differentially expressed in control and TCF7L1-overexpressing HCT116 cells, we identified 397 genes that were repressed directly, or indirectly, by TCF7L1. Gene set enrichment analysis found genes associated with epithelial-mesenchymal transition amongst those that are differentially expressed. By silencing and overexpressing TCF7L1 in CRC cell lines, we found that TCF7L1 promoted migration, invasion, and adhesion in vitro. Chromatin immunoprecipitation followed by sequencing (ChIP-sequencing) localized 3661 TCF7L1 binding sites within the CRC genome. Comparison of genes whose expression was downregulated by TCF7L1 and genes with TCF7L1 binding sites revealed 41 novel targets directly regulated by TCF7L1. Among these, we localized a TCF7L1 promoter-proximal binding site within the growth arrest specific 1 (GAS1) gene. We found that ectopic GAS1 expression rescued the TCF7L1-mediated increase in migration and invasion in CRC cells. These findings uncover a novel role for TCF7L1 in repressing GAS1 expression to promote migration and invasion of CRC cells in vitro.

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Genome-wide maps of chromatin state of WDR5 and KAT2A in gastric cancer BGC823 cells [ChIP-seq]

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