Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Identification of super-enhancers in colorectal cancer cell lines

PROVIDER: PRJNA378753 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5333010.fastq.gz	Fastqsanger.gz
	SRR5333003.fastq.gz	Fastqsanger.gz
	SRR5333004.fastq.gz	Fastqsanger.gz
	SRR5333005.fastq.gz	Fastqsanger.gz
	SRR5333006.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

ChIP seq for p63, H3K27ac and BRD4 in L3.6pl, BxPC-3 pancreatic cancer cell lines and ChIP-seq of H3K27ac and BRD4 in Panc-1 pancreatic cell line

Project description:We investigated the regions that are occupied by deltaNp63 in BxPC-3 and L3.6pl and identification of super enhancers in different pancreatic cancer cell lines. Thereby, we identified a group of 45 super enhancers that are associated with poorer prognosis and are highly dependent on deltaNp63.

2018-12-18 | E-MTAB-7034 | biostudies-arrayexpress

Identification of super-enhancers in colorectal cancer cell lines

Project description:H3K27 acetylation statuses were analyzed in four colon cancer cell lines (RKO, Caco2, SW48, and SW620), and colorectal cancer-specific super-enhancers were identified.

2017-05-31 | GSE96069 | GEO

Homo sapiens

Project description:Colorectal Cancer Cell Lines aCGH

| PRJNA155319 | ENA

Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer [ChIP-seq]

Project description:We interrogated global super-enhancer landscape and sought to discover master regulators governing the liver metastasis of colorectal cancer (CRC). Using de novo analysis, we predicted motif enrichment of master transcription factor in super-enhancers. We show that transcription factor-binding sites of hepatocyte nuclear factor 1 (HNF1) family are enriched at super-enhancers identified in cell lines derived from liver metastases, but not those derived from primary tumors. Using ChIP-Seq of acetylated H3K27, the enrichment of HNF1 binding motifs in super enhancers was found in a cell line derived from xenografted liver metastasis but not the parental cell line. The prediction method was further extended to pancreatic cancer where liver metastasis is also a common finding, and a similar enrichment of HNF1 family motif in super-enhancers was found. We subsequently showed that HNF1A was prominently expressed and significantly upregulated in metastatic cell lines and clinical specimens of liver metastases. Collectively, our study implicates HNF1A as a master transcription factor involved in shaping global super-enhancer landscape in CRC liver metastasis.

2020-11-17 | GSE161558 | GEO

Homo sapiens

Project description:Genomewide miRNA profiling of colorectal cancer cell lines and colorectal cancer-derived induced pluripotent cancer cell lines

| PRJNA343975 | ENA

Homo sapiens

Project description:Expression profiling of colorectal cancer cell lines.

| PRJNA380413 | ENA

Homo sapiens

Project description:Expression profiles of colorectal cancer cell lines

| PRJNA214975 | ENA

Chromatin interactions involving super-enhancers associate with specific expression patterns of target genes

Project description:Super-enhancers may regulate target genes through chromatin looping. We connected super-enhancers in the K562 chronic myelogenous leukemia cell line with chromatin interactions identified from Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data. Gene expression at proximal elements that are connected with distal super-enhancers showed significantly higher cell-type specificity than at proximal elements connected with other elements or not involved in interaction. 4C and Episwitch analysis of chromatin interactions showed that certain chromatin interactions are cell-specific, but others are more general. While super-enhancers upstream of c-MYC at the MYC-335 element can be found in other cancers, only super-enhancers downstream of c-MYC can be found in K562. 4C analysis of the c-MYC promoter revealed no chromatin interactions that are directed upstream of c-MYC, but only downstream of c-MYC, in the PVT1 long non-coding RNA gene. Cell-specific usage of super-enhancers could explain why the MYC-335 element that is associated with many solid cancers such as colorectal cancer and breast cancer, but not with leukemia. Surprisingly, we found that a chromatin interaction between c-MYC and a c-MYC super-enhancer is lost in chronic myelogenous leukemia patient blood as compared with blood from individuals without the disease through Oxford Biodynamicsâ?? Episwitch analysis. These results provide evidence for fine-tuning of expression patterns, such as cell-specific regulation of target genes by distal super-enhancers through chromatin interactions and an association between chromatin interactions and disease, and highlight that super-enhancers are more complex than previously described. Examination of several chromatin interactions involving super-enhancers using 4C-Seq and Episwitch (TM)

2017-05-01 | E-GEOD-77125 | biostudies-arrayexpress

super-ehancer landscape shaped by master regulator in liver metastasis of colorectal cancer [RNA-seq]

2021-10-05 | GSE185331 | GEO

Homo sapiens

Project description:Methylation-silenced genes in colorectal cancer cell lines

| PRJNA99441 | ENA