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CUT&RUN experiment in colon cancer cells (HCT116, DLD1 and SW620), assessing TBX3 genomic occupancy

ABSTRACT: CUT&RUN experiment in colon cancer cells (HCT116, DLD1 and SW620), assessing TBX3 genomic occupancy

PROVIDER: PRJEB71412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12379506_1.fastq.gz	Fastqsanger.gz
	ERR12379506_2.fastq.gz	Fastqsanger.gz
	ERR12379507_1.fastq.gz	Fastqsanger.gz
	ERR12379507_2.fastq.gz	Fastqsanger.gz
	ERR12379508_1.fastq.gz	Fastqsanger.gz

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CUT&RUN experiment in colon cancer cells (HCT116, DLD1 and SW620), assessing TBX3 genomic occupancy

Project description:The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a prime example. While much work has been dedicated to uncovering effective therapeutics to block oncogenic Wnt signaling, such interventions have not proven trivial because of the broad activity of Wnt throughout the adult body and the difficulty in finding suitable molecular targets. We have previously identified the developmental transcription factor TBX3 as a participant of the Wnt-mediated transcriptional regulation. Here we examine the genome-wide binding pattern of TBX3 in the human CRC cells lines HCT116 (25 replicates), DLD1 (2 replicates) and SW620 (2 replicates), by employing CUT&RUN (C&R) with Low-Volume and Urea (LoV-U; Zambanini et al., 2022).

2024-01-01 | E-MTAB-13646 | biostudies-arrayexpress

Difference of gene expression among DLD1, oxaliplatin resistant clones derived from DLD1, HCT116, and oxaliplatin resistant clones derived from HCT116

Project description:Gene expression between DLD1 and DLD1 derived oxaliplatin resistant clones (DLD/OHP1, DLD/OHP4, and DLD/OHP5) was assessed Gene expression between HCT116 and HCT116 derived oxaliplatin resistant clones (HCT/OHP1, HCT/OHP3, and HCT/OHP5) was assessed

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Expression data form PI3K Knockout colon cancer cell lines (HCT116 and DLD1)

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CAGE-seq of human colon cancer cell line (HCT116) upon TBX3 overexpression

Project description:The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a prime example. While much work has been dedicated to uncovering effective therapeutics to block oncogenic Wnt signaling, such interventions have not proven trivial because of the broad activity of Wnt throughout the adult body and the difficulty in finding suitable molecular targets. We have previously identified the developmental transcription factor TBX3 as a participant of the Wnt-mediated transcriptional regulation. Here, we performed Cap-Analysis Gene Expression sequencing (CAGE-seq) to assess the genome-wide transcriptional consequences upon TBX3 overexpression in the human colorectal cancer cell line HCT116.

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DLD1

Project description:DLD1 is an APC mut, KRAS mut, P53 mut CRC cell line. PROX1 transcription factor, target of Wnt pathway in CRC, is our protein of interest.DLD1 cells are PROX1 negative. We overexpressed through lentiviral expression PROX1 protein or the empty vector psd44, through selection of the cells in puromycin resistance. Afterwards we compared the transcriptional program of the DLD1-PROX1 and DLD1-Control cells growing in monolayer in vitro.

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CAGE-seq of human colon cancer cell line (HCT116) upon TBX3 overexpression

Project description:CAGE-seq of human colon cancer cell line (HCT116) upon TBX3 overexpression

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Expression data from SW620/sh control and SW620/shMACC1

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