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RNA-seq of human colorectal cancer HCT116 and HT29 cells by the distinct conditions of trypsin digestion

ABSTRACT: RNA-seq of human colorectal cancer HCT116 and HT29 cells by the distinct conditions of trypsin digestion

PROVIDER: PRJEB82973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR14006000_1.fastq.gz	Fastqsanger.gz
	ERR14006000_2.fastq.gz	Fastqsanger.gz
	ERR14006001_1.fastq.gz	Fastqsanger.gz
	ERR14006001_2.fastq.gz	Fastqsanger.gz
	ERR14006002_1.fastq.gz	Fastqsanger.gz

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RNA-seq of human colorectal cancer HCT116 and HT29 cells by the distinct conditions of trypsin digestion

Project description:In the process of cell culture in vitro, we usually find that the cells show signs of aging, which is that the passed cells are unable to stick to the wall. Experience tells us that the time it takes for trypsin to digest the adherent cells is important. If the digestion time is too short, enough cells cannot be obtained for passage, while if the digestion time is too long, a large number of senescent cells will also be digested. The substances released by the death and decomposition of these senescent cells will affect the function of those active cells, resulting in the failure of the recovery of the whole daughter cell line. This project starts from the question of the global difference among cells undergoing the multiple rounds of mitosis in one culture dish. RNA sequencing was conducted to investigate the transcriptome signatures of cells with different sensitivity response to trypsin.

2024-12-21 | E-MTAB-14651 | biostudies-arrayexpress

Transcription profiling of human colorectal carcinoma cell lines HCT116 and HT29 treated with 5-ASA

Project description:Transcription profiling of human colorectal carcinoma cell lines HCT116 and HT29 treated with 5-ASA

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Whole genome expression microarray of cancer stem cells isolated from HT29 and HCT116 Human colorectal cancer cell lines

Project description:In the present study we have isolated and characterized cancer stem cells and non-cancer stem cells (bulk tumor cells) from high grade human colorectal cancer cell line HCT116 and low grade human colorectal cancer cell line HT29. For this study, cancer stem cells and non-cancer stem cells (bulk tumor cells) were isolated from HCT116 and HT29 human colorectal cancer cell line. For isolating cancer stem cells by FACS, CD44 and CD166 tagged with V450 and PE respectively were used. CD44+CD166+ was the cancer stem cell population and CD44-CD166- was designated as the non-cancer stem cell (bulk tumor cells) population for this study. RNA was isolated from the isolated cell populations and microarray was done to study the whole genome transcriptomic changes.

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Trypsin

Project description:Trypsin sequencing

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Gene expression profile of HCT116 and HT29 cells treated with D/L2HG

Project description:The oncometabolite, 2-hydroxyglutarate (2HG), has been directly implicated in carcinogenesis; however, the underlying molecular mechanisms remain poorly understood. To elucidate the molecular mechanisms through which 2HG contributes to cancer progression, we performed transcriptome analysis in 2HG-treated colorectal cancer HCT116 and HT29 cells.

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Expression data from mammary epithelial cells harvested from 8-9 week old C3H female mice - various isolation conditions

Project description:Numerous lineage analysis studies have used FACS sorting as a separation technique prior to measuring mRNA expression patterns. To assess if FACS sorting causes non-specific changes in gene expression, we collected a heterogeneous population of mammary epithelial cells from three biological replicates. We then performed gene expression analysis on each replicate either prior to trypsin digestion, immediately following trypsin digestion, or following both the trypsin digestion and a mock FACS sort. In this dataset, we include gene expression data obtained from isolated murine mammary epithelial cells either prior to trypsin digestion, immediately following trypsin digestion, or following the trypsin digestion and a mock FACS sort.

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Tandem LysC/trypsin digestion performs efficient in detergent conditions and under constant denaturating environments

Project description:All shotgun proteomics experiments rely on efficient proteolysis steps for sensitive peptide/protein identification and quantification. Continuous protocol improvement is therefore a constant topic in proteomics research. Previous reports suggest that the sequential tandem LysC/trypsin digest yields higher recovery of fully tryptic peptides than single-tryptic proteolysis. Based on the previous studies, it is assumed that the advantageous effect of tandem proteolysis requires a high sample denaturation state for the initial LysC digest. Therefore, to date, all systematic assessments of LysC/trypsin proteolysis were done in chaotropic environments such as urea. Here we show that the LysC/trypsin digestion can be carried with high efficiency in MS-compatible detergents resulting in higher yields of fully cleaved peptides. We show that higher cleavage efficiency of tandem digests has an impact on absolute protein quantification using iBAQ values. By additionally testing different urea tandem conditions our data implies that beneficial effects of the initial LysC digest do not depend on the sample denaturation state, but more likely, are due to different target specificities of LysC and trypsin. The observed detergent compatibility enables tandem digestion schemes to be implemented in efficient cellular solubilization proteomics procedures without the need for buffer exchange to chaotropic digestion environment.

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