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Methylated RNA Immunoprecipitation sequencing Quantitative Analysis of HCT116 Wild Type and TTC7B-KO Transcriptomes

ABSTRACT: Methylated RNA Immunoprecipitation sequencing Quantitative Analysis of HCT116 Wild Type and TTC7B-KO Transcriptomes

PROVIDER: PRJNA1108601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28960515_1.fastq.gz	Fastqsanger.gz
	SRR28960515_2.fastq.gz	Fastqsanger.gz
	SRR28960516_1.fastq.gz	Fastqsanger.gz
	SRR28960516_2.fastq.gz	Fastqsanger.gz
	SRR28960517_1.fastq.gz	Fastqsanger.gz

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Methylated RNA Immunoprecipitation sequencing Quantitative Analysis of HCT116 Wild Type and TTC7B-KO Transcriptomes

Project description:To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO cell lines. The purpose of this study aims to predict possible downstream target genes of TTC7B and to investigate the effects of TTC7B knockout on modification of gene RNA m6A methylated RNA site by MeRIP-seq

2024-10-10 | GSE266858 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

2022-12-15 | GSE190435 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-02-10 | GSE157951 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

Project description:To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO/OE cell lines. The purpose of this study is to utilize next-generation sequencing techniques to investigate the effects of TTC7B knockout or overexpression on the biological behavior of tumor cells.

2024-10-10 | GSE247502 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

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Effect for target mRNA degradation by methylated microRNAs

Project description:To confirme the function of methylated micro RNAs (miR-17 and let-7a), we transfected methylated or non-methylated microRNAs to DICER KO HCT116 cell line. mRNA were isolated at 48 houes after transfection. This data show that the function were different between methylated or non-methylated microRNAs.

2018-08-25 | GSE119013 | GEO

RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

Project description:RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

| PRJNA850418 | ENA

Epigenetically Silenced Genes Found Using Methylated DNA Immunoprecipitation in Colon Cancer Cells Deficient in DNMTs

Project description:CpG island promoter hypermethylation of tumor suppressor genes is a common hallmark of human cancer, and new large-scale epigenomic technologies might be useful in our attempts to define the complete DNA hypermethylome of tumor cells. Here we report a functional search for hypermethylated CpG islands using the colorectal cancer cell line HCT-116, in which two major DNA methyltransferases, DNMT1 and DNMT3b, have been genetically disrupted (DKOcells). Using methylated DNA immunoprecipitation (MeDIP) methodology in conjunction with promoter microarray analyses we found that DKO cells experience a significant loss of hypermethylated CpG islands. Further characterization of these candidate sequences demonstrates CpG island promoter hypermethylation and silencing of genes with potentially important roles in tumorigenesis, such as the Ras guanine-nucleotide release factor RASGRF2, the apoptosis-associated basic helixloop transcription factor BHLHB9, and the homeobox gene HOXD1. Hypermethylation of these genes occurs already in premalignant lesions and accumulates during tumorigenesis. Thus, our results demonstrate the usefulness of DNMT genetic disruption strategies combined with MeDIP in searching for unknown hypermethylated candidate genes in human cancer that might aid our understanding of the biology of the disease and be of potential translational use. Keywords: Human Proximal Promoter Array; DNA Methylation Comparative experiment: methylated DNA immunoprecipitated/INPUT(Total Genomic DNA) from the colon cancer cell line HCT116 wild type vs methylated DNA imonoprecipitated/INPUT from the colon cancer cell line HCT116 DNMT1/3b doubleknockout (DKO)

2010-05-27 | E-GEOD-9267 | biostudies-arrayexpress

HCT116 MYC 3' TBE1 (WT) and KO RNA-Seq

Project description:mRNA was sequenced from HCT116 MYC 3' TBE1 (WT) and KO cells to identify genes differentially expressed after deletion of the MYC 3' TBE1

2016-05-24 | GSE70833 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

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