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

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

PROVIDER: PRJNA1039246 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26788580_1.fastq.gz	Fastqsanger.gz
	SRR26788580_2.fastq.gz	Fastqsanger.gz
	SRR26788581_1.fastq.gz	Fastqsanger.gz
	SRR26788581_2.fastq.gz	Fastqsanger.gz
	SRR26788582_1.fastq.gz	Fastqsanger.gz

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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: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

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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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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.

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Next Generation Sequencing Facilitates Quantitative Analysis of Col, myb30 and MYB30-OE Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Col, myb30 and MYB30-OE Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Col, myb30 and MYB30-OE Transcriptomes

Project description:total mRNA profiles of 4-day-old Col (WT), MYB30 knockout mutant (myb30) and MYB30-OE were generated by deep sequencing, in triplicate, Sequencing was carried out with the Illumina HiSeq 2000 platform and the resulting reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10) with TopHat (http://tophat.cbcb.umd.edu). Transcript expression was evaluated by cuffdiff (http://cufflinks.cbcb.umd.edu), and transcript abundance was estimated by fragments per kilobase of exon model per million mapped fragments (FPKM). Differentially expressed genes were selected using Student’s t-test with P<0.05. qRT–PCR validation was performed using SYBR Green assays.

2020-04-14 | GSE141145 | 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

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

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Project description:RNA Sequencing Facilitates Quantitative Analysis of shL3MBTL2 ,CGA-OE and corresponding control Transcriptomes

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