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

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

PROVIDER: PRJNA787124 | ENA |

REPOSITORIES: ENA

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

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2022-12-15 | GSE190435 | 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.

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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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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 TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

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

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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

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Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP-N1 injected zebrafish embryos and untreated group transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP-N1 injected zebrafish embros transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: we injected the plasmid pEGFP-N1 into zebrafish zygotes by microinjection, and then when the embryos to develop to 1 hour-post-fertilization (hpf), 6 hpf and 12 hpf, these groups was collected respectively by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process (Fig.1A), endogenous immune response and tumor necrosis factor-mediated signaling pathways were abnormal up-regulation, mainly including isg15, foxo3b, phlda3, cdkn1a, zgc:136826, and si:dkey-204l11.1, compared with the non-injected group at 6hpf. These genes are found in somatic cells to deal with foreign plasmids invasion.

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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

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Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP-N1 injected zebrafish embryos and untreated group transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP-N1 injected zebrafish embryos and untreated group transcriptomes

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Next-generation sequencing facilitates quantitative analysis of miRNAs of cetuximab-resistant colorectal cancer (HCT116-R) cells

Project description:Total RNAs were isolated from three groups, including A group (0×10^9/mL PA-MSHA-treated HCT116 cells), B group (0.3×10^9/mL PA-MSHA-treated HCT116 cells) and C group (0.4×10^9/mL PA-MSHA-treated HCT116 cells). MiRNA sequencing was performed to assess differential expression using next-generation sequencing. The data showed that most miRNAs levels were different in A, B and C groups. Importantly, miR-7-5p was greatly increased in a dose-dependent manner.

2021-08-13 | GSE181843 | GEO

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