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Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO HK2 cells

ABSTRACT: Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO HK2 cells

PROVIDER: PRJNA744076 | ENA |

REPOSITORIES: ENA

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Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO HK2 cells

Project description:Purpose: We idenficied a circRNA, circBNC2, that was downregulated during tubular epithelial cell (TEC) injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in HK2 (a well recognized TEC) cells. Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO HK2 cells and wild-type HK2 cells.

2022-07-01 | GSE179505 | GEO

Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells

Project description:Purpose: We idenficied a circRNA, circBNC2, that was downregulated during hepatocytes injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in L-02 (a well recognized human hepatocytes) cells. Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO L-02 cells and wild-type L-02 cells.

2022-07-01 | GSE179620 | GEO

Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells

Project description:Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells

| PRJNA744392 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of IFNα Stimulated Transcriptomes in HepG2, SETD2-KO, STAT1-KO and STAT1-K525ARe HepG2 cells

Project description:Purpose: Using RNA-seq to analyze the different expressions induced by IFNα among the SETD2-KO HepG2 cells, STAT1-KO HepG2 cells and STAT1-K525A-Re HepG2 cells and HepG2 control cells Methods: mRNA profiles of HepG2 control cells and SETD2-KO cells, STAT1-KO cells, STAT1-K525A-Re cells were generated by deep sequencing, using BGISEQ-500RS. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).

2019-03-12 | GSE98372 | 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

Expression profiling of E14 cells overexpressing Hk2/Pkm2

Project description:Purpose: In this study, we compared transcriptome profiling (RNA-seq) between normal mouse embryonic stem cell (E14) and Hexokinase2 (Hk2)/ Pyruvate Kinase M2 (Pkm2) overexpressed E14 cell. Result: Using an optimized data analysis workflow, we mapped over 4 billion sequence reads per sample to the mouse genome (build mm9) and identified 28698 transcripts in 5 samples. Conclusion: Our study represents the first detailed analysis of Hk2/ Pkm2 overexpressed E14 cell transcriptomes, generated by RNA-seq technology We compared transcriptome profiling (RNA-Seq) between normal mouse embryonic stem cell (E14) and E14 cells over-expressing Hexokinase2 (Hk2)/Pyruvate Kinase M2 (Pkm2)

2016-07-03 | E-GEOD-65246 | biostudies-arrayexpress

RNA-seq analysis of transcriptomes in Wild Type and ANXA2 knockdown HK2 cells

Project description:We conducted this experiment to study the effects of Annexin A2 (ANXA2) on gene expression in human proximal tubular epithelial (HK2) cells in vitro. Short hairpin RNA targeting ANXA2 was designed and cloned into vector pGFP-B-RS for RNAi to generate the recombinant expression plasmids, which were transfected into HK2 cells. RNA-seq analysis were performed on HK2 cells, with or without ANXA2 knockdown, to reveal the differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). Then the DEGs and RASEs were validated by qRT-PCR. Using criteria of an absolute fold change of ≥2.0 or ≤ 0.5 and false discovery rate (FDR) of < 0.05 with the edgeR package, RNA-seq analysis of the transcriptomes revealed 220 upregulated and 171 downregulated genes related to ANXA2 knockdown.

2022-06-16 | GSE159360 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

| S-EPMC3233386 | biostudies-literature

Next Generation Sequencing Facilitates Quantitative Analysis of Wild-type (WT) and Uba3fl/fl-Lck Cre+ (KO) splenic CD44hiCD4+ T cell transcriptomes

Project description:We analyze the impact of T cell-specific deletion of Uba3 gene on CD4+ T cell responses during Plasmodium infection using the RNA-seq techonology. We isolated CD44hiCD4+ T cells in spleens from wild-type (WT) and Uba3fl/fl-LckCre+ (KO)mice at day 5 of Plasmodium yoelii 17XNL infection. RNA samples were prepared for deep-sequencing on an Illumina Hiseq platform and 150 bp paired-end reads were generated.Quanlity control was performed to generate high quality data for further analysis.By comparing gene expression levels of different CD4+ T cell lineages, we observed defects in the expression of several signature genes that related to Th1 and Tfh responses in KO mice.

2018-10-31 | GSE111066 | GEO

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