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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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			Action	DRS
	SRR15048696_1.fastq.gz	Fastqsanger.gz
	SRR15048696_2.fastq.gz	Fastqsanger.gz
	SRR15048697_1.fastq.gz	Fastqsanger.gz
	SRR15048697_2.fastq.gz	Fastqsanger.gz
	SRR15048698_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

| PRJNA744392 | ENA

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

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

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

Analyses of Human Brain Metastases of Breast Cancer Reveal the Association between HK2 Up-Regulation and Poor Prognosis

Project description:Analyses of Resected Human Brain Metastases of Breast Cancer Reveal the Association between Up-Regulation of Hexokinase 2 and Poor Prognosis. Brain metastases of breast cancer seem to be increasing in incidence as systemic therapy improves. Metastatic disease in the brain is associated with high morbidity and mortality. We present the first gene expression analysis of laser-captured epithelial cells from resected human brain metastases of breast cancer compared with unlinked primary breast tumors. The tumors were matched for histology, tumor-node-metastasis (TNM) stage, and hormone receptor status. Most differentially expressed genes were down-regulated in the brain metastases, which included, surprisingly, many genes associated with metastasis. Quantitative real-time PCR analysis confirmed statistically significant differences or strong trends in the expression of six genes: BMP1, PEDF, LAMγ3, SIAH, STHMN3, and TSPD2. Hexokinase 2 (HK2) was also of interest because of its increased expression in brain metastases. HK2 is important in glucose metabolism and apoptosis. In agreement with our microarray results, HK2 levels (both mRNA and protein) were elevated in a brain metastatic derivative (231-BR) of the human breast carcinoma cell line MDA-MB-231 relative to the parental cell line (231-P) in vitro. Knockdown of HK2 expression in 231-BR cells using short hairpin RNA reduced cell proliferation when cultures were maintained in glucose-limiting conditions. Finally, HK2 expression was analyzed in a cohort of 123 resected brain metastases of breast cancer. High HK2 expression was significantly associated with poor patient survival after craniotomy (P = 0.028). The data suggest that HK2 overexpression is associated with metastasis to the brain in breast cancer and it may be a therapeutic target. Common reference design, disease state design.

2010-01-21 | E-GEOD-20016 | 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 H1299 Wild Type and TTC28-KO Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of H1299 Wild Type and TTC28-KO Transcriptomes

| PRJNA1008342 | 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 CD46-KO/control vector, CD46-KO/CD46-CYT1 and CD46-KO/CD46-CYT2 EJ-1 cells’ Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of CD46-KO/control vector, CD46-KO/CD46-CYT1 and CD46-KO/CD46-CYT2 EJ-1 cells’ Transcriptomes

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