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Next Generation Sequencing Facilitates Quantitative Analysis of TICs with or without H19 knockdown.

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of TICs with or without H19 knockdown.

PROVIDER: PRJNA476367 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR7349386_1.fastq.gz	Fastqsanger.gz
	SRR7349386_2.fastq.gz	Fastqsanger.gz
	SRR7349387_1.fastq.gz	Fastqsanger.gz
	SRR7349387_2.fastq.gz	Fastqsanger.gz
	SRR7349388_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of TICs with or without H19 knockdown.

Project description:The goals of this study are to compare mRNA and miRNA profiling between Tumor Initiating hepatoCytes (TICs) with or without H19 knockdown by shRNA. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study showed that knockdown of H19 in TICs led to increased expression of TP53 and CDKN1A/p21 target genes, increased expression of genes which are normally suppressed by Akt, and decreased expression of Src target genes

2019-06-06 | GSE115888 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SiHa cells with or without circCDKN2B-AS1 knockdown

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of SiHa cells with or without circCDKN2B-AS1 knockdown

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Expression data from HCT116 cells following H19 knockdown

Project description:Knockdown of H19 leads to cell cycle arrest, reduced cell proliferation, and reduced cell migration in HCT116 cells. We used microarrays to detail the global programme of gene expression following H19 knockdown in HCT116 cells

2016-09-29 | GSE87430 | GEO

Expression data from DLD1 cells following H19 knockdown

Project description:Knockdown of H19 leads to cell cycle arrest, reduced cell proliferation, and reduced cell migration in DLD1 cells. We used microarrays to detail the global programme of gene expression following H19 knockdown in DLD1 cells

2016-09-29 | GSE87427 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SiHa cells with or without circCDKN2B-AS1 knockdown

Project description:circCDKN2B-AS1 is significantly upregulated circRNA in HPV16 positive cervical cancer tissues comprared with both HPV16 positive and HPV16 negative normal cervical tissues.So we chose it for further study.To explore the mRNA expression profiles following circCDKN2B-AS1 knockdown, we performed RNA sequencing analysis in SiHa cells with or without circCDKN2B-AS1 knockdown.We performed RNA sequencing in two pairs of RNA samples of SiHa cells with or without circCDKN2B-AS1 knockdown.

2020-12-21 | GSE147010 | GEO

Genome-wide DNA methylation change due to H19 knockdown and TET3 knockdown in UtLM

Project description:We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by H19 knockdown and TET3 knockdown in human UtLM. Following H19 and TET3 knockdown, we observed extensive genome-wide methylation pattern changes relative to siCon cells, with some genes showing increased methylation, others showing decreased methylation, and a third group with no significant change.

2021-07-16 | GSE117190 | GEO

Identification of genes regulated by Long noncoding RNA H19 in hepatic cells

Project description:We used high throughput sequencing to compare the differential gene expression of HepG2 cells with and without H19 knockdown. We found critical genes involved in glucose production changed significantly after H19 konckdown compared to control.

2018-08-30 | GSE103201 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Yeast Cells Treated with and without Proanthocyanidins

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Next Generation Sequencing Facilitates Quantitative Analysis of Macrophage (RAW264.7) with and without arctigenin treatment

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Macrophage (RAW264.7) with and without arctigenin treatment

| PRJNA525768 | ENA

Effect of H19 Knockdown by siRNA on gene expression in C2C12 cells

Project description:We used microarrays to characterize the global changes in gene expression in C2C12 cells due to siRNA knockdown of long non-coding RNA H19 Control siRNA or siRNA specific for mouse H19 were transfected into day1 differentiating C2C12 myoblasts in triplicates. 40 H later total RNAs were isolated and subjected with microarray analysis.

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