Project description:To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis. We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells. We cultured shlncTCF7 and shCtrl cells from hepatocellular carcinoma (HCC) clinical sample, then hybridized on Affymetrix microarrays. We sought to identify distinct target genes of lncTCF7 in liver cancer stem cells (CSCs).

2015-03-05 | E-GEOD-66515 | biostudies-arrayexpress

Expression data from shlncTCF7 and shCtrl of hepatocellular carcinoma (HCC) clinical sample

2015-03-05 | GSE66515 | GEO

Genome-wide profiling of genes during differentiation of wild (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs, and Strip2 silenced (KD) ESCs

Project description:The role of Striatin Interacting Protein 2 (Strip2) in differentiation of embryonic stem cells (ESCs) is still under debate. Strip2 silenced (KD) ESCs were differentiated for 4, 8, 12, and 16 days. We show that Strip2 is distributed in the perinucleus or nuclei of wild type (WT) undifferentiated ESCs, but is localized in high-density nuclear bodies in differentiated cells. CellNet analysis of microarray gene expression data for KD and scrambled control (SCR) embryoid bodies (EBs), as well as immunostainings of key pluripotent factors, demonstrated that KD ESCs remain undifferentiated. This occurs even in 16-day old EBs, which possessed a high tumorigenic potential. Correlated with very high expression levels of epigenetic regulator genes, Hat1 and Dnmt3, enzymatic activities of the histone acetyltransferase type B (HAT1) and DNA (cytosine-5)-methyltransferase 3 beta (DNMT3b) were higher in differentiated 16-day old KD EBs than in SCR or WT EBs. The expression levels of let-7, 290 and 302 microRNA families were opposed in KD ESCs, while KD EBs had levels comparable to WT and SCR ESCs during differentiation. This demonstrates that Strip2 is critical to the onset of differentiation, regulating expression of epigenetic regulators, HAT1 and DNMT3b, as well as microRNAs involved in pluripotency.

2017-03-26 | GSE96807 | GEO

Genome-wide profiling of miRNAs during differentiation of wild (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs, and Strip2 silenced (KD) ESCs

2017-03-26 | GSE96808 | GEO

Expression data of shDIDO1 and shCtrl HUVEC cell lines

Project description:DIDO1(Death inducer-obliterator) gene localizes in the nucleus and cytosol, which is required in the early steps during the tumor progression and metastasis. We analyzed the GeneChip expression profiles of human umbilical vein endothelial cells transfected by RNAi lentiviral vectors, shDIDO1 cell line and shCtrl cell lines

2022-01-07 | GSE156713 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' Transcriptomes in B cells lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' transcriptomes, 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 NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-10 | GSE143862 | GEO

Transcriptomic analysis of SiHa cells stably expressing shCtrl or shSYT7

Project description:GeneChip PrimeView Human PathArrayTM was performed using the SiHa cells-stably expressing shCtrl or shSYT7. To investigate the underlying mechanism of tumor-suppressive phenotypes of CESC with SYT7 knockdown, we used GeneChip PrimeView Gene Expression Array that could detect expression profiling of over 36,000 transcripts and variants using the SiHa-shCtrl and shSYT7-cDNAs

2022-04-11 | GSE200526 | GEO

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