Project description:BHLHE40-AS1 was cloned into pBABE-Puro. Empty vector and pBABE-BHLHE40-AS1 were used to generate retrovirus and infect MCF10A cells. Transduced cells were selected with 1ug/mL puromycin for 2 weeks.
Project description:Microarray data on TH17 cells from Bhlhe40-GFP reporter mice We used microarrays to detail the global programme of gene expression in polarized Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells Purified naïve CD4 T cells from spleen were polarized under TH17 condition in vitro. On day 4, cells were stimulated with PMA and ionomycin, and sorted by their Bhlhe40-GFP expression prior to microarray analysis
Project description:To assess the impact of hypoxia on global gene expression of beta cells, we performed bulk RNA-seq on mouse islets, human islets and MIN6 cells. Bhlhe40 was transcriptional repressor which was highly induced by hypoxia in beta cells. Thus, we established Bhlhe40 overexpressing MIN6 cells and performed RNA-seq to identify the targets of Bhlhe40.
Project description:Long noncoding RNAs (lncRNAs), one type of endogenous RNA longer than 200 nucleotides, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of lncRNAs in regulating neuroblastoma progression still remain elusive. We identify GATA2 antisense RNA 1 (GATA2-AS1), a lncRNA derived from GATA binding protein 2 (GATA2), as a novel suppressor of neuroblastoma progression. To investigate the mechanisms underlying the oncogenic functions of GATA2-AS1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma BE(2)-C cells in response to stable over-expression of GATA2-AS1. The results showed that stable over-expression of GATA2-AS1 led to altered expression of 1933 human mRNAs, including 857 up-regulated genes and 1076 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to GATA2-AS1 over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.
Project description:Microarray data on TH17 cells from Bhlhe40-GFP reporter mice We used microarrays to detail the global programme of gene expression in polarized Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells
Project description:Long noncoding RNAs (lncRNAs), one type of endogenous RNA longer than 200 nucleotides, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of lncRNAs in regulating neuroblastoma progression still remain elusive. We identify HNF4A antisense RNA 1 (HNF4A-AS1), a lncRNA derived from upstream region of hepatocyte nuclear factor 4 alpha (HNF4A), as a novel driver of neuroblastoma progression. To investigate the mechanisms underlying the oncogenic functions of HNF4A-AS1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to stable over-expression of HNF4A-AS1. The results showed that stable over-expression of HNF4A-AS1 led to altered expression of 4296 human mRNAs, including 2169 up-regulated genes and 2127 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to HNF4A-AS1 over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.
Project description:Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of publically available microarray datasets, we discovered a novel 963-bp lncRNA, named FOXD3 antisense RNA 1 (FOXD3-AS1), as an independent prognostic marker for favorable clinical outcome of NB patients. To investigate the mechanisms underlying the oncogenic functions of FOXD3-AS1, we employed the Illumina HiSeq PE125/PE150 as a discovery platform to analyze the transcriptome profiling changes of human BE(2)-C cells in response to stable over-expression of FOXD3-AS1. The results showed that stable over-expression of FOXD3-AS1 led to altered expression of 3191 human mRNAs, including 1542 up-regulated genes and 1650 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to FOXD3-AS1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.
Project description:Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of public datasets, we identified myeloid zinc finger 1 antisense RNA 1 (MZF1-AS1) as a novel lncRNA associated with the progression of NB. To investigate the mechanisms underlying the oncogenic functions of MZF1-AS1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of MZF1-AS1. The results showed that stable over-expression of MZF1-AS1 led to altered expression of 2920 human mRNAs, including 1476 up-regulated genes and 1444 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including proline synthesis, invasion, and metastasis by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to MZF1-AS1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.
Project description:We silenced FAM83H-AS1 shRNAs in cell line MCF7 carried a ~75% silencing compared to thenegative control (NC). We evaluated the role of FAM83H-AS1 on oncogenic phenotypes in the MCF7 breast cancer cell line model. The knockdown of FAM83H-AS1 was achieved with ~75% of silencing efficiency. A complete transcriptomic analysis after silencing of FAM83H-AS1 revealed an impact on the global expression.