Project description:To explore the downstream genes of HDAC4, we performed RNA-seq to screen after knocking down HDAC4 in 5-8F cells, a nasopharyngeal carcinoma cell line.

2022-01-28 | GSE125744 | GEO

Identification of the downstream target genes of TGFbeta

Project description:This study aimed to explore the downstream target genes of TGFbeta in normal gastric cell line GES-1.

2024-01-31 | GSE245557 | GEO

Downstream genes and pathways of ASH1-miR-375-YWHAZ axis in hepatocellular carcinoma

Project description:To explore the mechanism and downstream pathways of ASH1-miR-375-YWHAZ axis in hepatocellular carcinoma (HCC). We performed microarray assay to identify the downstream genes of YWHAZ. As a result, we obtained 507 (245 upregulation and 262 downregulation) differentially expressed genes significantly affected by YWHAZ knockdown. Function enrichment analysis showed that these genes were enriched in the “Regulation of actin cytoskeleton” pathway which is related with cell migration and tumor metastasis. We also find that most of the autophagy-associated genes, such as ATG3, ATG5 and ATG7 and EMT related gene E-cadherin were highly correlated with YWHAZ and changed by silencing YWHAZ. Real-time quantitative RT-PCR was performed to verify the microarray results. In conclusion, the expression profile of many genes were significantly affected by YWHAZ knockdown, which helps to further explore the mechanism of the effects of ASH1-miR-375-YWHAZ axis in HCC.

2022-10-05 | GSE98026 | GEO

Investigation of downstream genes regulated by ACOT12 in HCC cells

Project description:Investigation of downstream genes regulated by ACOT12 in HCC cells

| PRJNA438207 | ENA

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts

Project description:Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding of Pol II downstream of the 3' end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all expressed genes we observed Pol II occupancy downstream of the EAGs suggesting that Pol II pausing 3' from the transcription units is a rather common phenomenon. Downstream of EAGs Pol II transcripts can also be detected by global run-on and sequencing, suggesting the presence of functionally active Pol II. Based on Pol II occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts undergo polyA tail addition [poly(A)+], Pol II occupancy downstream of the EAGs can be detected up to 4-6 kb. Inhibition of polyadenylation significantly increased Pol II occupancy downstream of EAGs at poly(A)+ genes, but not at the EAGs of core histone genes. The differential genome-wide Pol II occupancy profiles 3' of the EAGs have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be independent of the phosphorylation status of the C-terminal domain of the large subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3' end processing mechanisms and consequent Pol II transcription termination processes. Examination of RNA Polymerase II in MCF-7 cell line

2012-06-15 | E-GEOD-34001 | biostudies-arrayexpress

Exploring the downstream genes of PKP2

Project description:Plakophilin 2 (PKP2), encodes a plakophilin protein that belongs to the member of desmosomal proteins.PkP2 regulates some cell biological functions, but its downstream genes are not clear, so we constructed a stable cell line using H460 cells and identified its downstream target genes by RNA-seq technology

2022-11-13 | GSE140509 | GEO

Identification of ENO2-targeted downstream genes by ChIP-seq in Arabidopsis

Project description:Identification of ENO2-targeted downstream genes by ChIP-seq in Arabidopsis

| PRJNA635414 | ENA