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ABSTRACT: RNA sequencing following TRIM27 knockdown in KYSE30 cells

PROVIDER: PRJNA1049157 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27107078_1.fastq.gz	Fastqsanger.gz
	SRR27107078_2.fastq.gz	Fastqsanger.gz
	SRR27107079_1.fastq.gz	Fastqsanger.gz
	SRR27107079_2.fastq.gz	Fastqsanger.gz
	SRR27107080_1.fastq.gz	Fastqsanger.gz

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Project description:RNA sequencing following KLF12 knockdown in KYSE30 cells

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RNA sequencing analysis of OTUD6B-knockdown KYSE30 and KYSE450 cells

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to test the effects of OTUD6B-knockdown on the mRNA of KYSE30 and KYSE450 cells. Methods: KYSE30 and KYSE450 cells were transfected with negative control or siOTUD6B for 48 hours in 1640 medium plus 10% serum. Three independent replicates were plated, transfected in parallel for each negative control and siOTUD6B. Results: Log-fold changes of mRNAs between negative control and siOTUD6B group were selected with a significance threshod of p<0.05. Conclusions: Our study determined the mRNA changes of OTUD6B-knockdown KYSE30 and KYSE450 cells.

2023-04-01 | GSE209521 | GEO

Transcriptomes Analysis of LHX2-knockdown in KYSE30 and KYSE510 cells

Project description:Purpose: To fully realize the potential molecular mechanism that LHX2 promotes ESCC progression Methods: Total RNA of LHX2-knockdown KYSE30/KYSE510 and control cells was extracted with TRIzol Reagent. RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol. A total of 150 base paired-end reads were sequenced using the Novaseq 6000 S4 platform. Results: We identified 26008 transcripts in KYSE30 control and KYSE30 LHX2-knockdown cells ,and 25561 transcripts in KYSE510 control and KYSE510 LHX2-knockdown cells. Conclusions: Our study represents the analysis of LHX2-knockdown ESCC cells, generated by RNA-seq.

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RNA sequencing analysis of OTUD6B-knockdown KYSE30 and KYSE450 cells

Project description:RNA sequencing analysis of OTUD6B-knockdown KYSE30 and KYSE450 cells

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Differentially expressed genes between ACh-stimulated KYSE30 cells and the respective control cells

Project description:Purpose:RNA sequencing explored the possible altered gene transcriptome and signal pathways between ACh-stimulated KYSE30 cells and the respective control cells. Methods:RNA sequencing explored the ACh-stimulated KYSE30 cells and the respective control cells.

2022-05-11 | GSE202482 | GEO

Project description:ChIP-seq Analysis of KLF12 in KYSE30 Cells with and without TRIM27 Overexpression

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Homo sapiens

Project description:RNA-seq in KYSE30 and KYSE150 cells following KLF12 overexpression

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The USP7-TRIM27 axis as part of non-canonical PRC1.1 is a druggable target in leukemia

Project description:In an attempt to unravel the functionality and targettability of the non-canonical PRC1.1 Polycomb complex in human leukemogenesis, we dissected the subunit composition of the PRC1.1 complex and show that USP7 and TRIM27 are integral components. USP7 interactome analyses show that PRC1.1 is the predominant Polycomb complex co-precipitating with USP7. USP7 inhibition results in PRC1.1 disassembly and loss of chromatin binding, coinciding with reduced H2AK119ub and H3K27ac levels and diminished gene transcription of active PRC1.1-controlled loci, whereas H3K4me3 levels remain unaffected. TRIM27 and USP7 are reciprocally required for incorporation into PRC1.1, and TRIM27 knockdown partially rescues USP7 inhibitor sensitivity. USP7 inhibitors effectively impair proliferation in (primary) AML cells in vitro, also independent of the USP7-MDM2-TP53 axis, and MLL-AF9-induced leukemia is significantly delayed in vivo in human leukemia xenografts. We propose a model where USP7 counteracts TRIM27 E3 ligase activity, thereby maintaining PRC1.1 integrity and function. Moreover, USP7 inhibition may be a promising new strategy to treat AML patients.

2021-06-14 | PXD018365 | Pride

Next generation sequencing facilitates transcriptome analyses of mock and RHCG transfected esophageal squamous cell carcinoma cell line KYSE30 cells

Project description:We obtained transcriptome profiling (RNA-seq) of human esophageal squamous cell carcinoma cell line KYSE30 cells stabley transfected with pIRES2-EGFP vector or human RHCG-expression vector by using next generation sequencing.

2019-09-26 | GSE87664 | GEO

TRIM27 mediates protective immunity against tuberculosis by activating host autophagy flux

Project description:Infectious diseases, such as Mycobacterium tuberculosis (Mtb)-caused tuberculosis (TB), remain a global health threat exacerbated by increasing drug resistance. Host-directed therapy (HDT) is a complementing strategy for infection treatment through targeting host immune mechanisms. However, the limited understanding of the host factors and their regulatory mechanisms involved in host immune defense against infections has impeded HDT development. Here, we identify the E3 ubiquitin ligase tripartite motif-containing 27 (TRIM27) elicits host protective immunity against Mtb. Mechanistically, TRIM27 enters host cell nucleus upon Mtb infection to function as a transcription activator of transcription factor EB (TFEB). TRIM27 binds to TFEB promoter and the TFEB transcription factor cAMP responsive element binding protein 1 (CREB1), thus enhancing CREB1-TFEB promoter binding affinity and promoting CREB1 transcription activity towards TFEB, eventually leading to autophagy activation and pathogen clearance. Thus, TRIM27 contributes to host anti-Mtb immunity and targeting TRIM27/CREB1/TFEB axis serves as a promising HDT-based TB treatment.

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