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Transcriptome profiling in USP7 inhibitor (P22077)-treated H1299 and HeLa cells

ABSTRACT: Transcriptome profiling in USP7 inhibitor (P22077)-treated H1299 and HeLa cells

PROVIDER: PRJNA883214 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21675560_1.fastq.gz	Fastqsanger.gz
	SRR21675560_2.fastq.gz	Fastqsanger.gz
	SRR21675561_1.fastq.gz	Fastqsanger.gz
	SRR21675561_2.fastq.gz	Fastqsanger.gz
	SRR21675562_1.fastq.gz	Fastqsanger.gz

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Transcriptome profiling in USP7 inhibitor (P22077)-treated H1299 and HeLa cells

Project description:To investigate the molecular pathway signature responsive to pharmacological inhibition of USP7, we analyzed transcriptome in P22077 (a USP7 selective inhibitor)-treated H1299 and HeLa cells.

2023-09-30 | GSE213931 | GEO

Genome-wide maps of acetylated lysine 27 of Histone 3 (ChIP-seq) and gene expression profiling (RNA-seq) in wildtype and USP7-KO H1299 lung cancer lines

Project description:Ubiquitin Specific Protease 7 (USP7), also named as herpesvirus-associated ubiquitin-specific protease (HAUSP), is one of the most abundant deubiquitinase and plays multifaceted roles in many cellular functions, including the protein homeostasis, DNA repair, gene transcription, and oncogenic pathways. To investigate the role of USP7 in p53-deficient lung cancer cells, the CRISPR/Cas9-mediated gene editing was employed to inactivate the USP7 locus in H1299 cells. The alterations of transcriptional enhancers and gene expression were analyzed by H3K27ac ChIP-seq and RNA-seq, respectively, in wildtype and USP7-KO H1299 lung cancer cells.

2021-09-16 | GSE172506 | GEO

Chromatin organization in T-ALL cells upon USP7 inhibitor with or without dexamethasone (Hi-C)

Project description:We report chromatin organization changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin organization change

2022-12-13 | GSE182682 | GEO

Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (ATAC-Seq)

Project description:We report chromatin accessibility changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin accessibility change

2022-12-13 | GSE182681 | GEO

Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (RNA-Seq)

2022-12-13 | GSE182680 | GEO

Reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines.

Project description:To better characterize the effects of USP7 on DNA methylation, we performed reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines. RRBS analysis showed increased DNA methylation in USK7-KO cells and loss of USP7 elevates DNA methylation on pre-existing sites and de novo methylation.

2020-09-07 | GSE136159 | GEO

YG001: A Usp7-Tip60 pathway regulates early adipogenesis

Project description:USP7, a dominant DUB activity in 3T3-L1 adipocytes and in mouse adipose tissue, increases Tip60 protein levels, and deubiquitinates Tip60 both in intact cells and in vitro. Treatment with a pan deubiquitinase (DUB) inhibitor, or knockdown of USP7, decreases adipogenesis. Transcriptome analysis reveals a common set of cell cycle genes to be co-regulated by both Tip60 and USP7. Knock down of either factor results in impaired mitotic clonal expansion, an early step in adipogenesis. These results therefore reveal deubiquitination of a transcriptional coregulator to be a key mechanism in the regulation of early adipogenesis Mature 3T3-L1 adipocytes were subjected to RNAi-mediated knock down with control(C), USP7(U)- or Tip60(T)-specific oligonucleotides. For this, 4 replicates of differentiated 3T3-L1 cells were transfected with Amaxa technology. Two days after transfection cells were washed twice with PBS twice and lysed in 0.5ml Trizol (Invitrogen). mRNA expression of Tip60 and USP7 was assessed by qRT-PCR. Amplified cRNA samples were labeled with either cy3 or cy5 and put on microarray together with and oppositely labeled common reference sample consisting of cRNA derived from undifferentiated 3T3-L1 cells.

2013-08-28 | E-GEOD-28587 | biostudies-arrayexpress

Effect of the USP7 inhibitor HBX41,108 on lipopolysaccharide induced gene expression in mouse bone marrow derived macrophages.

Project description:USP7 is a deubiquitinase enzyme that removes polyubiquitin chains form a number of substrates including MDM2, p53 and NF-κB. In this study we assessed the impact of the USP7 inhibitor HBX41,108 on lipopolysaccharide (LPS) induded transcriptional responses in murine bone marrow derived macrophages.

2020-06-15 | GSE149478 | GEO

Expression data from Hela cells treated with IHSF115, an inhibitor of HSF1.

Project description:Expression data from Hela cells treated with IHSF115, an inhibitor of HSF1.

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Novel, Selective Inhibitors of USP7 Uncover Multiple Mechanisms of Antitumor Activity in Vitro and in Vivo

Project description:The human lung tumor cell line, NCI-H526, was treated with DMSO vehicle control or 0.5 µM of the novel small molecule USP7 inhibitor, USP7-797. At 24 and 48 hour time points, cells were harvested and used for RNA-Seq analysis. In order to identify pathways impacted by USP7 (Ubiquitin Specific Peptidase 7) inhibition, we used RNASeq to profile transcriptomic changes in human lung cancer NCI-H526 cells following treatment with the novel, selective USP7 inhibitor, USP7-797, or control DMSO for 24 or 48 hours. USP7 inhibitor treatment resulted in upregulation of a large number of genes normally silenced by the polycomb repressive complex 2 (PRC2). PRC2, whose components include the proteins EZH2, SUZ12 and EED, trimethylates histone H3 at lysine 27 (H3K27me3). Gene set enrichment analysis showed that the top 10 significantly enriched gene sets are all regulated by this pathway. RNA was extracted from approximately 1 million cells using the Allprep DNA/RNA Mini Kit (Qiagen). Whole transcriptome non-stranded libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina). Sequencing was performed on Illumina NovaSeq using paired-end mode, 200 cycles, targeting 40 million reads per sample.

2020-08-17 | GSE151286 | GEO

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