Whole-genome sequencing of chromatin in Hacat cells overexpressing WT1
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ABSTRACT:
PROVIDER: PRJNA598847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10823730_1.fastq.gz | Fastqsanger.gz | |||
| SRR10823730_2.fastq.gz | Fastqsanger.gz | |||
| SRR10823731_1.fastq.gz | Fastqsanger.gz | |||
| SRR10823731_2.fastq.gz | Fastqsanger.gz | |||
| SRR10823732_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the application of chip sequencing in the search for target genes of transcription factor .Chip-seq efficiently detect genome-wide segments of DNA interacting with transcription factors.We overexpressed the transcription factor WT1 in hacat cells, and then performed chip experiments to collect the DNA fragments bound to WT1, which were then sequenced.Finally, we proved that interleukinin is the target gene of WT1, providing a new target for clinical research and treatment of skin diseases.
2023-01-03 | GSE142992 | GEO
Project description:Purpose: The aim was to find the differentially expressed genes between the WT1 overexpressed group and the control group Methods:Hacat cell was transfected with WT1 overexpressed plasmids and blank plasmids, then RNA from both groups of cells was sequenced. The data obtained from the sequencing is called raw reads, and then the raw reads are subject to quality control QC. After the quality control is passed, the filtered clean reads are compared to the reference genome, This was followed by gene Quantitative analysis, gene expression level based analyses, and more in depth mining analyses such as GO functional significance enrichment analysis and pathway significance enrichment analysis for the selected differentially expressed genes between samples. Conclusions:Our study was the first to analyze the transcriptome of Hacat cells overexpressing WT1 generated by RNA-seq technique and to conduct biological replication. Six samples were measured using BGISEQ-500 platform, and the average output of each sample was 21.89 m. The average ratio of sample to genome was 94.81% . A total of 17,693 genes were detected. A total of 181 differentially expressed genes between the two groups were analyzed by GO and Kegg.
2023-01-03 | GSE142985 | GEO
Project description:Transciptional heterogeneity of scar-orchestrating cells in liver fibrosis, defined by WT1 expression, after chronic tetrachloride injury in vivo (WT1-high and WT1-low) or activation in vitro (WT1-negative).
2019-08-21 | GSE103055 | GEO
Project description:Investigation of the transcriptional profile of SNAI2-overexpressing HaCaT cells.
2021-09-01 | GSE166199 | GEO
Project description:During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.
2022-03-08 | GSE179521 | GEO
Project description:During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.
2022-03-08 | GSE179520 | GEO
Project description:We identified binding sites of the Wilms' tumor suppressor protein WT1 in the mouse podocyte genome in vivo by ChIP-seq. Furthermore, we provide a podocyte transcriptome derived from primary podocytes that were isolated by FACS on mouse glomeruli. In short, we show that WT1 activates a highly specific podocyte transcriptome by binding to putative podocyte-specific enhancers and TSS of target genes. Genes bound by WT1 in podocytes include the majority of genes mutated in hereditary podocytopathies as well as components of the slit diaphragm, actin cytoskeleton, extracellular matrix, and within endocytosis pathways. Furthermore, we infer a podocyte TF network from DNA-binding motifs enriched at WT1-bound loci that includes Tead, Lmx1b, Mafb, Tcf21, and Fox-class transcription factors.
2014-12-11 | GSE64063 | GEO
Project description:K-ras is one of the most frequently mutated human oncogenes. Activation of K-ras can lead to either senescence or proliferation in primary cells. The precise mechanism governing these distinct outcomes remains unclear. Here we utilized a loss-of-function screen to assess the role of specific genes identified as potential key regulators of K-ras driven oncogenesis. Using this approach, we identify the transcription factor Wt1 as an inhibitor of senescence in primary cells expressing oncogenic K-ras. Deletion or suppression of Wt1 expression leads to senescence of primary cells expressing oncogenic K-ras under the control of the native promotor at physiological levels, but has no effect on cells expressing wild-type K-ras. Wt1 contributes to K-ras driven lung tumorigenesis in vivo and loss of Wt1 is specifically deleterious to human lung cancer cell lines that are dependent on oncogenic K-ras. Taken together, these observations reveal a novel role for Wt1 as a key regulator of the complex genetic network required for the oncogenic effect of the small GTPase K-ras. We compare the expression profiles of Wild type, K-ras mutant, Wt1-null, and double K-ras mutant/Wt1-null mouse embryonic fibroblasts (MEFs). The study provides insights into the transcriptional role of Wt1 in the context of oncogenic K-ras.
2010-03-01 | GSE15325 | GEO
Project description:The present study was designed to use small interfering RNA (siRNA) approach to identify the effects of NCSTN silencing on human immortal keratinocyte cell line, HaCaT. The alteration of gene expression profiles after NCSTN gene silencing in HaCaT cells was investigated employing Agilent whole genome microarray
2018-04-28 | GSE68346 | GEO
Project description:Interventions: A patient is vaccinated with Montanide ISA51-adjuvanted WT1 Trio cancer vaccine consisting of two WT1 CTL peptides (WT1-126 and WT1-235) and one WT1 HTL peptide (WT1-332) (2mg each) seven times at the interval of two weeks.
Primary outcome(s): Induction of WT1-specific immune responses assessed by WT1-related tests such as WT1-DTH skin reaction and serum levels of WT1 peptide IgG autoantibody at 1M, 2M, and 3M of WT1 Trio vaccine.
Study Design: Single arm Non-randomized
| 2638832 | ecrin-mdr-crc