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Pro-seq of shControl and shRUNX1-ETO Kasumi-1 cells

ABSTRACT: Pro-seq of shControl and shRUNX1-ETO Kasumi-1 cells

PROVIDER: PRJEB38093 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4084570.fastq.gz	Fastqsanger.gz
	ERR4084571.fastq.gz	Fastqsanger.gz
	ERR4084572.fastq.gz	Fastqsanger.gz
	ERR4084573.fastq.gz	Fastqsanger.gz

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Pro-seq of shControl and shRUNX1-ETO Kasumi-1 cells

Project description:RUNX1-ETO knockdown was performed in Kasumi-1 cells and Pro-seq analyses were performed. Control cells (Kasumi-1 shControl) were also analysed and all samples were analysed in duplicates.

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RNA-seq of shControl and shRUNX1-ETO Kasumi-1 cells

Project description:RUNX1-ETO knockdown was performed in Kasumi-1 cells and transcriptomic analyses by RNA-sequencing were performed at two different time points (day2 and day9). Control cells (Kasumi-1 shControl) were also analysed at day2 and day9. All samples were analysed in triplicates.

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RNA-seq of shControl and shRUNX1-ETO Kasumi-1 cells

Project description:RNA-seq of shControl and shRUNX1-ETO Kasumi-1 cells

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Kasumi-1 AML1-ETO knockdown samples

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ATAC-seq analysis of shCtrl and shAML1-ETO Kasumi-1 cells

Project description:Chromatin accessibility was analysed in Kasumi-1 cells after AML1-ETO knock-down and in controls by ATAC-sequencing. The experiments were done in triplicates.

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Project description:Amino Enhancer of Split (AES) is essential for AML1-ETO induced self-renewal and leukemogenesis. To study the effect of AES on transcription regulation in AML1-ETO expressing Kasumi-1 cells, nascent transcripts in control (shctr) and AES knockdown (shAES) Kasumi-1 cells were labelled with uridine analogue 4-thioduridine with subsequent nascent RNA purification and next generation sequencing (Nascent RNA-seq).

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Project description:Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. However, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. Utilizing CRISPR-based genome editing, we inserted a degron tag into the endogenous AML1-ETO locus of Kasumi-1 cells, as well as overexpressed a degradable AML1-ETO protein in CD34+ human cord blood cells. This allowed rapid AML1-ETO protein degradation upon addition of a proteolysis targeting chimera (PROTAC). Furthermore, by combining rapid degradation with nascent transcript analysis (PRO-seq), RNA-seq and Cut&Run, we have defined the core AML1-ETO regulatory network. De-repression of this small set of genes set off a cascade of transcriptional events resulting in myeloid differentiation.

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2009-05-08 | E-GEOD-15648 | biostudies-arrayexpress

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Project description:The goal of this study is to determine the difference in transcriptome expression profils between wild type and AML1-ETO related fusion circular RNA knockdown Kasumi-1 cells

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