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RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

ABSTRACT: RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

PROVIDER: PRJEB43341 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5377830.fastq.gz	Fastqsanger.gz
	ERR5377840_1.fastq.gz	Fastqsanger.gz
	ERR5377840_2.fastq.gz	Fastqsanger.gz
	ERR5377850_1.fastq.gz	Fastqsanger.gz
	ERR5377850_2.fastq.gz	Fastqsanger.gz

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RNA-seq of CN, CN/AML, and CN/AML BAALC KO iPSCs-derived HSPCs

Project description:Severe congenital neutropenia (CN) is a pre-leukemia syndrome that, in the majority of patients, is caused by heterogeneous ELANE mutations encoding neutrophil elastase (NE). To study leukemogenesis associated with CN we generated CN and CN/AML patient-specific induced pluripotent stem cells (iPSCs). Additional mutations in leukemia-relevant genes, CSF3R and RUNX1, were introduced using CRISPR/Cas9 gene-editing. Consequently, we performed in vitro embryoid body (EB)-based hematopoietic and myeloid differentiation of generated iPSC lines. On day 14-17 of EB-based differentiation, iPSC-derived CD45+CD34+ cells were harvested and mRNA was isolated using RNeasy Mini- or Micro Kit (Qiagen). Sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina). Poly (A) selected single-read and pair-read sequencing libraries were sequenced on the Illumina platform in order to compare the transcriptomes of CN and CN/AML iPSCs-derived HSPCs from 2 CN/AML patients. Next, we identified that BAALC knockout resulted in a dramatic induction of granulocytic differentiation and a significant reduction in proliferation of CN/AML iPSC-derived HSPCs. To identify BAALC-dependent leukemia-associated gene expression, we compared the transcriptomes of CN/AML iPSCs before and after BAALC KO using a similar approach described above for CN and CN/AML iPSCs-derived HSPCs.

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