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RNA-seq following shRNA-mediated knock-down of ETV6-RUNX1 in the B-ALL cell line Reh

ABSTRACT: RNA-seq following shRNA-mediated knock-down of ETV6-RUNX1 in the B-ALL cell line Reh

PROVIDER: PRJEB44088 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5643680_1.fastq.gz	Fastqsanger.gz
	ERR5643680_2.fastq.gz	Fastqsanger.gz
	ERR5643681_1.fastq.gz	Fastqsanger.gz
	ERR5643681_2.fastq.gz	Fastqsanger.gz
	ERR5643672_1.fastq.gz	Fastqsanger.gz

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RNA-seq following shRNA-mediated knock-down of ETV6-RUNX1 in the B-ALL cell line Reh

Project description:Stable derivatives of the Reh cell line carrying inducible shRNAs were generated by transducing with lentivirus harbouring the pTRIPZ vector and enabling doxycycline-inducible expression of shRNAs together with an RFP reporter. Two independent lines carrying different shRNAs targeting ETV6 or a vector control were generated. Cells were treated for 0 or 7 days with doxycycline, and harvested for bulk RNA-seq.

2022-04-10 | E-MTAB-10308 | biostudies-arrayexpress

Identification of ETV6 bound protein by affinity purification of ETV6-HA fusion protein in REH cells

Project description:To determine the protein partners of ETV6, we expressed ETV6 and HA-tagged ETV6 in Reh pre-B leukemic cells. Anti-HA magnetic beads were used for affinity purification of ETV6-HA (and ETV6 control) from the nuclear and cytoplasmic fraction. Following purification on-beads digest and LC-MS/MS experiments were performed at the Proteomics platform of the CHU de Quebec Research Center, Quebec, Canada.

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Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

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Expression data from ETV6-RUNX1-positive Reh leukemic cells after overexpression of miR-125b, miR-100 and miR-99a levels in different combinations

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Expression data from ETV6-RUNX1-positive Reh leukemic cells after overexpression of miR-125b, miR-100 and miR-99a levels in different combinations

Project description:Combined overexpression of miR-125b with miR-99a and/or miR-100 induced VCR resistance in ETV6-RUNX1-positive leukemic cells Reh. We used microarrays to detail the global changes in gene expression of Reh cells upon enforced expression of miR-125 per se compared with combination of overexpression of miR-125b, miR-100 and/or miR-99a MiR-99a and/or miR-100 were transiently overexpressed in stable miR-125b-expressing and stable scrambled miR-control-expressing Reh cells. Cellular resistance to VCR was determined by MTT assay after incubating the cells with 9 ng/mL VCR for 3 days. Changes in the gene expression pattern of Reh cells induced by miRNAs overexpression were measured using Affymetrix Arrays.

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Project description:Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. An ETV6/RUNX1 expression signature was established, consisting of 596 lncRNAs (434 up and 162 down) using expression analysis of a series of primary patient samples. Subsequently, RNA sequencing from BCP-ALL cell lines and shRNA-mediated silencing of ETV6/RUNX1, illustrated that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are bona fide ETV6/RUNX1 targets and could serve as novel biomarkers of this prevalent subtype of human leukemia.

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