Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 21
Release date: Apr 27 2018
Last update date: Nov 20 2018
Access: Public
Diseases: Leukemia, Leukemia, Myeloid, Precursor Cell Lymphoblastic Leukemia-Lymphoma
Genes: KMT2A, MLLT3, CD34, CD9
Dataset link MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing

Experimental Protocol


For RNA-sequencing, RNA was purified from xenografted leukemic mouse bone marrow and cultured cells using Trizol (Invitrogen) followed by RNeasy kit (Qiagen) as manufacturer’s instructions, and sample quality was evaluated using Agilent RNA 6000 nano chip and Agilent 2100 Bioanalyzer (Agilent, St. Laurent, QC, Canada). More than 2mg of total RNA per sample was submitted for RNA-sequening. For targeted exome sequencing, genomic DNA was extracted from cultured cells and mouse bone marrow cells using the DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany) and analyzed using the TruSight myeloid sequencing panel targeting 54 frequently mutated genes in blood cancers (Illumina, CA, USA). Paired-end sequencing runs were performed on a MiSeq (Illumina) with reagent kit v3 according to manufacturer’s instructions. Paired sequences obtained from each sample were mapped to human genome reference GRCh37/hg19. Variant calls were annotated by Variant Effect Predictor (VEP).

Repositories


GEO

GSE103811

ENA

SRP117581

BioProject

PRJNA407088

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Contact


Johan Jeong