Comment[ArrayExpressAccession]	E-GEOD-64545
MAGE-TAB Version	1.1	
Public Release Date	2015-01-15
Investigation Title	Msi2 sustains the MLL leukemia stem cell regulatory program	
Comment[Submitted Name]	Msi2 sustains the MLL leukemia stem cell regulatory program
Experiment Description	Leukemia stem cells (LSCs) are found in most aggressive myeloid diseases and contribute to therapeutic resistance. Genetic and epigenetic alterations cause a dysregulated developmental program in leukemia. The MSI2 RNA binding protein has been previously shown to predict poor survival in leukemia. We demonstrate that the conditional deletion of Msi2 results in delayed leukemogenesis, reduced disease burden and a loss of LSC function. Gene expression profiling of the Msi2 ablated LSCs demonstrates a loss of the HSC/LSC and an increase in the differentiation program. The gene signature from the Msi2 deleted LSCs correlates with survival in AML patients. MSI2’s maintains the MLL self-renewal program by interacting with and retaining efficient translation of Hoxa9, Myc and Ikzf2. We further demonstrate that shRNA depletion of the MLL target gene Ikzf2 also contributes to MLL leukemia cell survival. Our data provides evidence that MSI2 controls efficient translation of the oncogenic LSC self-renewal program and a rationale for clinically targeting MSI2 in myeloid leukemia. RNA-Seq was performed on sorted c-Kit high leukemic cells from 2 Msi2 -/- and 2 Msi2 f/f mice.	
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl
Person Last Name	Lu	Kharas
Person First Name	Yuheng	Michael
Person Mid Initials		G
Person Email	geo@ncbi.nlm.nih.gov	
Person Affiliation	Memorial Sloan Kettering Cancer Center	
Person Address	Memorial Sloan Kettering Cancer Center, 417 East 68th Street, New York, NY, USA	
Person Roles	submitter	
Protocol Name	P-GSE64545-2	P-GSE64545-1
Protocol Description	Paired-end RNA-Seq reads were first processed with Trimmomatic to remove TruSeq adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded. Trimmed reads were then aligned to mm9 genome with the STAR aligner. The number of uniquely mapped reads overlapping with each RefSeq gene was counted with HTSeq. We used DESeq to evaluate the differences in expression between Msi2 KO and control samples, which were represented with log2 fold change and Benjamini-Hocheberg corrected p-values. Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files including gene-wise read counts for each sample	RNA was extracted using Trizol and RNeasy RNA extraction kit. Samples were prepared with a standard Illumina kit using the TruSeq RNA SamplePrep Guide. mRNA fragments with a length of 200–300 bp were selected for library construction. Sequencing was performed on a Hiseq2000 platform using a standard paired-end protocol.
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol
Experimental Factor Name	genotype	
Experimental Factor Type	genotype	
Comment[SecondaryAccession]	GSE64545	
Comment[GEOReleaseDate]	2015-01-15	
Comment[ArrayExpressSubmissionDate]	2014-12-29	
Comment[GEOLastUpdateDate]	2015-03-27	
Comment[AEExperimentType]	RNA-seq of coding RNA	
Comment[SecondaryAccession]	SRP051590	
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1736005-SRR1736008	
SDRF File	E-GEOD-64545.sdrf.txt