Comment[ArrayExpressAccession]	E-MTAB-1628
MAGE-TAB Version	1.1
Investigation Title	Imprinting RNAseq
Comment[Submitted Name]	Imprinting RNAseq
Experiment Description	Long-term hematopoietic stem cells (HSCs), short-term HSCs and multipotent progenitor cells (MPPs) were isolated from bone marrow of four mouse strains (WT, H19-deletion, Igf1r-deletion, and double-deletion) and  expression profiled with RNAseq.  The behavior of the transcriptomes, and in particular the imprinted genes, was analyzed to see what might be involved in maintaining quiescence of long-term stem cells, and how H19 and Igf1r affected the expression of imprinted genes. Transcriptional profiling data of the same cells have been deposited in ArrayExpress under accession number E-MTAB-1644 (http://wwwdev.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1644/).
Experimental Design	cell_type_comparison_design	strain_or_line_design	reference_design	co-expression_design
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[AEExperimentDisplayName]	RNA-seq of coding RNA of mouse long term hematopoietic stem cells, short term hematopoietic stem cells and hematopoietic multipotent progenitor cells to investigate maternal-specific imprinting in the H19-Igf2 locus
Experimental Factor Name	genotype	cell type
Experimental Factor Type	genotype	cell type
Quality Control Type
Quality Control Term Source REF	EFO
Public Release Date	2013-08-12
Person Last Name	Paulson
Person First Name	Ariel
Person Mid Initials
Person Email	apa@stowers-institute.org
Person Phone
Person Address
Person Affiliation	Stowers Institute for Medical Research
Person Roles	submitter
PubMed ID	23863936
Publication Author List	Venkatraman A, He XC, Thorvaldsen JL, Sugimura R, Perry JM, Tao F, Zhao M, Christenson MK, Sanchez R, Yu JY, Peng L, Haug JS, Paulson A, Li H, Zhong XB, Clemens TL, Bartolomei MS, Li L
Publication Title	Maternal imprinting at the H19–Igf2 locus maintains adult haematopoietic stem cell quiescence
Publication Status	Under review
Protocol Name	P-MTAB-33139	P-MTAB-33140	P-MTAB-33141	P-MTAB-33142	P-MTAB-33143	P-MTAB-33144	P-MTAB-33145
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol	normalization data transformation protocol
Protocol Description	All mice used in this study were housed in the animal facility at the Stowers Institute for Medical Research (SIMR) and handled according to SIMR and National Institutes of Health (NIH) guidelines. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of SIMR. H19-DMR flDMR/flDMR mice on B6 background were kindly provided by Dr. Marisa S. Bartolomei (University of Pennsylvania Perelman School of Medicine). Conditional mutant Igf1rfl/+ was kindly provided by Thomas L Clemens (Center for Musculoskeletal Research, Johns Hopkins Medicine, 601 North Caroline Street, Baltimore, MD 21287). Interferon inducible Mx1-Cre or tamoxifen inducible Scl-Cre mouse strains were used to delete the floxed H19-DMR and Igf1r. For Mx1-Cre activation, 250ug of pIpC was injected intraperitoneal every other day for 14 days at 5 weeks of age. For Scl-CreER activation, 2mg tamoxifen dissolved in 0.1 ml of corn oil was injected intraperitoneal every day for 5 days. 		Illumina TruSeq RNA Sample Prep Kit (Catalog #: FC-122-1001)	The RNA-sequencing library was prepared from approximately 200 ng of total RNA (mH19dDMR/+  Igf1r-/- , mH19dDMR/+Igf1rf-/- and mH19flDMR/+) for each sample.  The fragment size in the generated library ranged from 220 to 500 bps with a peak at 280 bps.	A total of 10 fmol library fragments were loaded to cBot to generate clusters, followed by sequencing on an Illumina HiSeq 2000 to produce 10-30 million paired-end 100 bp reads per sample.	Reads were trimmed to 70bp due to quality and aligned to mm9 with Tophat 1.3.1 / Bowtie 0.12.7, using the Ensembl 63 GTF file for gene models.  Parameters were -g 1 --mate-inner-dist 200 --mate-std-dev 70 --segment-length 35 --segment-mismatches 2; this allows for 4 mismatches per read (two per read half) and unique alignments only.	Final gene expression quantitation was done with Cufflinks 1.3.0, Ensembl 66 GTF, additional parameter --max-mle-iterations 10000.
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Hardware					Illumina HiSeq 2000
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo	http://www.ebi.ac.uk/arrayexpress
Comment[SecondaryAccession]	ERP003264
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR296698-ERR296709
SDRF File	E-MTAB-1628.sdrf.txt