Unknown,Transcriptomics,Genomics,Proteomics

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Effects of the loss of transmembrane adaptor protein WBP1L on bone marrow transplantation efficiency in mouse analyzed using RNA-Seq

ABSTRACT: Murine WBP1L-deficient (Wbp1l-/-) hematopoietic stem and progenitor cells engraft significantly better than wild-type (WT) cells in competitive transplantation assays. To analyze the mechanism, Wbp1l-/- or WT bone marrow cells (both Ly5.2+Ly5.1-) were each mixed 1:1 with WT competitor cells (Ly5.2+Ly5.1+) and the mixture was transplanted into the lethally irradiated recipient mice. 22 weeks after the transplantation the donor Ly5.2+Ly5.1- LSK cells (Wbp1l-/- or WT) were purified from the bone marrow of recipient mice, RNA was extracted and subjected to RNA sequencing.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Jan Kubovčiak

PROVIDER: E-MTAB-13908 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The mitochondrial superoxide dismutase (SOD2) is a major antioxidant protein which detoxifies superoxide anion radicals generated by mitochondrial respiration (Weisiger and Fridovich, J. Biol. Chem. 1973). We designed a model of oxidative stress-induced anemia caused by SOD2-deficiency (Friedman et al. J. Exp. Med. 2001). Our previous work showed that mice reconstituted with SOD2-deficient hematopoietic stem cells develop an anemia with striking similarity to human sideroblastic anemia (SA) (Friedman et al. Blood 2004; Martin et al. Exp Hematol 2005). Our overall goal was to define early events in the pathogenesis of SOD2-deficiency SA and, in particular, to identify genes involved in the response of erythroid progenitors to oxidative stress. We compared gene expression of sorted TER-119+ CD71+ erythroblasts from SOD2-/- ('KO') versus Sod2+/+ ('WT') hematopoietic stem cell recipients using cDNA microarrays. Samples used in this study were re-hybridized with GLYCOv2 oligonucleotide arrays. GLYCOv2 oligonucleotide arrays are custom Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA) designed for the Functional Glycomics Gateway, collaboration between the Consortium for Functional Glycomics (CFG, http://www.functionalglycomics.org/) and Nature Publishing Group. A complete description of the array can be found at http://www.functionalglycomics.org/static/consortium/resources/resourcecoree.shtml . Hybridization results and quality control details can be found at https://www.functionalglycomics.org/glycomics/publicdata/microarray.jsp , by clicking on the âRaw Dataâ icon link for microarray experiment âJeff Friedman 1: Sod2 KO anemic miceâ. Briefly but importantly, one Sod2-/- sample, which was prepared separately, and whose GAPDH 3'/5' ratio was off range, was legitimately removed from the analysis of the GLYCOv2 and 430 2.0 arrays. Experiment Overall Design: We sorted Sod2-/- and Sod2+/+ size-matched mouse erythroblasts based on the expression of two developmental surface markers, CD71 and TER-119. Total RNA from 4 biological replicates per genotype were extracted and hybridized on 8 Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). After quality controls (see scan protocol), analysis was performed with GeneSifter (VizX Labs, Seattle, WA) using 4 Sod2+/+ (control samples, WT) and 3 Sod2-/- (KO) replicates.

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Effects of the loss of transmembrane adaptor protein WBP1L on bone marrow transplantation efficiency in mouse analyzed using RNA-Seq

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