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UMCG Stem Cells ILM6v1.1 (Apr09) original
Accession number: GN149
Summary
The UMCG Hematopoietic cells datasets allow to search for differential expression of mRNA transcripts across a large subset of the BXD recombinant inbred strains. Prior studies have indicated and collected many hematopoietic phenotypes for which the parental C57BL/6 and DBA/2 strains differ. Total RNA collected from four distinct bone marrow cell populations was hybridized to Illumina Sentrix Mouse-6 BeadChips.
About the cases used to generate this set of data
Samples were collected from BXD recombinant inbred strains.
About the tissue used to generate these data
Bone marrow cells were flushed from femurs and stained with a collection of antibodies to detect defined hematopoietic cell populations. Four datasets are available:
1. Hematopoietic stem cells. These cells were isolated by flowcytometry using a MoFlow high speed cell sorter. Cells were stained with a panel of antibodies directed against lineage-specific markers, in combination with antibodies directed against c-kit and Sca-1. Purified cells were Lin-, Sca1+, and ckit+ (LSK cells). All long term repopulating stem cells are contained in the fraction of cells.
2. Hematopoietic progenitor cells. These cells were similarly isolated but were defined by a Lin-Sca1-ckit+ phenotype. These Sca1- cells are devoid of long term repopulating activity, but are highly enriched for progenitors.
3. Erythroid cells. These cells were isolated based on the expression of the erythroid antigen Ter119.
4. Myeloid cells. These cells were isolated based on the expression of the myeloid antigen Gr-1.
Cells were immediately sorted in RNA lysis buffer and RNA was isolated using the Rneasy Mini Kit (Qiagen, www.qiagen.com). RNA samples were stored at -80 C, and were shipped to ServiceXS (Leiden, the Netherlands, http://www.servicexs.com/) where hybridizations were performed.
About the array platform
RNA samples were randomly distributed according to strain and cell type across Illumina Sentrix Mouse-6 BeadChips.
About data processing
The data were pre-processed using Illumina BeadStudio software. The AVG_Signal values from the Gene profiles of all 4 cell types samples were gathered and submitted to a quantile normalization using the Bioconductor Affy package (Bolstad et al, Bioinformatics (2003). The Apr09 datasets were hybridized in two large series. The Apr09 dataset has not yet been corrected for potential batch effects.
Data source acknowledgment
Cells and RNA were collected by Ellen Weersing, Bert Dontje, Alice Gerrits, Leonid Bystrykh and Gerald de Haan, at the Department of Cell Biology, University Medical Center Groningen, the Netherlands. Cells were flow-sorted at the central flowcytometry facility of the UMCG with technical assistance from Geert Mesander and Henk Moes. Hybridizations were carried out by ServiceXS (Leiden, the Netherlands, http://www.servicexs.com/). Normalizations and preprocessing was carried out by Bruno Tesson, Yang Li, Rainer Breitling and Ritsert Jansen at the Department of Bioinformatics, University of Groningen, the Netherlands.
Financial support for this project was provided through VICI-awards to Ritsert Jansen and Gerald de Haan by the Netherlands Organization for Scientific Research (NWO) and by a Horizon-grant awarded to GdH by the Netherlands Genomics Initiative (http://www.genomics.nl/).
Contact address
Gerald de Haan, Department of Cell Biology, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands. (g.de.haan@med.umcg.nl). (http://www.rug.nl/umcg/faculteit/disciplinegroepen/celbiologie/stamcelbiologie/index)
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