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Series GSE128743 Query DataSets for GSE128743
Status Public on Mar 01, 2020
Title EBF-1 mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Here, we investigate the role of Early B-cell factor 1 (EBF1) in MSCs to support hematopoiesis. Ebf1 deletion in Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+CD45-CD31-Lin- (PαS) cells in the bone marrow decreases the numbers of HSCs and myeloid cells. Single cell and bulk transcriptome analysis, combined with analysis of chromatin accessibility in EBF1-deficient MSCs revealed decreased expression of adhesion molecules and altered niche composition. In consequence, HSCs exposed to the EBF1-deficient niche, exhibit altered chromatin accessibility and impaired occupancy by myeloid regulators like AP-1, ETS and IRF.
Overall design Single cells from the bone marrow stroma as well as hematopoietic progenitors were sorted into 384-well plates and processed using a modified version of the CEL-Seq2 protocol (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8).
Contributor(s) Derecka M, Herman JS, Ramamoorthy S, Cauchy P, Lupar E, Grϋn D, Grosschedl R
Citation(s) 32066955
Submission date Mar 22, 2019
Last update date Jun 01, 2020
Contact name Josip Stefan Herman
Phone 00497615108725
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Quantitative Single Cell Biology
Lab Research Group Dominic Grün
Street address Stuebeweg 51
City Freiburg im Breisgau
ZIP/Postal code D-79108
Country Germany
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (74)
GSM3684264 CARko_5
GSM3684265 CARko_6
GSM3684266 CARko_7
BioProject PRJNA528662
SRA SRP189280

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Supplementary file Size Download File type/resource
GSE128743_RAW.tar 31.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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