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Series GSE127970 Query DataSets for GSE127970
Status Public on Mar 01, 2020
Title EBF1-mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Crosstalk between mesenchymal stromal cells (MSCs) and hematopoietic stem and cells (HSCs) is essential for hematopoietic homeostasis and lineage output. Ebf1-deficient MSCs have reduced mesenchymal lineage potential. Ebf1 deletion in Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+CD45-CD31-Lin- (PαS) cells in the bone marrow decreased the numbers of HSPCs and myeloid cells. EBF1 in the bone marrow niche regulates a transcriptional program that determines the functional interactions with HSCs and the long-term balance between the myeloid and lymphoid cell fates.
Overall design Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. For the MSC cells isolation, the bone chips were digested with 0.3% collagenase type II and 0.02% DNase I at 37°C for 45 min with gentle shaking. After enzymatic digestion, the cells were filtered, washed with FACS buffer, and stained accordingly. CAR cells were identified as CD45-CD31-Lin-PDGFRα+Sca1-, PαS cells were identified as CD45-CD31-Lin-PDGFRα+ Sca1+. BD FACSAria Fusion was used for fluorescence-activated cell sorting.
Contributor(s) Derecka M, Ramamoorthy S, Grosschedl R
Citation(s) 32066955
Submission date Mar 06, 2019
Last update date Mar 30, 2020
Contact name Senthilkumar Ramamoorthy
Phone 00497615108731
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Cellular & Molecular Immunology
Lab Laboratory Rudolf Grosschedl
Street address Stübeweg 51
City Freiburg
ZIP/Postal code D-79108
Country Germany
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (20)
GSM3659297 CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 1
GSM3659298 CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 2
GSM3659299 CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 3
BioProject PRJNA525888
SRA SRP187777

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Supplementary file Size Download File type/resource 122.5 Mb (ftp)(http) BW 142.2 Mb (ftp)(http) BW
GSE127970_RAW.tar 650.2 Mb (http)(custom) TAR (of BW, TXT) 132.9 Mb (ftp)(http) BW 107.8 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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