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Series GSE184432 Query DataSets for GSE184432
Status Public on Sep 22, 2021
Title Scalable Production of Mouse Erythroid Cells using an in vitro Embryoid Body differentiation System [Capture-C]
Organism Mus musculus
Experiment type Other
Summary Mouse embryonic stem (mES) cells can be manipulated ex-vivo to recapitulate the process of erythropoiesis, whereby multipotential haematopoietic stem cells undergo lineage specification, differentiation and maturation to produce functional erythroid cells. Although very useful for identifying specific progenitors and precursors, this cell system has not been fully exploited as a source of cells to analyse erythropoiesis, compared with primary erythroid cells or immortalised cell lines. Here we have established a protocol in which erythroid cells can be isolated in a scalable manner from differentiated embryoid bodies (EBs). Using transcriptional and epigenetic analysis, we show that all purified erythroid cells in this system are derived from the primitive haematopoietic lineage. Finally, we show that this system faithfully recapitulates normal erythropoiesis in the embryonic mouse and fully mimics the effects of natural and engineered mutations seen in full mouse models. Data deposited here comprises chromatin profiling of the EB derived CD71+ erythroid cells; chromatin accessibility (ATAC-Seq), characterisation of the open chromatin by associated histone modifications (ChIP-Seq), chromatin structure (CTCF ChIP-Seq and Capture C interaction data). WT CD71+ cells were compared to either mutant CD71+ cells or other erythroid tissues (mouse adult spleen, E13.5 fetal liver, early embryonic circulating blood) representing both definitve and primitive erythroid lineages.
 
Overall design NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments (DpnII fragment), in this case the Alpha Globin R1 enhancer and promoters of Rhbdf1 and Mpg genes. Purified CD71+ erythroid cells derived from differentiated Wildtype (WT) or mutant mouse Embryonic Stem (mES), D3839, deleted for the CTCF boudary elements at HS-38 and HS-39.5 positions at the Alpha Globin locus (Hanssen L et al, Nature Genetics, 2017) were used in this assay. The profiles produced from WT and D3839 CD71+ cells were then compared.
 
Contributor(s) Kassouf M, Gosden M
Citation(s) 34995303
Submission date Sep 20, 2021
Last update date Jan 12, 2022
Contact name Mira Tony Kassouf
E-mail(s) mira.kassouf@imm.ox.ac.uk
Organization name University of Oxford
Department Weatherall Institute of Molecular Medicine
Lab Doug Higgs
Street address John Radcliffe Hospital, Headly way
City Oxford
State/province England
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (12)
GSM5588950 WT EBd7 CD71+ R1 Capture sample 1(WT_EB8_Enhancers)
GSM5588951 WT EBd7 CD71+ R1 Capture sample 2 (WT_EB9_Enhancers)
GSM5588952 WT EBd7 CD71+ R1 Capture sample 3 (WT_EB11_Enhancers)
This SubSeries is part of SuperSeries:
GSE184435 Scalable Production of Mouse Erythroid Cells using an in vitro Embryoid Body differentiation System
Relations
BioProject PRJNA764670
SRA SRP337859

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE184432_RAW.tar 6.3 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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