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Series GSE108961 Query DataSets for GSE108961
Status Public on Jun 22, 2019
Title Single-cell transcriptomics reveals chemotaxis mediated intra-organ crosstalk during cardiogenesis [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We used single-cell RNA-seq to reconstruct differentiation paths of cardiac progenitors in two sequential waves during early heart development. Further analysis identified six major cell types and multiple differentiation trajectories of cardiac progenitors derived from distinct heart fields. We also constructed TF regulatory networks controlling SHF CPC differentiation. Interlineage crosstalk through signaling pathways and chemotactic guidance played a potent role in SHF CPC deployment. The mechanisms regulating SHF CPC migration and differentiation was further confirmed by Nkx2-5 enhancer knock out. Our work provides a cardiac lineage hierarchy and new insights into SHF CPC development. Mechanistically, NKX2-5 directly bound the Cxcr2 genomic locus and activated its transcription.
Overall design We performed NKX2-5 ChIP-seq using an Nkx2-5 allele in which the endogenous gene has been modified to incorporate FLAG and bio (flbio) epitope tags, where bio is specifically biotinylated by the enzyme BirA (He et al. 2014; Zhou et al. 2017). SHF (largely SpM and pharyngeal mesoderm) and HT regions were separately micro-dissected for a modified bioChIP-seq in Nkx2-5flbio/+::Rosa26BirA/+ mouse embryos at E8.25-8.75.
Contributor(s) Xiong H, Luo Y, He A
Citation(s) 31221018
Submission date Jan 09, 2018
Last update date Jun 22, 2019
Contact name Haiqing Xiong
Organization name Peking University
Street address 5 Yiheyuan Road, Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (10)
GSM3637960 flbioNkx2-5_E8.75_FHF_rep1
GSM3637961 flbioNkx2-5_E8.75_FHF_rep2
GSM3637962 flbioNkx2-5_E8.75_FHF_rep3
This SubSeries is part of SuperSeries:
GSE108963 Single-cell transcriptomic analysis reveals lineage hierarcies and communications for second heart lineage deployment
BioProject PRJNA429248
SRA SRP128551

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

Supplementary file Size Download File type/resource
GSE108961_RAW.tar 1.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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