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Series GSE186425 Query DataSets for GSE186425
Status Public on Jun 06, 2023
Title Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT-seq]
Organism Danio rerio
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis.
Overall design Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but where and how HSPC heterogeneity occurs remain unclear. Here, we performed scRNA-seq and scATAC-seq with zebrafish 36 hpf VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish, we performed STRT-seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency, we performed scRNA-seq with the sorted ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC, we examined genome-wide spi2 binding by cut-tag assay in fli1a-flag-spi2-EGFP+ cells sorted from trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.
Contributor(s) Xia J
Citation(s) 37016019
Submission date Oct 22, 2021
Last update date Jun 20, 2023
Contact name Zhixin Kang
Phone +86-01064807562
Lab Group of Hematopoiesis and Cardiovascular Development
Street address 1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
Platforms (1)
GPL24995 Illumina NovaSeq 6000 (Danio rerio)
Samples (3)
GSM7083138 DP1_36hpf
GSM7083139 DP2_36hpf
GSM7083140 SP_36hpf
This SubSeries is part of SuperSeries:
GSE186427 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity
BioProject PRJNA773778
SRA SRP342737

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

Supplementary file Size Download File type/resource
GSE186425_Barcodes_and_Cell_information.xlsx 112.9 Kb (ftp)(http) XLSX
GSE186425_Zebrafish.STRT-seq.txt.gz 604.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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