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ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

ABSTRACT: ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

PROVIDER: PRJNA601524 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10901452_1.fastq.gz	Fastqsanger.gz
	SRR10901452_2.fastq.gz	Fastqsanger.gz
	SRR10901453_1.fastq.gz	Fastqsanger.gz
	SRR10901453_2.fastq.gz	Fastqsanger.gz
	SRR10901454_1.fastq.gz	Fastqsanger.gz

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ATACseq of kdrl-GFP+ endothelial cells in 28hpf zebrafish embryos

Project description:The goal of this study is to analyse the open chromatin regions via ATACseq in zebrafish embryonic endothelial cells at 26-27hpf using Tg(Kdrl:GFP) transgenic zebrafish embryos. 40000-50000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.

2020-01-16 | GSE143763 | GEO

Runx+ HSPC, kdrl+ endothelial, and negative cells sorted from DMSO- or Lycorine-treated 3 dpf zebrafish embryos

Project description:The zebrafish is a powerful model for the study of hematopoietic stem and progenitor cells (HSPC). We have developed a novel HSPC-specific transgenic line (Runx1+23:GFP). We have used this line in time-lapse live imaging studies to track the migration of HSPC during development. We have also performed a chemical genetic screen to find small molecules that modulate HSPC numbers during development. Treating embryos from 2-3 days post fertilization (2-3 dpf) then fixing for in situ staining with HSPC probes cmyb and runx1, we found the compound lycorine increased HSPC numbers. Applying this compound during time-lapse live imaging showed increased accumulation of Runx+ HSPC in the caudal hematopoietic tissue (CHT). Treatment from 2-3 dpf, then washing off the compound, had a sustained effect on the size of the HSPC with Runx+ numbers higher at 5 and 7 dpf. We have performed microarray analysis to elucidate the molecular changes within HSPC and endothelial cells after Lycorine treatment. We treated Runx1+23:GFP;kdrl:DsRed2 embryos from 2-3 dpf with 75 uM lycorine in 1% DMSO. We then dissociated the embryos and sorted the Runx+ GFP cells, the kdrl+ DsRed2 cells, and the non-fluorescent negative cells from the total embryo as a comparator population. Total RNA was amplified and biotin labled for hybridization on Affymetrix microarrays. 18 samples were collected and analyzed. There are 3 biological replicates. There are 3 cell type populations: 1) Runx+ HSPC; 2) kdrl+ endothelial cells; 3) non-fluorescent negative cells. There are cell populations from dissociated Lycorine-treated embryo pools, and control DMSO-treated embryo pools.

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| PRJNA946665 | ENA

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