Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Danio rerio

PROVIDER: GSE143763 | GEO | 2020/01/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ATACseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

Project description:The goal of this study is to analyse the open chromatin regions via ATACseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. 2000-3000 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. Genomic control DNA was isolated from 30.000 cells using the DNeasy Blood & Tissue kit (Qiagen) and eluted with EB buffer. Tagmentation was performed as described. Fragments were amplified for 9 cycles. Sequencing was performed on a NextSeq machine. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).

2019-06-06 | GSE132258 | GEO

kdrl:eGFP+ ECs isolated from wildtype, etsrp-null, npas4l-null, and sox32-null zebrafish embryos

Project description:Microarray analysis of triplicate RNA samples isolated from kdrl:eGFP-sorted ECs of wildtype, npas4l-/-, etsrp-/-, and sox32-/- zebrafish embryos in Tg(kdrl:EGFP) transgenic background between 18 and 18.5 hpf.

2020-10-20 | E-MTAB-9698 | biostudies-arrayexpress

MCGILL_R4.ATAC-SEQ - samples

Project description:McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)

| EGAD00001001300 | EGA

Loss of kdrl marks the shift from embryonic to adult HSPCs

Project description:Loss of kdrl marks the shift from embryonic to adult HSPCs in zebrafish embryos

2021-04-30 | GSE173100 | GEO

Comparison of the expression profiles of kdrl:mCherry-positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin-positive cells upon injury compared to the rest of cardiac cells.

Project description:Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart, and activated endocardial kdrl:mCherry cells, postnb:citrine fibroblasts and the rest of the cells at 7 days post injury.

2018-03-21 | GSE101200 | GEO

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

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

| PRJNA601524 | ENA

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.

2015-01-15 | E-GEOD-56015 | biostudies-arrayexpress

Gene expression profile at single cell level of kdrl+ FACS sorted cells from WT or flt1 mutant Tg(kdrl:EGFP) zebrafish embryos (3dpf).

Project description:Gene expression profile at single cell level of kdrl+ FACS sorted cells from WT or flt1 mutant Tg(kdrl:EGFP) zebrafish embryos (3dpf).

| PRJNA946665 | ENA

Transcription factor induction of vascular blood stem cell niches in vivo [scRNA-Seq.Adult-Kidney]

Project description:We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):mCherry or kdrl(flk1):GFP positive cells collected from adult kidneys.

2023-03-23 | GSE227115 | GEO

Transcription factor induction of vascular blood stem cell niches in vivo [RNA-Seq]

Project description:We report gene expression data for FACS sorted zebrafish kdrl(flk1):GFP + and kdrl:mCherry+;sele(5.3kb):GFP+ double positive cells collected from whole embryos at 72 hours post fertilization (hpf). We also report gene expression data for the kdrl:GFP negative fraction.

2023-03-23 | GSE124148 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data