Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription factor induction of vascular blood stem cell niches in vivo [ATAC-Seq 2]

ABSTRACT: We report accessible chromatin genomic regions using ATAC-sequencing of zebrafish double transgenic for kdrl(flk1):mCherry and sele:GFP from FACS-isolated double positive, single positive, and double negative cells collected from whole embryos at 72 hours post fertilization (hpf).

ORGANISM(S): Danio rerio

PROVIDER: GSE227113 | GEO | 2023/03/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

Project description:We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hours post fertilization (hpf).

2023-03-23 | GSE227117 | GEO

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

Project description:We report ATAC-seq data for FACS sorted zebrafish kdrl(flk1):mCherry+;mrc1a(1.3kb):GFP+ double positive cells collected from whole embryos at 72 hours post fertilization (hpf). We also report ATAC-seq data for the single positive fractions and the remaining, transgene negative, portion of the same embryos. The experiment was performed in triplicate.

2023-03-23 | GSE124147 | GEO

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

Project description:We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):GFP positive cells collected from whole embryos at 72 hours post fertilization (hpf).

2023-03-23 | GSE124149 | GEO

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 [scRNA-Seq.Whole-tail]

Project description:We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hours post fertilization (hpf).

2023-03-23 | GSE227118 | GEO

Distinct roles for matrix metalloproteinases 2 and 9 in hematopoietic stem cell emergence, migration and niche colonization

Project description:We report gene expression data for FACS sorted zebrafish mpeg1:mCherry + and mpx:EGFP + cells collected from whole embryos at 72 hours post fertilization (hpf). We also report gene expression data for the remaining, transgene negative, portion of these embryos.

2017-05-19 | GSE93818 | 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

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 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

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