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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Danio rerio

PROVIDER: GSE132260 | GEO | 2019/06/06

REPOSITORIES: GEO

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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

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

Project description:The goal of this study is to perform RNAseq 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. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used to generate SMARTer libraries for low-input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. 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). Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1). To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).

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

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

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

Project description:ATACseq and RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

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

Project description:RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

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