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| Status |
Public on Jun 06, 2019 |
| Title |
ATACseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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).
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| Overall design |
Analysis of 5 different cell types; DN (double negative), SP-kdrl (single positive), DP-R1lo (double positive runx1 low expression), DP-R1med (runx1 medium expressionand) and DP-R1hi (runx1 high expression) in TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, in triplicates, NextSeq with a 75 bp paired end
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| Contributor(s) |
Bonkhofer F, Rispoli R |
| Citation(s) |
31395869 |
| |
| Submission date |
Jun 05, 2019 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Florian Bonkhofer |
| Organization name |
Oxford University
|
| Street address |
John Radcliffe Hospital/Headley Way
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE132260 |
ATACseq and RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
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| Relations |
| BioProject |
PRJNA547065 |
| SRA |
SRP200562 |
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