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| Status |
Public on Jan 29, 2016 |
| Title |
ATAC-seq_tet123_MO_rep2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 24hpf
genetic background: mixed AB and Tübingen
transgenic embryos: Morpholino against Tet1/Tet2/Tet3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq experiments were performed as previously described (Buenrostro et al. 2013). Briefly, 10 zebrafish embryos were manually dechorionated and disrupted in 500 µl of Ginzburg Fish Ringers (55 mM NaCl, 1.8 mM KCl, 1.25 mM NaHCO3). After washing with cold PBS, 75.000 cells were lysed (lysis buffer: 10 µM Tris pH7.4, 10 µM NaCl, 3 µM MgCl2, 0.1% IGEPAL) and incubated for 30 min at 37ºC with the TDE1 enzyme. The sample was then purified with Qiagen Minelute kit, and a PCR was performed with 13 cycles using Ad1F and Ad2.1R primers and KAPA HiFi hotstart enzyme (Kapa Biosystems).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ATAC-seq
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| Data processing |
ATAC-seq library was sequenced on the Illumina Hi-seq 2000 sequencing platform. Reads were aligned using zebrafish July 2010 assembly (danRer7) as the reference genome. Duplicated pairs or those ones separated by more than 2Kb were removed. The enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
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| Submission date |
Aug 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ozren Bogdanovic |
| E-mail(s) |
o.bogdanovic@gmail.com
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| Organization name |
Garvan Institute of Medical Research
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| Department |
Genomics and Epigenetics
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| Street address |
384 Victoria Street
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE68087 |
Active DNA demethylation at enhancers during the vertebrate phylotypic period |
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| Relations |
| BioSample |
SAMN04009184 |
| SRA |
SRX1162716 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1859510_ATAC-seq_tet123_MO_rep2.bed.gz |
139.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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