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Status |
Public on Nov 06, 2015 |
Title |
Atac-seq_4hpf |
Sample type |
SRA |
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Source name |
zebrafish embryos
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Organism |
Danio rerio |
Characteristics |
tissue: 4hpf embryos chip antibody: none
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Extracted molecule |
genomic DNA |
Extraction protocol |
phenol/chloroform Ovation Ultralow Library System V2 Workflow (NuGEN)
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
data was mapped using bowtie 1.1.1 Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome v.2 software package was used for peak-calling (FDR < 0.05). In the case of the Atac-Seq the called peaks were not used in the manuscript, however the provided BED file for the ATAC-seq sample was used to generate the figure. Genome_build: zv9 Supplementary_files_format_and_content: cod files with called peaks. The BED files for the H3K4me2 ChIP and ATAC-sq samples were used to generate figures.
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Submission date |
Oct 21, 2015 |
Last update date |
May 15, 2019 |
Contact name |
lucas kaaij |
E-mail(s) |
l.kaaij@imb-mainz.de
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Organization name |
IMB
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Department |
RNA silencing
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Lab |
Rene Ketting
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Street address |
ackermannweg 4
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City |
mainz |
ZIP/Postal code |
55128 |
Country |
Germany |
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Platform ID |
GPL18413 |
Series (2) |
GSE74231 |
Enhancers reside in a unique epigenetic environment during early zebrafish development [ChIP-seq & ATAC-seq] |
GSE74617 |
Enhancers reside in a unique epigenetic environment during early zebrafish development |
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Relations |
BioSample |
SAMN04201227 |
SRA |
SRX1360672 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1915040_Atac-Seq_4hpf_peak.cod.gz |
471.1 Kb |
(ftp)(http) |
COD |
GSM1915040_imb_ketting_2014_02_06_Nextera_43hpf_11_sorted_unique.bed.gz |
27.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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