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Sample GSM1915040 Query DataSets for GSM1915040
Status Public on Nov 06, 2015
Title Atac-seq_4hpf
Sample type SRA
 
Source name zebrafish embryos
Organism Danio rerio
Characteristics tissue: 4hpf embryos
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol phenol/chloroform
Ovation Ultralow Library System V2 Workflow (NuGEN)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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.
 
Submission date Oct 21, 2015
Last update date May 15, 2019
Contact name lucas kaaij
E-mail(s) l.kaaij@imb-mainz.de
Organization name IMB
Department RNA silencing
Lab Rene Ketting
Street address ackermannweg 4
City mainz
ZIP/Postal code 55128
Country Germany
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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