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Sample GSM2120818 Query DataSets for GSM2120818
Status Public on Nov 14, 2016
Title brain_H3K27ac_ChIP-seq_R1
Sample type SRA
Source name Adult brain, H3K27ac ChIP
Organism Danio rerio
Characteristics strain/background: AB
genotype/variation: wild type
Sex: male
age: adult
tissue: brain
chip antibody: H3K27ac (Abcam ab4729, lot# GR259887-1)
Extracted molecule genomic DNA
Extraction protocol Whole brains, hearts, intestines and testis were dissected from adult male AB zebrafish (brains, hearts and testis = 10-month-old; hearts and intestines = 1-year-old). Two biological replicates were prepared from brain, heart (1-year-old), intestine and testis, whereas one biological replicate was prepared from 10-month-old heart. Each biological replicate was prepared using: 12 brains, 20 hearts, 5 intestines and 8 testis. All tissues were homogenized and cross-linked in 1% formaldehyde, washed and lysed. Chromatin was sheared using a Covaris S220 ultrasonicator to a DNA fragment size of 175 bp (10-month-old samples) or 200 bp (1-year-old samples). ChIP-seq was performed as previously described (Guenther et al. 2008) using 5 ug Abcam H3K27ac antibody (ab4729, lot# GR259887-1) bound to Dynal Protein A linked beads (Invitrogen). Reverse cross-linked and phenol:chloroform purified chromatin was used for single-end library preparation following standard Illumina protocols.
DNA fragments with an average size of 175 bp or 200 bp were used for single-end library preparation following standard Illumina protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description Processed data file: adult_brain_H3K27ac_drerio_super_enhancers.bed
Processed data file: adult_brain_H3K27ac_drerio_typical_enhancers.bed
Processed data file: adult_brain_drerio_H3K27ac_normalized.wig
Data processing Basecalls were performed using CASAVA.
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2-2.1.0 configured for global alignment and allowing 1 mismatch in the seed alignment (seed size = 22). If a read aligned more than once in the genome, only the alignment with the best score was saved for further analyses. Aligned reads were saved in BAM format using samtools (version 0.1.8).
BAM files from biological replicates were merged with samtools and converted to BED format with bedtools (v2.24.0).
Peak calling was performed using SICER (V1.1) with the following parameters: redundancy threshold = 1, window size = 200, fragment size = 175 or 200, effective genome fraction = 0.7, gap size = 600 and FDR = 0.05.
After peak calling, peaks were discarded if 50% of the peak overlapped with the regions comprising 2 Kb upstream and 2 Kb downstream of TSSs (based on RefSeq annotations) and if the peak summit was within these regions.
To identify typical enhancers and super-enhancers, the ROSE algorithm was applied (Whyte et al. 2013; Lovén et al. 2013), setting the -t parameter to 2000.
Genome_build: Zv9
Supplementary_files_format_and_content: BED files with annotations for typical enhancers and super-enhancers were generated using ROSE. Scores represent the H3K27ac density in each enhancer region.
Supplementary_files_format_and_content: WIG file with the H3K27ac profile generated by SICER and normalized by library size per million.
Submission date Apr 12, 2016
Last update date May 15, 2019
Contact name Yuvia Alheli Perez Rico
Organization name Institut Curie
Street address 26 rue d'Ulm
City Paris
ZIP/Postal code 75005
Country France
Platform ID GPL18413
Series (1)
GSE75734 Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
BioSample SAMN04687581
SRA SRX1700604

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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