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Status |
Public on Nov 14, 2016 |
Title |
intestine_1year_H3K27ac_ChIP-seq_R1 |
Sample type |
SRA |
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Source name |
intestine_1year_H3K27ac_ChIP-seq
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Organism |
Danio rerio |
Characteristics |
strain background: AB genotype/variation: wild type Sex: male age: adult tissue: intestine chip antibody: H3K27ac (Abcam ab4729)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
processed data file adult_1year_intestine_H3K27ac_drerio_super_enhancers.bed adult_1year_intestine_H3K27ac_drerio_typical_enhancers.bed adult_1year_intestine_drerio_H3K27ac_normalized.wig.gz
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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 for 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 region. Supplementary_files_format_and_content: WIG file with the H3K27ac profile generated by SICER and normalized by library size per million.
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Submission date |
Nov 10, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Yuvia Alheli Perez Rico |
E-mail(s) |
yuvia.perez-rico@embl.de
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Organization name |
Institut Curie
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Street address |
26 rue d'Ulm
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City |
Paris |
ZIP/Postal code |
75005 |
Country |
France |
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Platform ID |
GPL18413 |
Series (1) |
GSE75734 |
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes |
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Relations |
BioSample |
SAMN06008943 |
SRA |
SRX2341454 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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