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Sample GSM2152259 Query DataSets for GSM2152259
Status Public on May 13, 2016
Title Uninjured zebrafish hearts H3K27Ac ChIP-Seq, 2
Sample type SRA
 
Source name Uninjured zebrafish hearts
Organism Danio rerio
Characteristics injury conditions: Whole hearts following treatment of ZCAT fish with vehicle
days post injury: 7 days post incubation with vehicle
antibody: H3K27Ac (Active Motif)
Extracted molecule genomic DNA
Extraction protocol Ablation protocol: bact2:loxP-mCherry-stop-loxP-DTA;cmcl2:CreER zebrafish were treated with tamoxifen or vehicle
Hearts were extracted 7 days post incubation. Ventricles were dissected and rinsed in heparin.
ChIP was performed after sonication using the MagnifyChIP kit using. ChIP was done using an antibody directed against H3K27Ac (ActiveMotif).
Bowman, S. K. et al. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics 14, 466 (2013)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description differential_ac_genome_corrected_control_afterfiting_all.wig.gz
Data processing Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2
Differential peaks were identified using MACS with parameters effective genome size = 1.70e+09; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05; Range for calculating regional lambda is: 1000 bps and 10000 bps
Genome_build: zv9
 
Submission date May 13, 2016
Last update date May 15, 2019
Contact name Ravi Karra
E-mail(s) ravi.karra@duke.edu
Organization name Duke
Department Cell Biology
Lab Poss
Street address 464 Nanaline Duke, 307 Research Drive
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL14875
Series (1)
GSE75894 Modulation of tissue repair by regeneration enhancer elements.
Relations
BioSample SAMN04998962
SRA SRX1760527

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

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