|
| Status |
Public on May 13, 2016 |
| Title |
Regenerating zebrafish hearts H3K27Ac ChIP-Seq, 2 |
| Sample type |
SRA |
| |
|
| Source name |
Regenerating zebrafish hearts
|
| Organism |
Danio rerio |
| Characteristics |
injury conditions: Whole hearts following genetic ablation of cardiomyocytes by recombination of ZCAT fish with tamoxifen
days post injury: 7 days post incubation with tamoxifen
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_treat_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 |
SAMN04998959 |
| SRA |
SRX1760525 |
