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Sample GSM1953851 Query DataSets for GSM1953851
Status Public on Feb 01, 2016
Title Zcrest H3K27Ac
Sample type SRA
Source name zebrafish melanoma tumor cell line zcrest 1
Organism Danio rerio
Characteristics cell type: zebrafish melanoma tumor cell line
passages: > 20 passages
chip antibody: H3K27Ac (ab4729) (Abcam)
genotype of founder fish: p53/BRAF/Na; crestin:EGFP, MiniCoopR alone
Growth protocol Zebrafish melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 3-5X10^7 cells were formaldehyde crosslinked and collected. The primary melanoma was generated in a p53/BRAF/Na zebrafish injected with MiniCoopR;mitf:EGFP control Tol2 plasmid as in Ceol, Houvras, et al, Nature, 2011. The bulk tumor was carefully dissected and manually dissociated with a razor blade and trypsinized prior to formaldehyde crosslinking.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed using the methods of T. I. Lee, S. E. Johnstone, R. A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 1, 729–748 (2006).
Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description ChIP'ed genomic DNA
Data processing ChIP-Seq aligned to zebrafish Zv9 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: Zv9
Supplementary_files_format_and_content: called peaked in narrowPeak bed file
Submission date Nov 24, 2015
Last update date May 15, 2019
Contact name Leonard Zon
Organization name Boston Children's Hospital
Department Oncology/Hematology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL18413
Series (2)
GSE75353 A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish ChIP-seq]
GSE75356 A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation
BioSample SAMN04292917
SRA SRX1451237

Supplementary file Size Download File type/resource
GSM1953851_CKK2_11_peaks.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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