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Sample GSM1953839 Query DataSets for GSM1953839
Status Public on Feb 01, 2016
Title LOX IMVI H3K27Ac
Sample type SRA
 
Source name human melanoma cell lines
Organism Homo sapiens
Characteristics cell line: LOX IMVI
cell type: melanoma
passages: long term culture
chip antibody: H3K27Ac (ab4729) (Abcam)
Growth protocol Human melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 1X108 cells were formaldehyde crosslinked and collected.
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 hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
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
E-mail(s) zon@enders.tch.harvard.edu
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 GPL16791
Series (2)
GSE75352 A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [human cell line ChIP-seq]
GSE75356 A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation
Relations
BioSample SAMN04292905
SRA SRX1451225

Supplementary file Size Download File type/resource
GSM1953839_CKK3_peaks.narrowPeak.gz 2.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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