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Sample GSM3362306 Query DataSets for GSM3362306
Status Public on Dec 31, 2018
Title B16F12_H3K14me3
Sample type SRA
 
Source name mouse melanoma cell
Organism Mus musculus
Characteristics cell line: melanoma cell line B16-F12
chip antibody: H3K14me3 (homemade)
Extracted molecule genomic DNA
Extraction protocol Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing base_calling: CASAVA package (Illumina v1.6)
alignment: Bowtie 2 (version 2.2.5) with -p 8 -k 1 -X 1000 and other default parameters
peak_calling: macs2 (version 2.1.1.20160309) with -p 0.00001 --nomodel
Genome_build: mm10
Supplementary_files_format_and_content: bed files including peak locations
 
Submission date Aug 30, 2018
Last update date Dec 31, 2018
Contact name Fei Lan
E-mail(s) fei_lan@fudan.edu.cn
Organization name Fudan university
Street address 130 Dong An Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (2)
GSE119251 H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases [Mm]
GSE119252 H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases
Relations
BioSample SAMN09937941
SRA SRX4625892

Supplementary file Size Download File type/resource
GSM3362306_B16F12_H3K14me3_peaks.bed.gz 156.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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