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Sample GSM3362305 Query DataSets for GSM3362305
Status Public on Dec 31, 2018
Title HEK293T_Input
Sample type SRA
 
Source name HEK293T
Organism Homo sapiens
Characteristics cell line: embryonic kidney cell line HEK293T
chip antibody: none
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 Illumina HiSeq 2500
 
Data processing base_calling: CASAVA package (Illumina v1.6)
alignment: Bowtie (version 1.2.1.1) with -m 1 and other default parameters
peak_calling: macs14 (1.4.2 20120305) with -p 0.00001 --nomodel
Genome_build: hg19
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 GPL16791
Series (2)
GSE119250 H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases [Hs]
GSE119252 H3K14me3 Genomic Distributions and its regulation by KDM4 family demethylases
Relations
BioSample SAMN09937904
SRA SRX4625891

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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