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| Status |
Public on Dec 31, 2018 |
| Title |
HEK293T_H3K14me3 |
| Sample type |
SRA |
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| Source name |
HEK293T
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| Organism |
Homo sapiens |
| Characteristics |
cell line: embryonic kidney cell line HEK293T
chip antibody: H3K14me3 (homemade)
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Aug 30, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Fei Lan |
| E-mail(s) |
fei_lan@fudan.edu.cn
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| Organization name |
Fudan university
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| Street address |
130 Dong An Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN09937901 |
| SRA |
SRX4625890 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3362304_HEK293T_H3K14me3_peaks.bed.gz |
140.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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