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Status |
Public on Sep 03, 2014 |
Title |
HeLa_H33_FLAG_Input |
Sample type |
SRA |
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Source name |
HeLa cells
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa cell type: C-terminal FLAG-tagged H3.3 stably expressing HeLa chip antibody: None
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Treatment protocol |
FLAG-H3.3 stably expressing HeLa cells was established using a retroviral expressing system.
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Growth protocol |
Cells were maintained in Dulbecco’s modified Eagle’s medium (Hyclone) containing 10% FBS (Hyclone).
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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) ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0 peaks were called using macs2 with the following setting:--qvalue=0.05 --broad -g hs Genome_build: hg19 Supplementary_files_format_and_content: peak list
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Submission date |
Mar 11, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Yang Shi |
E-mail(s) |
yshi@hms.harvard.edu
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Organization name |
Fudan university
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Street address |
NO. 138, Yi-Xue-Yuan Road
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City |
Shanghai |
ZIP/Postal code |
200032 |
Country |
China |
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Platform ID |
GPL16791 |
Series (1) |
GSE51672 |
A histone H3.3 Lysine 36 Trimethylation Reader Connects Chromatin to Regulated Pre-mRNA Processing |
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Relations |
BioSample |
SAMN02687930 |
SRA |
SRX484651 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not applicable for this record |
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