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| Status |
Public on Feb 24, 2017 |
| Title |
Flag_CTCF_Pool1 |
| Sample type |
SRA |
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| Source name |
HCT116
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| Organism |
Homo sapiens |
| Characteristics |
genotype: C-terminal Flag tagging of SP1, clone 1
cell line: HCT116
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| Growth protocol |
Mouse embryonic stem cell lines E14 and Mll3/4 double knockout were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP-seq has been carried out as previously described6,7. Briefly, 2 million cells were crosslinked with 1% formadehyde for 10 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit.
TruSeq
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
SRC430
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| Data processing |
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq
Genome_build: hg19
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| Submission date |
Feb 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Yan |
| E-mail(s) |
jian.yan618@gmail.com
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| Organization name |
City University of Hong Kong
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| Department |
Biomedical Sciences
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| Lab |
Jian Yan
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| Street address |
83 Tat Chee Ave
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| City |
Kowloon |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE78064 |
A Scalable Epitope Tagging Approach for High Throughput ChIP-seq Analysis |
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| Relations |
| BioSample |
SAMN06445432 |
| SRA |
SRX2586450 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2507346_Flag_CTCF_Pool1_SRC430.bw |
144.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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