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| Status |
Public on Sep 22, 2017 |
| Title |
TFCP2_ChIPseq_rep2 |
| Sample type |
SRA |
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| Source name |
liver cancer cell
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Bel-7402
cell type: Hepatocellular carcinoma
antibodies: anti-TFCP2 (CST #80784)
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| Growth protocol |
Bel-7402 cells were were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS) (GIBCO, Carlsbad, CA, USA) and penicillin/streptomycin (GIBCO).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to hg19 genome assembly using Bowtie version 0.12.7 with default parameters. Only the concordant pairs with mapq > 3 were retained.
Wig files were generated from the filtered alignments. Briefly, the genome were divided into 10 bp windows. Reads Per Kilobase per Million mapped reads (RPKM) value was calculated in eary window and the adjacent windows were used for smooth the values.
The high-confidence sets of YAP and TFCP2 were obtained by using the IDR (Irreproducible Discovery Rate) pipeline2: Firstly, we used MACS2 version 2.1.03 to call peak sets on individual replicates, pseudo-replicates and pooled data. Then we run an IDR analysis on these peak sets and an IDR threshold of 0.01 was used to filter and obtain optimal sets of peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
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| Submission date |
May 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Weisheng Zheng |
| E-mail(s) |
wisense@2008.sina.com
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| Organization name |
Tongji University
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| Department |
Department of Bioinformatics
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| Lab |
Jiang Lab
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| Street address |
Siping Road, No.1239
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE99314 |
Genome-wide analysis of YAP and TFCP2 binding DNA in liver cancer cells |
| GSE99315 |
Genome-wide analysis of YAP and TFCP2 occupancy and regulated expression in liver cancer cells |
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| Relations |
| BioSample |
SAMN07168871 |
| SRA |
SRX2858137 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2641033_TFCP2-2_ChIP-seq.bigwig |
275.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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