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Series GSE84637 Query DataSets for GSE84637
Status Public on Oct 20, 2016
Title Base-resolution analysis of cisplatin-DNA adducts at the genome scale
Organisms Homo sapiens; synthetic construct
Experiment type Other
Summary Cisplatin, one of the most widely used anticancer drugs, crosslinks DNA and ultimately induces cell death. However, the genomic pattern of cisplatin-DNA adducts remains unknown, due to the lack of a reliable and sensitive genome-wide method. Here we present “cisplatin-seq” to identify genome-wide cisplatin crosslinking sites at base-resolution. Cisplatin-seq reveals that mitochondrial DNA is a preferred target of cisplatin. For nuclear genome, cisplatin-DNA adducts are enriched within promoters and regions harboring transcription termination sites. While the density of GG dinucleotide determines the initial crosslinking of cisplatin, binding of proteins to the genome largely contributes to the accumulative pattern of cisplatin-DNA adducts.
 
Overall design Developing a method "Cisplatin-seq" to profile cisplatin-crosslinking site in human genome, using cells treated with cisplatin for 3h, 12h, 24h respectively.
 
Contributor(s) Shu X, Xiong X, Yi C
Citation(s) 27736024
Submission date Jul 20, 2016
Last update date May 15, 2019
Contact name Xushen Xiong
E-mail(s) xiongxs@zju.edu.cn
Organization name Zhejiang University
Department Medical Center
Street address Wenyi Road West
City Hangzhou
State/province Zhejiang
ZIP/Postal code 311121
Country China
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (10)
GSM2243405 Hela_input
GSM2243406 Hela_IP_ctrl_rep1
GSM2243407 Hela_IP_ctrl_rep2
Relations
BioProject PRJNA330713
SRA SRP079003

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE84637_RAW.tar 3.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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