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Series GSE125254 Query DataSets for GSE125254
Status Public on Dec 01, 2020
Title Genome-wide profiling reveals the distribution pattern of abasic sites in mammalian genomes
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary The AP-seq provides a genome-wide method for detecting abasic sites among the human and mouse genomes
Purpose: Abasic sites are one of the most frequent DNA damage among the genome , which often carries harmful consequences for the genome stability and the normal cell functions. So it is necessary to develop a whole genome abasic sites (AP sites) profiling method to detect all the AP sites among the genome, which we called the AP-seq.
Methods: The human and mouse genome are processed with enzymatic fragmentation, damage repair, biotin-dU labeling, and pull-down steps. After the sequencing library preparation, the FASTQ files are produced by the Illumina HiSeq XTen platform. To guarantee the reproducibility, each case of the experiment is present with two biological replicates.
Results: The reproducibility of our two biological replicates shows a high correlation which larger than 0.95. And the overlap AP site peaks between the HEK293T and MCF-7 cell line are over 50%, which show a great similarity between the different cell lines. Totally, we identified more than 2000 and 1000 abasic site peaks in human, and mouse cell lines separately. Moreover, the distribution of these AP sites prefer to locate in the intergenic regions and introns.
 
Overall design We explored a genome-wide efficient method to map the abasic sites in human and mouse genome called AP-seq. And perform the AP-seq with human HEK293T, MCF-7, and mouse embryo stem cells (mESC).
 
Contributor(s) Menghao L, Haowei M, Zhicong L, Chengqi Y
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Submission date Jan 17, 2019
Last update date Dec 04, 2020
Contact name Howard MENG
E-mail(s) menghaowei@pku.edu.cn
Organization name Peking University
Department School of Life Sciences
Lab Yi Chengqi Lab
Street address No.5 Yiheyuan Road Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (12)
GSM3567250 293T-AP-Input_rep1
GSM3567251 293T-AP-Input_rep2
GSM3567252 293T-AP-PD_rep1
Relations
BioProject PRJNA515700
SRA SRP179985

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Supplementary file Size Download File type/resource
GSE125254_RAW.tar 7.8 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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