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Series GSE116345 Query DataSets for GSE116345
Status Public on Apr 12, 2019
Title Improved SALP-seq method for construct next-generation sequencing library of cell free DNA
Organism Homo sapiens
Experiment type Other
Summary Cell free DNA (cfDNA) in human plasma carries abundant information on physiological condition, especially in cancer patients such as esophageal cancer. Next-generation sequencing (NGS) as a rapidly developed technology could decode the information effectively. As a key step of NGS, using existing methods to construct cfDNA sequencing libraries is limited by several shortcomings. In this study, we developed a new NGS library construction method for highly degraded DNA, cfDNA as example, based on Single strand Adaptor Library Preparation (SALP). With the high ligation efficiency of single strand adaptor (SSA) which overhangs 3 random bases at 3' end of a double-strand DNA, the new method could construct the sequencing library with high sensitivity without using specific enzymes except T4 DNA ligase and Taq polymerase. With the special designed barcode T adaptor (BTA), multiple libraries constructed from different samples can be amplified in unbiased strategy and facility to compare. Using this method, this study successfully sequenced and compared totally 20 cfDNA samples derived from esophageal cancer patients and healthy people in whole genome scale. This study also compared the chromatin state between cancer patients and healthy people using cfDNA, identified the significant difference between different health condition. Our findings extend the application of cfDNA beyond the analysis with degraded DNA fragments itself, to the transcription regulation level, which also provide an important clue for biopsy of esophageal cancer and other diseases.
Overall design The cell free DNA of 20 samples were sequenced with adapted SALP-seq.
Contributor(s) Wu J, Dai W, Wu L, Xia X, Wang J
Citation(s) 30746694
Submission date Jun 27, 2018
Last update date Apr 12, 2019
Contact name Jian Wu
Organization name Southeast University
Street address Sipailou 2#, Sipailou 2#
City NanJing
State/province Jiangsu
ZIP/Postal code 210096
Country China
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (20)
GSM3229515 cfDNA1
GSM3229516 cfDNA2
GSM3229517 cfDNA3
BioProject PRJNA478222
SRA SRP151466

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Supplementary file Size Download File type/resource
GSE116345_Barcodes_on_Barcoded_T_adaptors_for_labeling_different_cell_free_DNA_samples.xlsx 8.7 Kb (ftp)(http) XLSX
GSE116345_RAW.tar 849.5 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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