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Sample GSM3541203 Query DataSets for GSM3541203
Status Public on Jan 05, 2019
Title Maternal plasma
Sample type SRA
Source name plasma
Organism Homo sapiens
Characteristics tissue: plasma
Extracted molecule genomic DNA
Extraction protocol The cfDNA was purified from a DENQCMs sample and a clinical plasma sample respectively with the Cell-Free DNA Extraction Kit (Annoroad) as per the manufacturer’s protocol.
Libraries were prepared with Detection Kit for Noninvasive Fetal Trisomy (Annoroad) according to the manufacturer’s recommendations. Samples were individually indexed during library preparation. The pooled libraries were sequenced using a 150-bp paired-end (PE) run on the Illumina NovaSeq platform following the manufacturer's protocols.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description cell-free DNA
Data processing Library strategy: DNA-Seq
Basecalls performed using bcl2fastq software
Reads were aligned to the human reference genome GRCh37 using BWA version 0.7.10
The aligned paired-end data was stored in BAM format using the SAMtools
We selected non-duplicated mapped reads with 167 bp length from BAM files, separately extended with 100 bp upstream and downstream to the aligned region, and extracted the sequences of each extended region using bedtools v2.20.1. Both the number of A/T (including AA/AT/TA/TT) and C/G (including CC/CG/GC/GG) dinucleotides were counted in these regions and the fraction of A/T and C/G were calculated using a sliding 2 bp window and reference alleles at each position.
Fragment endpoint coordinates were extracted from BAM files and non-duplicated mapped reads within 120-180 bp were selected using bedtools v2.20.1. A fragment’s coverage is defined as all positions between the two ends. Reads spanning the window were defined as the reads covering the whole genomic window, while non-spanning reads with an endpoint within the window as the reads partially covering the genomic window.
The nucleosome protection peaks were identified based on genome-wide windowed protection score (WPS) distribution. Regions started from the position with above-zero WPS and allowing up to three consecutive positions with below-zero WPS were considered as candidates for nucleosome protection peaks. If the median WPS value of a candidate was equal to or larger than 1, it was regarded as a nucleosome protection peak, and its start, end and centre coordinates were reported.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: Tar archives include the following files:
WPS score of neighbouring bins overlalpping with TSS (*WPS_overlapped_TSS.tsv)
Nucleosome Protection length of all chromosome (*chrAll.NP.tsv)
WPS score of all chromosome bins (*hrAll.WPS.tsv)
Di-nucleotide frequency of all chromosome bins (*diNucleotideFreq.tsv)
Frequency table of fregment insert size (*fragLengthDist.tsv)
Median WPS score of each distance group relatitve to TSS (*median_WPS_of_TSS.tsv)
Submission date Jan 04, 2019
Last update date Jan 05, 2019
Contact name Ziyang Li
Organization name Wenzhou Medical University
Street address University-town, Chashan
City Wenzhou
State/province Zhejiang Province
ZIP/Postal code 325035
Country China
Platform ID GPL24676
Series (1)
GSE124686 Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma
BioSample SAMN10693355
SRA SRX5205644

Supplementary file Size Download File type/resource
GSM3541203_WBJPE18018556.tar.gz 169.5 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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