{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Miao Dang"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16905"],"description":["Fragment data of GC,HC,GB in paper titled Circulating Cell-Free mtDNA Fragmentomics for Early Detection of Gastric Cancer and Precancerous Lesions"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Circulating cell‑free DNA (cfDNA) was extracted from 1–2 mL plasma using the VAMNE MagUltra Circulating Cell‑free DNA Isolation Kit (Vazyme, China) following the manufacturer’s protocol. The cfDNA concentration was quantified using Qubit 4.0 (Thermo Fisher, USA).","Sequencing - The captured mtDNA libraries were sequenced on an Illumina NovaSeq 6000 platform using paired‑end 150 bp (PE150) chemistry. Each sequencing batch included a pooled cfDNA standard derived from ten healthy individuals to monitor inter‑batch consistency.","Library Construction - NGS libraries were prepared using 10–20 ng cfDNA. Biotinylated mtDNA capture probes (120‑mer RNA oligonucleotides, tiled at 1× density across the entire mitochondrial genome, NC_012920.1) were hybridized with the libraries. Captured mtDNA fragments were amplified and purified according to the manufacturer’s instructions.","Sample Collection - Peripheral blood samples (5 mL each) were collected from all participants into K2-EDTA tubes. Within 2 hours after collection, plasma was separated using a standard two-step centrifugation protocol (first centrifugation at 1,600 × g for 10 min at 4°C, second centrifugation at 16,000 × g for 10 min at 4°C) and stored at −80°C until DNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing data were processed using Fastp (v0.20.0) to trim adapters and low-quality bases (quality score < 30). Reads were aligned to the revised Cambridge Reference Sequence (rCRS) using BWA (v0.7.12). Only uniquely mapped reads with mapping quality MAPQ = 60 were retained. PCR duplicates were removed with Picard MarkDuplicates (v1.81). Fragment sizes were determined using Picard Tools. The proportion of fragments in the 70–90 bp range, fragment size distribution profiles, 5′ end base preferences, and motif diversity scores were calculated as described in the manuscript."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Illumina NovaSeq 6000"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_title":["Circulating Cell-Free mtDNA Fragmentomics for Early Detection of Gastric Cancer and Precancerous Lesions"],"pubmed_authors":["Miao Dang"],"additional_accession":[]},"is_claimable":false,"name":"XJ Fragmentomics Features","description":"Fragment data of GC,HC,GB in paper titled Circulating Cell-Free mtDNA Fragmentomics for Early Detection of Gastric Cancer and Precancerous Lesions","dates":{"release":"2026-04-08T00:00:00Z","modification":"2026-04-08T19:35:05.519Z","creation":"2026-04-07T10:48:37.588Z"},"accession":"E-MTAB-16905","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}