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Sample GSM4988380

Query DataSets for GSM4988380

Status

Public on Jun 15, 2022

Title

3B-46

Sample type

SRA

Source name

Acute Myeloid Leukemia_Plasma

Organism

Homo sapiens

Characteristics

diagnosis: Acute Myeloid Leukemia
training/validation group in diagnostic model: Training
training/validation group in survival analysis: Train
age: 68.47
gender: male
vital status (0: censored; 1: event): 1
survival (months): 34.36

Extracted molecule

genomic DNA

Extraction protocol

Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

NextSeq 550

Data processing

Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg19 genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for all sample with raw reads count summarised to genebody region.

Submission date

Dec 24, 2020

Last update date

Jun 15, 2022

Contact name

Zejuan Li

E-mail(s)

[email protected]

Phone

3462385129

Organization name

Houston Methodist Hospital