|
| Status |
Public on Jul 01, 2022 |
| Title |
W4 |
| Sample type |
SRA |
| |
|
| Source name |
Water control
|
| Organism |
blank sample |
| Characteristics |
group: NTC
time point: T0
tissue: Water control
molecule type: cell-free DNA
|
| Treatment protocol |
Plasma was separated from blood by centrifugation
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cfDNA was extracted from plasma using QIAamp circulating nucleic acid kit (QIAGEN)
single-strand DNA library preparation with custom sequencing primers
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: metagenomics DNA sequencing library
Illumina Casava1.7 software used for basecalling.
Raw reads were first trimmed to 2x75bp using Cutadapt (version 1.18) and rarefied to 30M to ensure equal library size except for non-template controls due to its low input. Duplicates were then removed using PRINSEQ (version 0.20.4) in a paired-end mode with entropy-based strategy. The threshold of entropy was set as 20. Adapters and bases with quality lower than 20 were then trimmed using BBMap (version 35.74). Reads shorter than 25bp were discarded.
Quality-controlled reads were mapped to human reference GRCh38 downloaded from NCBI RefSeq database using Bowtie2 (version 2.2.6) in a very-sensitive mode. Duplicates were marked and removed using Picard Tools (version 2.18.7). Then both mapped and unmapped reads were extracted using SAMtools (version 1.3.1) for analysis of human fragments and microbial compositions respectively.
Mapped human bam files were firstly sorted using SAMtools (version 1.3.1) and then converted to bed files using BEDtools (version 2.15.0). Human autosome reference was segmented into 1-megabase non-overlap bins using BEDtools. Ratio of fragments of different length overlapped with each bin were calculated using custom script.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file containg the number of fragments with different length within 1M bins across autosomes
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Qiuyu JING |
| E-mail(s) |
[email protected]
|
| Phone |
+85261579677
|
| Organization name |
The Hong Kong University of Science and Technology
|
| Department |
Division of Life Science
|
| Lab |
Prof. Angela Wu's lab
|
| Street address |
Room 6202C, Academic Building, The Hong Kong University of Science and Technology
|
| City |
Hong Kong |
| State/province |
Hong Kong |
| ZIP/Postal code |
999999 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL29107 |
| Series (1) |
| GSE179037 |
Cell-free DNA as biomarker for sepsis by integration of microbial and host information |
|
| Relations |
| BioSample |
SAMN19918727 |
| SRA |
SRX11243327 |
