|
| Status |
Public on Apr 24, 2024 |
| Title |
C16 |
| Sample type |
SRA |
| |
|
| Source name |
Plasma separated from blood
|
| Organism |
Homo sapiens |
| Characteristics |
race: White
age: 79
gender: Male
group: CRC
tissue: Plasma separated from blood
fraction: cfDNA
|
| Extracted molecule |
other |
| Extraction protocol |
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 1 ng cfDNA was used for library construction.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
other |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome hg19 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Assembly: hg19
Supplementary files format and content: bismark output cov files
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE186007 |
LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA |
|
| Relations |
| BioSample |
SAMN35355213 |
| SRA |
SRX20503486 |
