|
| Status |
Public on Jan 25, 2024 |
| Title |
B2MW059 |
| Sample type |
SRA |
| |
|
| Source name |
circulating cell-free DNA (cfDNA)
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: high-grade serous ovarian cancer (HGSOC)
platinumsensitivity: Sensitive
chemonaive: Y
tissue: circulating cell-free DNA (cfDNA)
|
| Extracted molecule |
other |
| Extraction protocol |
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
other |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to hg19 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Uniquely mapped reads were counted on gene-bodies by FeatureCounts.
Assembly: hg19
Supplementary files format and content: Bigwig files normalized to show RPKM.
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Jan 25, 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 |
GPL24676 |
| Series (1) |
| GSE240535 |
5-Hydroxymethylcytosine signals in serum are a predictor of chemoresistance in high-grade serous ovarian cancer |
|
| Relations |
| BioSample |
SAMN36931555 |
| SRA |
SRX21325888 |
