|
Status |
Public on Jan 25, 2024 |
Title |
B2MW068 |
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: N 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 |
SAMN36931550 |
SRA |
SRX21325893 |