|
Status |
Public on Aug 07, 2019 |
Title |
blood_416 |
Sample type |
SRA |
|
|
Source name |
Plasma
|
Organism |
Homo sapiens |
Characteristics |
tissue: plasma training/validation group: Validation-1
|
Extracted molecule |
genomic DNA |
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 |
genomic |
Library selection |
5-methylcytidine antibody |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Bcl2fastq v2.17 software used to change the bcl files to fastq files. Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using bowtie v2.26 Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3. Genome_build: hg19 Supplementary_files_format_and_content: txt file for each sample with raw reads count summarised to genebody region.
|
|
|
Submission date |
Apr 04, 2018 |
Last update date |
Jun 05, 2023 |
Contact name |
Zhou Zhang |
E-mail(s) |
zhou.zhang@northwestern.edu
|
Organization name |
Northwestern University
|
Department |
Preventive Medicine
|
Street address |
680 North Lake Shore Drive, Suite 1400
|
City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60611 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE112679 |
Genome-wide Mapping of 5-Hydroxymethylcytosines in Circulating Cell-free DNA as a Non-invasive Approach for Early Detection of Hepatocellular Carcinoma |
|
Relations |
BioSample |
SAMN08869151 |
SRA |
SRX3890426 |