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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 28, 2022 |
| Title |
Lane1_cfDNA1 |
| Sample type |
SRA |
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| Source name |
Cell free DNA
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
condition: Esophageal cancer patient pre-operation
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The plasma was separated from whole blood, then cell free DNA was isolated with the Plasma Circulating DNA Kit (TIANGEN, DP339).
The denatured cell free DNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and ligated with barcoded T overhanging adaptors. After purified with Ampure XP beads, amplification was performed with Illumina compatible primers.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The raw reads data were separated according to the barcode using a homemade Perl scripts.
The constant sequence (19 bp) and barcode (6 bp) sequences were removed from the 5สน end of the pair-end sequencing reads 2 then mapped to human genome (hg19) using Bowtie2 (version 2.2.6).
Genome_build: hg19
Supplementary_files_format_and_content: bw files
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| Submission date |
Aug 28, 2019 |
| Last update date |
Aug 28, 2022 |
| Contact name |
Shicai Liu |
| E-mail(s) |
liushicainj@yeah.net
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| Organization name |
Southeast University
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| Street address |
Sipailou 2#, Sipailou 2#
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210096 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE136541 |
Inferring Epigenetic and Genetic Biomarkers of cancer in cell-free DNA |
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| Relations |
| BioSample |
SAMN12647258 |
| SRA |
SRX6777860 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4051273_Lane1_cfDNA1.bw |
18.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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