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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 12, 2019 |
| Title |
cfDNA14 |
| Sample type |
SRA |
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| Source name |
Cell free DNA
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
tissue compartment: plasma
sequenced molecule: Cell free DNA
condition: Esophageal cancer patient post-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 |
Library strategy: SALP-seq
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: bigwig files
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| Submission date |
Jun 27, 2018 |
| Last update date |
Apr 12, 2019 |
| Contact name |
Jian Wu |
| E-mail(s) |
wujian2010@outlook.com
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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) |
| GSE116345 |
Improved SALP-seq method for construct next-generation sequencing library of cell free DNA |
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| Relations |
| BioSample |
SAMN09501786 |
| SRA |
SRX4313244 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3229528_cfDNA14.bigwig |
53.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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