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| Status |
Public on Jan 01, 2020 |
| Title |
COAD.ct-200 |
| Sample type |
SRA |
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| Source name |
blood serum
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| Organism |
Homo sapiens |
| Characteristics |
sample type: cell-free DNA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions
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| Submission date |
Apr 18, 2017 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Kang Zhang |
| E-mail(s) |
kangzhanglab@gmail.com
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| Organization name |
UCSD
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE97923 |
Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (COAD) |
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| Relations |
| BioSample |
SAMN06761827 |
| SRA |
SRX2743052 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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