|
| Status |
Public on Nov 01, 2016 |
| Title |
A13-Pr2_rep2 [BS-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Patient A13
|
| Organism |
Homo sapiens |
| Characteristics |
patient: Patient A13
tissue: primary tumor
|
| Growth protocol |
Unless otherwise stated, cells were grown to 70% (A38-Lg) or 100% (A38-Per) confluence in DMEM with 10% Fetal Bovine Serum (FBS)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with MasterPure kits
Whole genome bisulfite sequencing libraries were generated using TruSeq DNA Sample preparation protocol (Illumina) with modifications. Bisulfate conversion was done after gel size selection using EZ DNA Methylation-Gold Kit (Zymo Research). To amplify bisulfate converted library Kapa Hifi Uracil+ (Kapa Biosystems) polymerase was used.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned by BSmooth bisulfite alignment pipeline (version 0.7.1) as previously described in detail. Briefly, reads were aligned by Bowtie2 (version 2.0.1) against human genome (hg19) as well as the lambda phage genome.
After alignment, methylation measurements for each CpG were extracted from aligned reads. We filtered out measurements with mapping quality < 20 or nucleotide base quality on cytosine position < 10 and we also removed measurements from the 5’ most 10 nucleotides of both mates.
bsseq package in BSmooth was used to identify small and large differentially methylated regions (DMRs).
Genome_build: hg19
Supplementary_files_format_and_content: text file, methylated read count and total read count at each CpG site and each sample
|
| |
|
| Submission date |
Apr 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Li |
| E-mail(s) |
lixin4306ren@gmail.com
|
| Organization name |
Sun Yat-sen University
|
| Department |
School of Medicine
|
| Street address |
132 Daxuecheng Outer Ring E Rd
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510006 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63123 |
Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [BS-Seq] |
|
| Relations |
| BioSample |
SAMN04889846 |
| SRA |
SRX1723242 |
