|
| Status |
Public on Mar 15, 2023 |
| Title |
tumor brain, CAPS+ |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
Sex: female
disease: glioblastoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA of human normal brain and glioblastoma samples were obtained from the Amsbio
Genomic DNA was spiked with 0.5% of CpG-methylated lambda DNA and 0.25% of unmodified 2 kb spike-in control. DNA samples were fragmented by Covaris M220 and size-selected to 300–500 bp with 0.55–0.85× Ampure XP beads according to the manufacturer’s protocol. The sonicated DNA was additionally spiked with 0.05% of 144 mer spike-in after size-selection with Ampure XP beads. End-repair and A-tailing reaction and ligation of NEBNext Adaptor for Illumina were prepared with KAPA HyperPrep Kit according to the manufacturer’s protocol. The uracil in the loop of NEBNext Adaptor was removed by adding 6 ml of USER Enzyme (New England Biolabs) to the ligation reaction and incubating at 37 °C for 45 min. The reaction was purified with 0.8× Ampure XP beads by washing twice with 80% acetonitrile/water (v/v).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
brain_tumor_astair_CpG.filtered.bedGraph.gz
|
| Data processing |
Fastp (v.0.12.4) was used to filter bad reads, trim low-quality bases and cut adaptors
Trimmed reads were then aligned to either mm9 (for mESC samples) or hg38 (for human healthy brain and glioblastoma samples) reference genome using BWA mem (v.0.7.17)
PCR duplicates were removed by MarkDuplicate in Picard tools (v.2.23.0) (http://broadinstitute.github.io/picard/)
Methylation calling was performed by asTair (v3.3.2) using reads with MAPQ > 10. Regions prone to cause mapping artefacts were excluded from subsequent analysis(https://sites.google.com/site/anshulkundaje/projects/blacklists)
For mESC samples, known single nucleotide variants in E14 cell lines (http://epigenetics.hugef-research.org/data.php) were also excluded. For human normal brain and glioblastoma samples, CpG sites overlapping with common single nucleotide polymorphisms (SNPs) (dbSNP153) and centromeres were further excluded from downstream analysis
Assembly: mm9, hg38
Supplementary files format and content: Tab-delimited bedGraph files include chr (first column), start position (second), end position (third), modification level (fourth), unmodified reads (fiveth) and modified reads (sixth)
|
| |
|
| Submission date |
Sep 23, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Linzhen Kong |
| E-mail(s) |
linzhen.kong@ndm.ox.ac.uk
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Nuffield Department of Medicine
|
| Lab |
Dr. Chunxiao Song's group
|
| Street address |
University of Oxford Old Road Campus Research Building
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7FZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE214006 |
Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine |
|
| Relations |
| BioSample |
SAMN30974469 |
| SRA |
SRX17680437 |
