|
| Status |
Public on Mar 01, 2024 |
| Title |
Sample 1: G06 cells, normoxia, RRBS |
| Sample type |
SRA |
| |
|
| Source name |
G06
|
| Organism |
Canis lupus |
| Characteristics |
cell line: G06
cell type: glioma cell
treatment: normoxia
|
| Treatment protocol |
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using Zymo Research Quick DNA Mini-prep Plus kit.
40 ng of starting input genomic DNA was digested with 30 units of MspI (NEB). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™-5 (Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™-5 (Cat#: D4003) for sequencing on an Illumina NovaSeq 6000 platform (150 bp PE reads).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads from bisulfite-treated Classic RRBS libraries were identified using standard Illumina base calling software and then raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore 0.6.4. FastQC 0.11.9 was used to assess the effect of trimming and overall quality distributions of the data.
Alignment to the Canis lupus familiaries reference genome was performed using Bismark 0.22.3
Methylated and unmethylated read totals for each CpG site were called using MethylDackel 0.5.0. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Assembly: canFam3
Supplementary files format and content: bedgraph files contain methylated regions
|
| |
|
| Submission date |
Jan 27, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Ryan Toedebusch |
| E-mail(s) |
ryantoedebusch@gmail.com
|
| Organization name |
University of California
|
| Street address |
1 Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL33062 |
| Series (1) |
| GSE223852 |
Effect of hypoxia on canine glioma stem-like cells metabolism |
|
| Relations |
| BioSample |
SAMN32938619 |
| SRA |
SRX19198062 |
