|
| Status |
Public on May 29, 2024 |
| Title |
tp53 R242H/R242H, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole larvae
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole larvae
Stage: 5 dpf
strain: AB
genotype: tp53 R242H/R242H
|
| Growth protocol |
Larvae were maintained at 28C and samples were collected at 5 dpf.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Thirty pooled 5 dpf larvae were flash frozen, then DNA extraction andmethylation libraries were generatedusing the Post-Bisulfite Adapter Ligation method.
Starting material of 100ng of gDNA from bulk samples, one round DNA generation/random priming was used with four rounds of PCR following with a size selection step enriched for larger fragments of DNA.
Uniquely indexed libraries were pooled and submitted for sequencing on the NovaSeq6000.
Alignment and fractional methylation calls were generated using GemBS.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
coverageR242H1_PBAL
|
| Data processing |
MethylKit was used to filtered out regions with less than 10 reads and the highest 0.1% coverage regions as recommended and coverage was normalized between samples.
The genome was binned across in 1,000bp bins with a step size of 1,000bp and used Fisher’s Exact test to determine differentially methylated bins between the groups.
Assembly: GRCz11
Supplementary files format and content: tab-delinated text file includes filtered matrix of methylation information for regions that are covered in all samples.
|
| |
|
| Submission date |
May 24, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Kim Kobar |
| E-mail(s) |
kkobar.30@gmail.com
|
| Organization name |
Children's Hospital of Eastern Ontario Research Institute
|
| Lab |
Berman Lab
|
| Street address |
401 Smyth Rd
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H 8L1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE268283 |
tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [WGBS] |
|
| Relations |
| BioSample |
SAMN41523265 |
| SRA |
SRX24682099 |
