|
| Status |
Public on Jan 01, 2022 |
| Title |
Skin BPT17 |
| Sample type |
SRA |
| |
|
| Source name |
Skin tissue
|
| Organism |
Balaenoptera physalus |
| Characteristics |
oc concentration: high
group: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction with Quick-DNA Miniprep Plus Kit (Zymo Research, ZR).
Libraries were prepared from 300 ng of genomic DNA digested with 30 units of MspI (NEB) and then extracted with Zymo Research DNA Clean & Concentrator™-5 kit. The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR) for sequencing on an Illumina HiSeq.
Reduced representation bisulfite sequencing (RRBS)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a ZR proprietary analysis pipeline, which is written in Python and used Bismark to perform the alignment.
Index files were constructed using the bismark_genome_preparation command and the entire reference genome.
The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off during methylation calling.
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.
The methylation ratio (Mr) is defined as the number of reads overlapping a particular CpG comprising a C or a T at the first position of the CpG. If x is the number of C's and y the number of T's, the formula Mr = x/(x + y) then gives the methylation ratio for each CpG.
Genome_build: BalAcu1.0
Supplementary_files_format_and_content: Excel file including methylation data for every C for each sample including methylation differentiation and p value related to Comparison (group1 vs group2)
Supplementary_files_format_and_content: Matrix table with raw methylation counts for every gene and every sample
Supplementary_files_format_and_content: Comparison 1 CHH_result_table.xls: Comparison CHH
Supplementary_files_format_and_content: Comparison 1 CHG_top result_table.xls: Comparison CHG
Supplementary_files_format_and_content: Comparison CpG_top result_table.xls: Comparison CpG
Supplementary_files_format_and_content: CHH_all result_table.txt: All data CHH
Supplementary_files_format_and_content: CHG_all result_table.txt: All data CHG
Supplementary_files_format_and_content: CpG_all result_table.txt: All data CpG
Supplementary_files_format_and_content: Strongly Hypo-Hyper_CpG_CHH_CHG-xls: Selected data files for CpG_CHH_CHG
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Jan 01, 2022 |
| Contact name |
Annalaura Mancia |
| E-mail(s) |
annalaura.mancia@unife.it
|
| Organization name |
University of Ferrara
|
| Department |
Life Sciences and Biotechnology
|
| Street address |
via L.Borsari, 46
|
| City |
Ferrara |
| ZIP/Postal code |
44121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL28794 |
| Series (1) |
| GSE153525 |
DNA methylation profile of the Mediterranean fin whale (Balaenoptera physalus) exposed to organochlorine contaminants. |
|
| Relations |
| BioSample |
SAMN15401472 |
| SRA |
SRX8635307 |
