|
| Status |
Public on Jul 03, 2023 |
| Title |
sc10 |
| Sample type |
SRA |
| |
|
| Source name |
tumour tissue
|
| Organism |
Equus caballus |
| Characteristics |
tissue: tumour tissue
|
| Treatment protocol |
The collected material was transferred into tubes and stored at -20°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from tissue using a Sherlock AX (A&A Biotechnology) kit
To quantify DNA methylation levels across the genome RRBS methodology was used following the Ovation RRBS Methyl-Seq System (NuGEN) protocol. 24 DNA libraries were pooled in two pools and sequenced on the NexSeq 500 platform (Illumina) using a 75-bp single-end read and High-Output Flow Cell. The sequencing was performed along with a balanced control library obtained from the viral DNA (PhiX, Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-quality set to 20 and a minimum read length of 36 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The aligned to the horse reference genome (EquCab3.0) using BSMAP (Yuanxin and Wei, 2009) with default options recommended for RRBS data, specifying the enzyme cleavage site (MspI) and mapping only to two forward strands.
The percentage of methylation of individual CpG sites with coverage higher than 5 reads was determined using Methylation Caller software provided in BSMAP package. Then, the files were processed in R to obtain input files for Methylkit software.
Assembly: EquCab3.0
Supplementary files format and content: Files containing the percentage of methylation of individual CpG sites determined using Methylation Caller software followed by the conversion in R to be viable as input files for Methylkit software
|
| |
|
| Submission date |
Jul 21, 2022 |
| Last update date |
Jul 03, 2023 |
| Contact name |
Ewelina Semik-Gurgul |
| E-mail(s) |
ewelina.semik@iz.edu.pl
|
| Organization name |
National Research Institute of Animal Production
|
| Department |
Department of Animal Molecular Biology
|
| Lab |
Laboratory of Genomics
|
| Street address |
Krakowska 1
|
| City |
Balice |
| ZIP/Postal code |
32083 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21401 |
| Series (1) |
| GSE208778 |
Reduced representation bisulfite sequencing of equine sarcoid andhorse skin samples |
|
| Relations |
| BioSample |
SAMN29878195 |
| SRA |
SRX16387446 |
