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Sample GSM6369231 Query DataSets for GSM6369231
Status Public on Jul 03, 2023
Title sc12
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 SAMN29878193
SRA SRX16387448

Supplementary file Size Download File type/resource
GSM6369231_sc12.txt.gz 30.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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