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Sample GSM5737979 Query DataSets for GSM5737979
Status Public on Dec 31, 2022
Title 27p
Sample type SRA
 
Source name lung
Organism Equus caballus
Characteristics individual: horse 1
tissue: lung
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. 12 DNA libraries were pooled in one pool 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-trimming set to 20, quality set to 20 and a minimum read length of 20 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.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: Files containing the percentage of methylation of individual CpG sites determined using Methylation Caller software.
 
Submission date Dec 16, 2021
Last update date Dec 31, 2022
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)
GSE191047 Reduced representation bisulfite sequencing of equine tissue
Relations
BioSample SAMN24116530
SRA SRX13438171

Supplementary file Size Download File type/resource
GSM5737979_p27p.txt.gz 13.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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