|
| Status |
Public on Sep 29, 2023 |
| Title |
HA-D |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Hampshire breed
|
| Treatment protocol |
Muscle tissues were removed using biopsy from pigs belonging to Hampshire and Mali breeds of pigs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A was isolated from muscle tissues using a commercial kit (Thermofisher, USA) .The methylated regions were precipitated and used for sequencing.
MeDIP libraries were prepared for sequencing using standard Illumina protocols
The enriched fragments with methylation were purified and amplified through adaptor-mediated PCR. Later, 8.5pmol of the MeDIP library was subjected to paired-end sequencing using an Illumina HiSeq 2500 and a 100-bp read length.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The quality of the raw sequences generated from MeDIP sequencing were assessed with FastQC (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). With respect to the FastQC report, the low quality bases were removed using custom made perl script and the adaptor sequences were removed using cutadapt (version 3.3). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment. Uniquely mapped reads with high mapping quality (reads with a mapping quality score of ≥10) were analyzed using the MEDIPS software package (version 1.44) (BWA) (version 0.7.17).
The wiggle files were generated using "exportWIG" function in MEDIPS to export genome wide coverage profiles for visualization in the UCSC genome browser
Genome_build: Sus scrofa 11.1 reference genome
Supplementary_files_format_and_content: tab-delimited text files containing chromosome wise differentially methylated regions
Supplementary_files_format_and_content: CPG informtion in DNA isolated two different breeds of animals
|
| |
|
| Submission date |
Sep 29, 2021 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Narayana H Mohan |
| E-mail(s) |
mohan.nh@icar.gov.in
|
| Organization name |
Indian Council of Agricultural Research
|
| Department |
ICAR-National Research Centre on Pig
|
| Lab |
Physiology laboratory
|
| Street address |
Rani
|
| City |
Guwahati |
| State/province |
Assam |
| ZIP/Postal code |
781 131 |
| Country |
India |
| |
|
| Platform ID |
GPL19176 |
| Series (2) |
| GSE184969 |
MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity |
| GSE184970 |
Muscle from two pig breeds with varying muscularity |
|
| Relations |
| BioSample |
SAMN21895015 |
| SRA |
SRX12400047 |
