|
| Status |
Public on Sep 29, 2023 |
| Title |
HA1 |
| 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
|
| Growth protocol |
Muscletranscriptome of two different breeds of pigs were compared.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from muscle tissues using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were removal of adaptor sequences, and phred scores abov 30, then mapped to Sus scrofa 11.1 reference genome using Hisat 2 and bowtie v0.12.2 and picard tools.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) and DEGs were calculated using CuffDiff data analysis pipeline.
Genome_build: Sus scrofa 11.1 reference genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for RNA seq data
|
| |
|
| 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 |
GPL11429 |
| Series (2) |
| GSE184968 |
Transcriptome analysis of muscle from two pig breeds with varying muscularity |
| GSE184970 |
Muscle from two pig breeds with varying muscularity |
|
| Relations |
| BioSample |
SAMN21895012 |
| SRA |
SRX12400044 |
