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Sample GSM5602638 Query DataSets for GSM5602638
Status Public on Sep 29, 2023
Title HA
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 SAMN21895011
SRA SRX12400043

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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