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| Status |
Public on May 01, 2013 |
| Title |
male muscle after exercise MF2P |
| Sample type |
SRA |
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| Source name |
muscle
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| Organism |
Equus caballus |
| Characteristics |
sampling position: right leg
subject: F2P
treatment: after exercise
tissue: muscle
Sex: male
birth date: 05.06.2006
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from muscle and blood were prepared using TRIzol (Invitrogen) and a RNeasy RNA Purification Kit with DNase treatment (Qiagen), according to the instruction manual. One microliter of cleaned total RNA was consumed to check RNA quality using BioAnalyzer 2011 with an RNA chip (RIN > 7 and 28S:18S ratio > 1.0). Messenger RNA sequencing libraries were generated using an mRNA Seq Sample Prep Kit following the manufacturer’s manual (Illumina). 5 ug of poly(A) mRNA was isolated from the total RNA using oligo-dT beads. The mRNA was then fragmented and randomly primed for reverse transcription, followed by the second-strand synthesis to create double-stranded cDNA fragments. The double-stranded short cDNA fragments were purified with a QiaQuick PCR extraction kit (Qiagen) and resuspended in an EB buffer. Each end of cDNA was repaired with a combination of fill-in reactions and blunted by exonuclease. The addition of A-base was applied to the blunt end DNA followed by sequencing adaptor ligation. The required fragments were purified by agarose gel electrophoresis and a QIAquick Gel Extraction Kit (Qiagen), and enriched by PCR amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequences reads were mapped to the EquCab2 reference genome using BWA. Briefly, the reference genome was indexed using “bwa index –a bwtsw”, fastq-formatted reads were aligned using “bwa aln”, and sored, merged BAM files were generated using “bwa sampe” followed by reference genome sorting with “picard-tools”. And, statistics on apparently miscalled bases are gathered from the initial BAM files, conditional on specified covariates, excluding sites likely to be polymorphic. As covariates we used the raw quality scores, the machine cycle number (read position), and the dinucleotide context. Then, reads around indels identified from the initial BAM files are realigned using “picard-tools”.
fragments per kilobase of exon per million fragments mapped (FPKM) value for expression level of gene and isoform were calculated using Cufflinks (v. 1.3.0)
Genome_build: EquCab2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
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| Submission date |
May 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
HYEONGMIN KIM |
| E-mail(s) |
lazenca01@gmail.com
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| Phone |
082-10-7147-6494
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| Organization name |
Seoul National University
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| Department |
College of Agriculture Sciences
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| Lab |
biopop
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| Street address |
Seoul National Univ., Daehak-dong, Gwanak-gu,
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| City |
Seoul |
| ZIP/Postal code |
151-921 |
| Country |
South Korea |
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| Platform ID |
GPL15545 |
| Series (1) |
| GSE37870 |
Whole transcriptome analyses of six thoroughbred horses before and after exercising using RNA-Seq |
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| Relations |
| SRA |
SRX147019 |
| BioSample |
SAMN00991821 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM929206_MF2P.genes_fpkm.txt.gz |
695.0 Kb |
(ftp)(http) |
TXT |
| GSM929206_MF2P.isoforms_fpkm.txt.gz |
904.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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