Comparative analyses of transcriptome during skeletal muscle development between pig breeds differing in muscle growth rate by deep-sequencing

Experiment ID:SRP006209
Technology:RNA-Seq
Description:Obese and lean pig show breed-specific traits in muscle growth and meat quality. However, the mechanisms underlying remains unclear. Here, we reported the first genome-wide muscle development research from embryonic to 6 months old between Lantang (obese) and Landrace (lean) using Solexa/Illumina's Genome Analyzer. We obtained 4.22±0.9×107 total reads per sample with approximately 5×106 distinct tags. Filtered adaptor tags, empty reads, low quality tags and tags of copy number =1, we obtained 3.84±0.9×107 clean total tags with 1.5±0.5×106 clean distinct tags. Overall design: 20 libraries of longissimus muscle samples were sequenced in Lantang and Landrace at days 35, 49, 63, 77, 91 prenatal and 2, 28, 90, 120, 180 postnatal days.
Source:SRP006209 SRA

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entries

Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX054595UBERON:0001401 longissimus thoracis musclelongissimus dorsi muscleSscrDv:0000025 28-day-old stage (pig)postnatal day 28maleLandraceNANASus scrofaNAIlluminaIllumina Genome AnalyzerFULL_LENGTH35single313687715994300681014996Browse results
SRX054606UBERON:0001401 longissimus thoracis musclelongissimus dorsi muscleSscrDv:0000044 12-week-old stage (pig)postnatal day 90maleLantangNANASus scrofaNAIlluminaIllumina Genome AnalyzerFULL_LENGTH35single433857022912800758915418Browse results
SRX054608UBERON:0001401 longissimus thoracis musclelongissimus dorsi muscleSscrDv:0000059 6-month-old stage (pig)postnatal day 180maleLantangNANASus scrofaNAIlluminaIllumina Genome AnalyzerFULL_LENGTH35single319128022164000690815061Browse results