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Series GSE14584 Query DataSets for GSE14584
Status Public on Nov 24, 2009
Title MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing
Organism Sus scrofa
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNAs (miRNA) are short single-stranded RNA molecules that regulate gene expression post-transcriptionally by binding to complementary sequences in the 3' untranslated region (3' UTR) of target mRNAs. MiRNAs participate in the regulation of myogenesis, and identification of the complete set of miRNAs expressed in muscles is likely to significantly increase our understanding of muscle growth and development. To determine the identity and abundance of miRNA in porcine skeletal muscle, we applied a deep sequencing approach. This allowed us to identify the sequences and relative expression levels of 212 annotated miRNA genes, thereby providing a thorough account of the miRNA transcriptome in porcine muscle tissue. The expression levels displayed a very large range, as reflected by the number of sequence reads, which varied from single counts for rare miRNAs to several million reads for the most abundant miRNAs. Moreover, we identified numerous examples of mature miRNAs that were derived from opposite sides of the same predicted precursor stem-loop structures, and also observed length and sequence heterogeneity at the 5' and 3' ends. Furthermore, KEGG pathway analysis suggested that highly expressed miRNAs are involved in skeletal muscle development and regeneration, signal transduction, cell-cell and cell-extracellular matrix communication and neural development and function.
 
Overall design Examination of small RNA profiles in 7 isolates of porcine muscle

The raw sequences were trimmed to 30 nucleotides, and it was set as a requirement that any sequence must appear at least three times and be present in at least two of the seven libraries. All identical reads within a library were grouped and converted into unique sequences. Reads containing Ns or long tracks (¡Ý8) of As were removed and the sequences were trimmed for adaptor-sequences. To annotate the unique sequences, a Decypher Tera-BLASTN Search was performed against a database of mature miRNAs obtained from miRBase (release 12.0). Hits with a match of 16 or more nucleotides to a miRNA from the database were gathered, and the count of each miRNA was normalized to the total number of sequence reads per lane. The outcome of this procedure can be seen in the Aarhus_University_GBI_FC208D2AAXX_blast_mirbase table below.
 
Contributor(s) Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C, Thomsen B
Citation(s) 19917043
Submission date Jan 27, 2009
Last update date May 15, 2019
Contact name Jakob Hedegaard
E-mail(s) Jakob.Hedegaard@ki.au.dk
Phone (+45)89991363
Organization name Aarhus University, Faculty of Agricultural Sciences
Department Department of Genetics and Biotechnology
Lab Molecular Genetics and System Biology
Street address PO-box 50
City Tjele
ZIP/Postal code DK-8830
Country Denmark
 
Platforms (1)
GPL9126 Illumina Genome Analyzer (Sus scrofa)
Samples (7)
GSM364843 Muscle_animal_4363
GSM364844 Muscle_animal_4365
GSM364845 Muscle_animal_5342
Relations
SRA SRP001751
BioProject PRJNA111701

Aarhus_University_GBI_FC208D2AAXX_blast_mirbase_hits header descriptions
DESCRIPTION miRNA
TOTAL total count
GSM364843
GSM364844
GSM364845
GSM364846
GSM364847
GSM364848
GSM364849

Data table
DESCRIPTION TOTAL GSM364843 GSM364844 GSM364845 GSM364846 GSM364847 GSM364848 GSM364849
aga-let-7 23 0 5 0 3 8 3 4
ath-miR156a 4 0 0 0 0 2 1 1
bta-miR-139 19 9 2 0 1 4 3 0
bta-miR-140 9002 406 732 997 805 1511 3152 1399
bta-miR-181a 1010 49 228 155 98 217 113 150
bta-miR-181b 145 12 23 42 14 23 7 24
bta-miR-181c 16 1 1 3 1 3 6 1
bta-miR-192 130 14 38 18 16 28 10 6
bta-miR-195 50 7 6 3 8 12 8 6
bta-miR-21 2075 186 284 357 206 398 292 352
bta-miR-22-5p 591 99 45 80 84 126 110 47
bta-miR-26b 1653 123 208 263 177 473 260 149
bta-miR-29a 117 13 16 18 17 32 12 9
bta-miR-29b 6 1 1 1 1 0 2 0
bta-miR-30a-5p 2271 146 291 298 209 397 433 497
bta-miR-30d 4501 99 441 486 310 639 1196 1330
bta-miR-30e-5p 1048 77 111 145 119 190 237 169
bta-miR-345 26 2 3 0 4 6 7 4
bta-miR-423 103 1 8 5 7 17 22 43
bta-miR-425-3p 37 6 2 4 4 5 6 10

Total number of rows: 305

Table truncated, full table size 10 Kbytes.




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Processed data are available on Series record
Raw data are available in SRA

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