Open Access Highly Accessed Research article

Identification of differences in microRNA transcriptomes between porcine oxidative and glycolytic skeletal muscles

Yingkai Liu1, Mingzhou Li1, Jideng Ma1, Jie Zhang1, Chaowei Zhou1, Tao Wang1, Xiaolian Gao2 and Xuewei Li1*

Author Affiliations

1 Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya’an, Sichuan, China

2 Department of Biology & Biochemistry, University of Houston, Houston, TX, USA

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BMC Molecular Biology 2013, 14:7  doi:10.1186/1471-2199-14-7

Published: 18 February 2013

Additional files

Additional file 1: Figure S1:

Summary of the sequencing results. (A) Distribution of the sequencing data in each library after applying a series of filters. LDM, longissimus dorsi muscle; PMM, psoas major muscle. (B) Distribution for the other known classes of RNA sequences. (C) Mappable reads were divided into three groups. (D) Length distribution and frequency percentage of the unique miRNAs. The Y-axis indicates the ratio of miRNA (numbers of each stage divided by total numbers in a library). LDM, longissimus dorsi muscle; PMM, psoas major muscle.

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Additional file 2: Table S1:

Statistics of the distribution for small RNAs during a series of filters in order.

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Additional file 3: Table S2:

Proportion of sequ-seqs mapping to known RNA classes.

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Additional file 4: Table S3:

Statistics based on the counts of the mappable sequences.

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Additional file 5: Table S4:

Profile of the known porcine miRNAs (miRBase 17.0) with genome locations. Table S4.2. Profile of the known other mammalian miRNAs (miRBase 17.0). Table S4.3. Profile of porcine candidate miRNAs.

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Additional file 6: Table S5:

Unique porcine miRNAs.

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Additional file 7: Table S6:

List of the top 20 enriched Gene Ontology (GO) terms.

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Additional file 8: Table S7:

KEGG pathways enriched for the predicted protein coding target genes of miR-378, -148a, -143, and -27b.

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Additional file 9: Figure S2:

Relative expression levels of metabolism-related miRNAs. LDM, longissimus dorsi muscle; PMM, psoas major muscle. **P <0.001, Fisher’s exact test.

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Additional file 10: Figure S4:

Correlation of miRNA expression among three biological replicates within two libraries. (A) A scatter plot and trend line (Pearson’s correlation) revealed a correlation between the log10 of miRNA expression of each biological replicate. Line represents linear regression. (B) Heat map matrix of Pearson’s correlation between individuals and tissues.

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Additional file 11: Figure S3:

Deep sequencing and microarray data correlations. The data shows the fold change of relative expression between longissimus dorsi muscle (LDM) and psoas major muscle (PMM). (A) Correlation of the 151 known porcine miRNAs. (B) Correlation of the top ten co-expressed miRNAs.

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