Open Access Highly Accessed Research article

Identification and analysis of pig chimeric mRNAs using RNA sequencing data

Lei Ma12, Shulin Yang1, Weiming Zhao1, Zhonglin Tang1, Tingting Zhang2 and Kui Li1*

Author Affiliations

1 The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China

2 College of Life Science, Shihezi University, Xinjiang, 832000, P. R. China

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BMC Genomics 2012, 13:429  doi:10.1186/1471-2164-13-429

Published: 28 August 2012

Additional files

Additional file 1:

Putative chimeric mRNAs. The file lists the information on the putative chimeric mRNAs, including GenBank identifier, fusion type, overlap or gap between partners, junction site in the transcript, trans-splicing signals, and annotation in GenBank, as well as the chromosome location of the partners.

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Additional file 2:

Putative chimeric mRNAs validated by RT-PCR. The file shows the results of the RT-PCR assay.

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Additional file 3:

Putative chimeric mRNAs validated by ESTs. The table lists the chimeric mRNAs validated by ESTs. The columns of the table consist of the GenBank ID of putative chimeric mRNAs, the number of ESTs that overlap at least 20 nt of the sequence on either side of a putative fusion point, as well as the GenBank ID of each EST.

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Additional file 4:

Pig putative chimeric mRNAs similar to known human chimeric mRNAs. Pig putative chimeric mRNAs were aligned to known human chimeric transcripts. The table represents the BLAST results and the annotations of human chimeric mRNAs in ChimeraDB version 2.0.

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Additional file 5:

Information on RNA-seq reads. The raw reads, the cleaned reads, the uniquely mapped reads on the genome, the multi-mapped reads on the genome, the un-mapped reads on the genome, and the junction reads are shown in the table.

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Additional file 6:

Pig chimeric mRNAs validated by RNA-seq reads. The table shows the pig chimeric mRNAs validated by the RNA-seq reads derived from liver tissue and skeletal muscle. A fusion junction mapped by junction reads derived from at least three different start positions or at least three samples was considered a validated chimeric event. The junction reads should overlap with at least 5 nt of the sequence on either side of the chimeric junction.

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Additional file 7:

Evaluation on the junction reads. Figure (A) shows the count of the fusion junctions based on the count of junction reads. Figure (B) represents the count of the fusion junctions based on the count of positions that junction reads start.

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Additional file 8:

Putative DNA motifs shared in the genomic regions of the partners. The table gives some information on the putative DNA motifs shared in the genomic regions of the partners.

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Additional file 9:

Similar DNA sequences that match known DNA motifs in the JASPAR CORE database. The table shows similar DNA sequences matched known DNA motifs in the JASPAR CORE database.

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Additional file 10:

Potential CTCF binding motifs. The table shows potential CTCF binding motifs.

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