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refseq noncoding gene 9030619p08rik  (Biotechnology Information)
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Biotechnology Information refseq noncoding gene 9030619p08rik
Mouse liver–expressed lncRNAs. (A) Pipeline used for discovery of 15,558 liver-expressed lncRNAs, based on Melia et al. (22), except only gene structures whose exons overlap protein-coding gene exons transcribed in the same direction were removed. Of the 15,558 lncRNAs, 13,343 did not overlap any protein-coding gene and, therefore, were designated intergenic; 1,966 lncRNAs were designated antisense on the basis of their overlap with the antisense strand of a protein-coding gene; and 249 lncRNAs were designated intragenic (i.e., they were transcribed in the same direction as an overlapping protein-coding gene, but without any exonic region overlap). Data characterizing the 15,558 liver-expressed lncRNAs are presented in Supplemental Table 2A (44). (B) Principal component analysis of 186 RNA-seq samples used to discover liver-expressed lncRNAs. The first principal component separates the livers by the age of the mice from young to old (right to left; ages are indicated on the right). (C–G) Examples of sex-specific lncRNAs discovered in this study. Gene structures of lncRNAs are shown in green. Shown are wig files based on sequencing reads for male and female nuclear RNA-seq samples. (C) Intergenic lncRNA showing strong female-biased gene expression. (D, E) Intergenic lncRNAs showing strong male-biased gene expression. Additional details about these two lncRNAs are shown in Table 2 and Supplemental Fig. 2 (44). (F) Female-specific lncRNA, ncRNA_inter_chr15_12684, that is transcribed on the reverse strand and overlaps ncRNA_inter_chr15_12685, which is transcribed on the forward strand. Corresponds to RefSeq noncoding gene <t>9030619P08Rik.</t> (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a, which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.
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Mouse liver–expressed lncRNAs. (A) Pipeline used for discovery of 15,558 liver-expressed lncRNAs, based on Melia et al. (22), except only gene structures whose exons overlap protein-coding gene exons transcribed in the same direction were removed. Of the 15,558 lncRNAs, 13,343 did not overlap any protein-coding gene and, therefore, were designated intergenic; 1,966 lncRNAs were designated antisense on the basis of their overlap with the antisense strand of a protein-coding gene; and 249 lncRNAs were designated intragenic (i.e., they were transcribed in the same direction as an overlapping protein-coding gene, but without any exonic region overlap). Data characterizing the 15,558 liver-expressed lncRNAs are presented in Supplemental Table 2A (44). (B) Principal component analysis of 186 RNA-seq samples used to discover liver-expressed lncRNAs. The first principal component separates the livers by the age of the mice from young to old (right to left; ages are indicated on the right). (C–G) Examples of sex-specific lncRNAs discovered in this study. Gene structures of lncRNAs are shown in green. Shown are wig files based on sequencing reads for male and female nuclear RNA-seq samples. (C) Intergenic lncRNA showing strong female-biased gene expression. (D, E) Intergenic lncRNAs showing strong male-biased gene expression. Additional details about these two lncRNAs are shown in Table 2 and Supplemental Fig. 2 (44). (F) Female-specific lncRNA, ncRNA_inter_chr15_12684, that is transcribed on the reverse strand and overlaps ncRNA_inter_chr15_12685, which is transcribed on the forward strand. Corresponds to RefSeq noncoding gene 9030619P08Rik. (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a, which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.

Journal: Endocrinology

Article Title: Sex-Biased lncRNAs Inversely Correlate With Sex-Opposite Gene Coexpression Networks in Diversity Outbred Mouse Liver

doi: 10.1210/en.2018-00949

Figure Lengend Snippet: Mouse liver–expressed lncRNAs. (A) Pipeline used for discovery of 15,558 liver-expressed lncRNAs, based on Melia et al. (22), except only gene structures whose exons overlap protein-coding gene exons transcribed in the same direction were removed. Of the 15,558 lncRNAs, 13,343 did not overlap any protein-coding gene and, therefore, were designated intergenic; 1,966 lncRNAs were designated antisense on the basis of their overlap with the antisense strand of a protein-coding gene; and 249 lncRNAs were designated intragenic (i.e., they were transcribed in the same direction as an overlapping protein-coding gene, but without any exonic region overlap). Data characterizing the 15,558 liver-expressed lncRNAs are presented in Supplemental Table 2A (44). (B) Principal component analysis of 186 RNA-seq samples used to discover liver-expressed lncRNAs. The first principal component separates the livers by the age of the mice from young to old (right to left; ages are indicated on the right). (C–G) Examples of sex-specific lncRNAs discovered in this study. Gene structures of lncRNAs are shown in green. Shown are wig files based on sequencing reads for male and female nuclear RNA-seq samples. (C) Intergenic lncRNA showing strong female-biased gene expression. (D, E) Intergenic lncRNAs showing strong male-biased gene expression. Additional details about these two lncRNAs are shown in Table 2 and Supplemental Fig. 2 (44). (F) Female-specific lncRNA, ncRNA_inter_chr15_12684, that is transcribed on the reverse strand and overlaps ncRNA_inter_chr15_12685, which is transcribed on the forward strand. Corresponds to RefSeq noncoding gene 9030619P08Rik. (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a, which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.

Article Snippet: Corresponds to RefSeq noncoding gene 9030619P08Rik. (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a , which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.

Techniques: RNA Sequencing, Sequencing, Gene Expression