gene refseq Search Results


refseq gene model  (OmicSoft Corporation)
90
OmicSoft Corporation refseq gene model
Refseq Gene Model, supplied by OmicSoft Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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refseq summary of human irf7 gene (nm_004029.2)  (Biotechnology Information)
90
Biotechnology Information refseq summary of human irf7 gene (nm_004029.2)
Refseq Summary Of Human Irf7 Gene (Nm 004029.2), supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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extracellular domain of tlr2  (Unigene)
90
Unigene extracellular domain of tlr2
Extracellular Domain Of Tlr2, supplied by Unigene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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refseq noncoding gene 9030619p08rik  (Biotechnology Information)
90
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.
Refseq Noncoding Gene 9030619p08rik, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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national center for biotechnology information refseq assembly and gene annotations  (Biotechnology Information)
90
Biotechnology Information national center for biotechnology information refseq assembly and gene annotations
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.
National Center For Biotechnology Information Refseq Assembly And Gene Annotations, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ucsc genome browser refseq gene track  (Nature Biotechnology)
90
Nature Biotechnology ucsc genome browser refseq gene track
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.
Ucsc Genome Browser Refseq Gene Track, supplied by Nature Biotechnology, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gene models refseq omyk_1.0  (Genoscope)
90
Genoscope gene models refseq omyk_1.0
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.
Gene Models Refseq Omyk 1.0, supplied by Genoscope, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gene (refseq)  (Integragen sa)
90
Integragen sa gene (refseq)
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.
Gene (Refseq), supplied by Integragen sa, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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human refseq gene models  (Nature Biotechnology)
90
Nature Biotechnology human refseq gene models
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.
Human Refseq Gene Models, supplied by Nature Biotechnology, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/gene+refseq/human+refseq+gene+models/us09428811-519-5-0
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gene refseq  (Hasegawa Co Ltd)
90
Hasegawa Co Ltd gene refseq
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.
Gene Refseq, supplied by Hasegawa Co Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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plasmid dna containing the rptp gene (refseq nm_002841.3) encoding the cytoplasmic portion (amino acids 790–1445) of the rptp protein  (Lexicon Pharmaceuticals)
90
Lexicon Pharmaceuticals plasmid dna containing the rptp gene (refseq nm_002841.3) encoding the cytoplasmic portion (amino acids 790–1445) of the rptp protein
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.
Plasmid Dna Containing The Rptp Gene (Refseq Nm 002841.3) Encoding The Cytoplasmic Portion (Amino Acids 790–1445) Of The Rptp Protein, supplied by Lexicon Pharmaceuticals, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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plasmid dna containing the rptp gene (refseq nm_002841.3) encoding the cytoplasmic portion (amino acids 790–1445) of the rptp protein - by Bioz Stars, 2026-11
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refseq_id gene_id  (Chrom Tech)
90
Chrom Tech refseq_id gene_id
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.
Refseq Id Gene, supplied by Chrom Tech, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


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