Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA266000 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.
2016-03-24 | E-GEOD-70419 | biostudies-arrayexpress
Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.
2016-03-24 | E-GEOD-79541 | biostudies-arrayexpress
Project description:We report that head to head long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and classified to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differentiation by removing LIF or neural differentiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors.
2016-10-31 | GSE62899 | GEO
Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors.
2016-03-24 | GSE70419 | GEO
Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors.
2016-03-24 | GSE79541 | GEO
Project description:We report that head to head long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and classified to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we deleted the promoter and exon1 region which shared by Evx1as/Evx1 XH pair in embryonic stem cells by two sgRNAs-mediated CRISPR. Two homozygous mutants came out from 46 single clones with high efficiency, while two control clones were picked from cells which were only Cas9 transfected. These two mutants failed to activate Evx1 in -LIF differentiation compared to control cells, while Evx1as still have 30% mRNA residual. Meanwhile, we characterized gene expression level among different stages of ESC differentiation and found many differentiated related makers exhibited aberrant regulation, especially endodermal genes. We propose that XH lncRNA and its coding neighbor could regulate each other, and function as a unit to promote ESC differentiation and biological development.
2016-03-24 | GSE58801 | GEO
Project description:Long non-coding RNAs (lncRNAs) can have potential roles in development of tissues and organs. We selected breast muscle of fast-growing White Recessive Rock chicken (WRR) and slow-growing Xing Hua chicken (XH) to identify lncRNA transcripts by LncRNA-Seq. This study identified 21,993 novel lncRNAs. Among 7,339 differentially expressed lncRNAs, 723 up-regulated and 6,616 down-regulated lncRNAs were found in WRR compared with XH. Of them, five novel lncRNA were antisense transcripts for growth-related genes CACNA1D (unigene 14689_all), IL4I1 (unigene 15355_all), LEF-1 (unigene 19525_all) and FABP1 (unigenes 17536_all and 17537_all) respectively. Meanwhile, 12 other novel lncRNAs were found in the intron or downstream of some known growth-related genes (IGF1, IGF2BP2, IGF2BP3, CACNA1D, IL4I1, LEF-1 and FABP1). In addition, 4,043 SSRs and 200,049 SNPs were identified. Our data revealed the global lncRNA expression pattern in muscle tissue, and contributed a useful genomic resource towards studying the effects of lncRNAs in regulating chicken growth. Two RNA pool for WRR and XH strains
2014-06-24 | E-GEOD-58755 | biostudies-arrayexpress
Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
| S-EPMC8784167 | biostudies-literature
Project description:Long non-coding RNAs (lncRNAs) can have potential roles in development of tissues and organs. We selected breast muscle of fast-growing White Recessive Rock chicken (WRR) and slow-growing Xing Hua chicken (XH) to identify lncRNA transcripts by LncRNA-Seq. This study identified 21,993 novel lncRNAs. Among 7,339 differentially expressed lncRNAs, 723 up-regulated and 6,616 down-regulated lncRNAs were found in WRR compared with XH. Of them, five novel lncRNA were antisense transcripts for growth-related genes CACNA1D (unigene 14689_all), IL4I1 (unigene 15355_all), LEF-1 (unigene 19525_all) and FABP1 (unigenes 17536_all and 17537_all) respectively. Meanwhile, 12 other novel lncRNAs were found in the intron or downstream of some known growth-related genes (IGF1, IGF2BP2, IGF2BP3, CACNA1D, IL4I1, LEF-1 and FABP1). In addition, 4,043 SSRs and 200,049 SNPs were identified. Our data revealed the global lncRNA expression pattern in muscle tissue, and contributed a useful genomic resource towards studying the effects of lncRNAs in regulating chicken growth.
2014-06-24 | GSE58755 | GEO
Project description:Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
| S-EPMC11335981 | biostudies-literature