RNA-seq in 4 tissues of 10 mammals
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Rattus norvegicus
SUBMITTER: Masa Roller
PROVIDER: E-MTAB-8122 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To study the tissue-specific evolution of regulatory elements in the mammalian lineage, we created a comprehensive map of promoters and enhancers in 4 tissues of 10 mammalian species. To map in-vivo promoters and enhancers, we performed ChIP-seq experiments for H3K4me3, H3K27ac and H3K4me1 in adult liver, muscle, brain and testis of all 10 species. The species included in the study are: macaque, marmoset, mouse, rat, rabbit, pig, dog, cat, horse and opossum. To correlate regulatory evolution to expression, we also performed RNA-seq experiments in all tissues and species submitted separately to ArrayExpress.
2020-09-30 | E-MTAB-7127 | biostudies-arrayexpress
Project description:The origin and stability of germline noncoding RNAs remain largely uncharacterized in mammals. Here, we demonstrate that the vast majority of pachytene piRNAs originate from less than 100 bi- and unidirectionally transcribed loci in the mouse genome. These loci show features characteristic of transcribed protein-coding genes, including primary transcription by RNA polymerase II, H3K4 trimethylation marking the transcription initiation site, and H3K36 trimethylation present at elongation regions in a highly tissue-specific manner. We identified MYBL1, a spermatocyte-enriched transcription factor, as a potential driver of piRNA precursor transcripts. By similarly mapping piRNA clusters in testes of dog and opossum, we revealed that the regulatory architectures generating piRNAs appear to be highly conserved in mammals. Finally, we discovered that apparently neutral chromosomal rearrangements in evolution can act as an unexpected mechanism to generate novel piRNA clusters in diverse mammals. Thus, our results demonstrate how an integrated, multi-species approach can help define the genomic features and evolutionary mechanisms underlying mammalian germline noncoding RNAs.
2015-09-01 | E-MTAB-1265 | biostudies-arrayexpress
Project description:RNA-seq of total RNA was produced to aid in re-annotation of genes in horse, mouse, opossum, macaque, rat and pig. The RNA-seq was isolated from brain, liver and/or muscle.
2019-09-01 | E-MTAB-8118 | biostudies-arrayexpress
Project description:Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family. Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present. Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids. In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable. Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation. A testicular tissue sample from dog, horse, and two different Eptesicus fuscus individuals. Four samples total.
2014-05-19 | E-GEOD-47593 | biostudies-arrayexpress
Project description:Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. However, not all species have clear PMD/HMDs in their placentas. Instead what is conserved is higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification compared with the rest of the genome. As in human placenta, high gene body methylation is associated with higher gene expression across species. Analysis of DNA methylation in mouse and cow oocytes shows the same pattern of gene body methylation over many of the same genes as in the placenta, suggesting that this conserved pattern of active gene body methylation of the placenta may be established very early in development. MethylC-seq on placentas of 7 mammals, trophoblasts of rhesus, brains of 3 mammals, oocytes of cow, and human cordblood
2015-08-05 | E-GEOD-63330 | biostudies-arrayexpress
Project description:Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. However, not all species have clear PMD/HMDs in their placentas. Instead what is conserved is higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification compared with the rest of the genome. As in human placenta, high gene body methylation is associated with higher gene expression across species. Analysis of DNA methylation in mouse and cow oocytes shows the same pattern of gene body methylation over many of the same genes as in the placenta, suggesting that this conserved pattern of active gene body methylation of the placenta may be established very early in development.
2015-08-05 | GSE63330 | GEO
Project description:RNA sequencing (RNA-seq) was used to annotate chimpanzee, gorilla, gibbon, and marmoset genome and transcript isoforms in adult testis. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11074 | biostudies-arrayexpress
Project description:Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family. Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present. Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids. In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable. Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation.
2014-05-19 | GSE47593 | GEO
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 9,926 nuclei in opossum adult testis. This dataset includes three samples from three different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11072 | biostudies-arrayexpress
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 7,318 nuclei in marmoset adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11069 | biostudies-arrayexpress