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Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq)

ABSTRACT: Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq)

PROVIDER: PRJNA556201 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9825000.fastq.gz	Fastqsanger.gz
	SRR9825010.fastq.gz	Fastqsanger.gz
	SRR9825020.fastq.gz	Fastqsanger.gz
	SRR9825030.fastq.gz	Fastqsanger.gz
	SRR9825001.fastq.gz	Fastqsanger.gz

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Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq)

Project description:Here we characterize microglia transcriptional program across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, while humans express significant microglia heterogeneity. In addition, we observed notable differences in complement, phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders, including Alzheimer’s and Parkinson’s disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia-based therapies in humans.

2019-12-12 | GSE134705 | GEO

Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq)

2019-12-12 | GSE134706 | GEO

Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program

Project description:Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program

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Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq)

Project description:Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq)

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Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-12-12 | GSE134707 | GEO

Conservation of human microsatellites across 450 million years of evolution.

Project description:The sequencing and comparison of vertebrate genomes have enabled the identification of widely conserved genomic elements. Chief among these are genes and cis-regulatory regions, which are often under selective constraints that promote their retention in related organisms. The conservation of elements that either lack function or whose functions are yet to be ascribed has been relatively little investigated. In particular, microsatellites, a class of highly polymorphic repetitive sequences considered by most to be neutrally evolving junk DNA that is too labile to be maintained in distant species, have not been comprehensively studied in a comparative genomic framework. Here, we used the UCSC alignment of the human genome against those of 11 mammalian and five nonmammalian vertebrates to identify and examine the extent of conservation of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites found in human sequences, 85.39% were conserved in at least one other species, whereas 28.65% and 5.98% were found in at least one and three nonprimate species, respectively. An exponential decline of microsatellite conservation with increasing evolutionary time, a comparable distribution of conserved versus nonconserved microsatellites in the human genome, and a positive correlation between microsatellite conservation and overall sequence conservation, all suggest that most microsatellites are only maintained in genomes by chance, although exceptionally conserved human microsatellites were also found in distant mammals and other vertebrates. Our findings provide the first comprehensive survey of microsatellite conservation across deep evolutionary timescales, in this case 450 Myr of vertebrate evolution, and provide new tools for the identification of functional conserved microsatellites, the development of cross-species microsatellite markers and the study of microsatellite evolution above the species level.

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A 450 million years long latitudinal gradient in age-dependent extinction.

Project description:Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age-dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age-dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern.

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Southern African ancient genomes estimate modern human divergence to 350,000-260,000 years ago

Project description:Southern African ancient genomes estimate modern human divergence to 350,000-260,000 years ago

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RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle, androgen, androgen and IMTPPE, androgen and JJ-(+)-450, androgen and JJ-(-)450, androgen and enzalutamide

Project description:RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle (C), androgen (R), androgen and IMTPPE (R + IMTPPE), androgen and JJ-(+)-450 (androgen + (-)450), androgen and JJ-(-)450 (androgen + (-)450), androgen and enzalutamide (androgen +Enz). To evaluate if our compounds can inhibit AR function specifically and completely, LNCaP mRNA profiles of cells treated with IMTPPE, (+)-JJ-450 and (-)-JJ-450, comparing to enzalutamide. RNA isolation was performed using RNeasy Mini kit (Qiagen), RNA Sequencing was carried out by Genomics Research Core of University of Pittsburgh using Illumina NextSeq 500 system. The sequence reads that passed FASTQC were analyzed at the transcript level. Each sample was mapped to the Human Ensembl reference genome GRCh38. We definied different expression genes with a fold change ≥2.0 and FDR <0.05. Both (-)-JJ-450 and enzalutamide are very specific to AR, with 56 and 186 DE genes comparing to control samples respectively. IMTPPE and (+)-JJ-450 can inhibit most of the androgen responsive genes, but also some other genes were affected. (-)-JJ-450 is a novel compound inhibts AR function specifically and completely, and it is a potential lead compound for the treatment of CRPC, including those resistant to enzalutamide.

2019-06-06 | GSE115395 | GEO

60 million years of co-divergence in the fig-wasp symbiosis.

Project description:Figs (Ficus; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant-pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant-insect co-divergence over a geological time frame spanning at least 60 million years.

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