GEO DataSets

(Submitter supplied) Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.

Organism:

Notamacropus eugenii; Orycteropus afer; Sarcophilus harrisii; Loxodonta africana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

7 related Platforms

15 Samples

Download data: BEDGRAPH, TSV, TXT

(Submitter supplied) Contrast the genomes of different elephants species to find genetic differences underlying species differences like immune system differences that impact disease resistance.

Organism:

Loxodonta africana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18016

4 Samples

Download data: TXT

(Submitter supplied) The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. more...

Organism:

Loxodonta africana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24284

12 Samples

Download data: TXT

(Submitter supplied) The placenta is arguably the most anatomically variable organ in mammals. Understanding gene expression patterns among placentas from multiple species can illuminate the molecular basis of placenta function as well as potentially enrich our knowledge of the biology of obstetrical syndromes. We measured the expression profiles of the term placenta of multiple therian mammals using RNA-Seq. We identified multiple genes and transcripts which are differentially expressed across lineages including prolactin, relaxin, and galectins, as well as identifying the non-housekeeping genes which are core to placenta function (such as components of annexin complexes) in all species studied.

Organism:

Loxodonta africana; Bos taurus; Ateles fusciceps; Mus musculus; Pan paniscus; Canis lupus familiaris; Monodelphis domestica; Dasypus novemcinctus

Type:

Expression profiling by high throughput sequencing

8 related Platforms

8 Samples

Download data: FASTA, FPKM_TRACKING

(Submitter supplied) We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts. For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. more...

Organism:

Notamacropus eugenii; Loxodonta africana; Callithrix jacchus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT