GEO DataSets

(Submitter supplied) MAF from pika Epas1-3FLAG knock-in mice were extracted and immortalized. After 12h DMOG treatment, cells were conducted for the ChIP-seq (Bmal1,Flag). We found that in knock-in mice fibroblasts, EPAS1-3FLAG can bind to similar E-box locus compared with BMAL1. Fibroblasts from mouse, rat, rabbit and Tibetan pika were extracted (and Tibetan pika fibroblasts were immortalized). RNA was extracted at 90% confluency. more...

Organism:

Rattus norvegicus; Ochotona curzoniae; Oryctolagus cuniculus; Mus musculus

Type:

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

5 related Platforms

18 Samples

Download data: BW, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus; Sus scrofa; Oryctolagus cuniculus; Bos taurus; Ovis aries; Mus musculus; Rattus norvegicus; Danio rerio; Felis catus; Macaca mulatta; Homo sapiens; Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing; Other

12 related Platforms

54 Samples

Download data: BED, HDF5, XLS

(Submitter supplied) Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. more...

Organism:

Gallus gallus; Sus scrofa; Oryctolagus cuniculus; Mus musculus; Danio rerio; Macaca mulatta; Homo sapiens; Canis lupus familiaris; Felis catus; Bos taurus; Ovis aries; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

12 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. more...

Organism:

Homo sapiens; Mus musculus; Felis catus; Bos taurus; Ovis aries; Oryctolagus cuniculus; Rattus norvegicus; Canis lupus familiaris; Danio rerio; Gallus gallus; Macaca mulatta

Type:

Other

11 related Platforms

25 Samples

Download data: BED, HDF5, XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Sus scrofa; Mus musculus; Gallus gallus; Macaca mulatta; Homo sapiens; Canis lupus familiaris; Cavia porcellus; Felis catus; Ovis aries; Oryctolagus cuniculus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

19 related Platforms

553 Samples

Download data: HIC, TXT

(Submitter supplied) Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. more...

Organism:

Macaca mulatta; Felis catus; Mus musculus; Rattus norvegicus; Gallus gallus; Ovis aries; Oryctolagus cuniculus; Canis lupus familiaris; Cavia porcellus

Type:

Expression profiling by high throughput sequencing

9 related Platforms

142 Samples

Download data: TXT