GEO DataSets

(Submitter supplied) Although the chromatin regulator CTCF is enriched at genes escaping from X-chromosome inactivation (XCI), molecular mechanisms remain elusive. We examined CTCF and epigenetic features at escape genes on the inactive X (Xi) in mouse F1 hybrid cells and tissues. We found that escape genes are located inside topologically insulated domains limited by convergent arrays of CTCF binding sites, suggesting loop formation. more...

Organism:

Mus musculus; Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33375

2 Samples

Download data: BW

(Submitter supplied) Cellular senescence is a program of permanent cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in mammalian cells. Landmark studies in laboratory mice have established master senescence regulators, including p16INK4a, p21, NF-kB, p53, and C/EBPβ. To discover other molecular players in cellular senescence, we developed an approach that harnessed the natural divergence between distant mouse species. more...

Organism:

Mus musculus; Mus spretus; Mus musculus x Mus spretus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32187 GPL24247 GPL29827

42 Samples

Download data: TXT

(Submitter supplied) Here, we mapped cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic 'B2NeuN+' megabase-scaling subcompartment. Comparative chromosomal conformation mapping in Mus spretus and Mus musculus revealed neuron-specific reconfigurations tracking recent ERV2 retrotransposon expansions in the murine germline, with significantly higher B2 megadomain contact frequencies at sites with ongoing ERV2 insertions in Mus musculus. more...

Organism:

Mus musculus; Mus spretus

Type:

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

5 related Platforms

72 Samples

Download data: HIC, TXT, XLS

(Submitter supplied) We investigated the cis-regulatory divergences in alternative splicing and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid mouse. By obtaining more than 240 million read pairs on average in each sample from 5 organs and ESC as well as published data in liver, we comprehensively analyzed the allelic splicing patterns across tissues in hybrid mice. We find that tissue-dependent regulation causing large splicing differences is highly conserved and likely functional, while splicing divergence mainly affects genes under relaxed selective constraints. more...

Organism:

Mus musculus; Mus spretus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28894 GPL28893 GPL28892

18 Samples

Download data: TXT

(Submitter supplied) Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted genes is the leading candidate mechanism. However, direct evidence for the involvement of imprinted genes in hybrid growth dysplasia is limited. more...

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus domesticus x Mus spretus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL26185 GPL26184 GPL26187

29 Samples

Download data: TXT

(Submitter supplied) The increase of aged population makes it necessary to find effective prevention and treatment procedures to help the elderly to enjoy a healthy and long life. The organochlorine compound p,p´-DDE (1,1-dichloro-2,2-bis(p-chlorophenyl) ethylene) is a DDT metabolic byproduct that generates great concern because its deleterious effects on both human and environment health. It is an endocrine disruptor agent and causes alterations in immune response, reproductive system, development, nervous system and endocrine homeostasis. more...

Organism:

Mus spretus; Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

12 Samples

Download data: TXT

(Submitter supplied) The mammalian placenta is both the physical interface between mother and fetus, and the source of endocrine signals that target the maternal hypothalamus, priming females for parturition, lactation and motherhood. Despite the importance of this connection, the effects of altered placental signaling on the maternal brain are understudied. Here, we show that placental dysfunction alters gene expression in the maternal brain, with the potential to affect maternal behavior. more...

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus domesticus x Mus spretus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26185 GPL26184 GPL26187

44 Samples

Download data: CSV, TXT

(Submitter supplied) The complexity of environmental systems requires the use of holistic methodologies to conduct studies of contamination effects over individuals who inhabit specific polluted areas. Microarrays are an appropriate tool since they allow the simultaneous expression analysis of thousand genes. As an omic and unbiased technology, it allows for the identification of novel biological responses within certain environmental conditions. more...

Organism:

Mus musculus; Mus spretus

Type:

Expression profiling by array

Platform:

GPL10333

8 Samples

Download data: GPR

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

Organism:

Homo sapiens; Mus spretus; Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21697 GPL21626 GPL23505

61 Samples

Download data: BW

(Submitter supplied) In this study, we show that evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy concomitantly rewire DNA cleavage sites to novel contact domain boundaries. While transcription and replication coupled genomic rearrangements have been well documented, we demonstrate that DSBs at loop anchors are transcription-, replication-, and cell type- independent. more...

Organism:

Mus musculus; Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21626 GPL23505

18 Samples

Download data: BW

(Submitter supplied) In this study, we show that evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy concomitantly rewire DNA cleavage sites to novel contact domain boundaries. While transcription and replication coupled genomic rearrangements have been well documented, we demonstrate that DSBs at loop anchors are transcription-, replication-, and cell type- independent. more...

Organism:

Homo sapiens; Mus musculus; Mus spretus

Type:

Other

Platforms:

GPL23505 GPL21697 GPL21626

32 Samples

Download data: BW

(Submitter supplied) The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. more...

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL17106 GPL22153 GPL17637

35 Samples

Download data: BW

(Submitter supplied) We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from Doñana Biological Reserve (“Santa Olalla” lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. more...

Organism:

Mus musculus; Mus spretus

Type:

Expression profiling by array

Dataset:

GDS5331

Platform:

GPL4134

19 Samples

Download data: TXT

Analysis of Mus spretus livers from the polluted Domingo Rubio stream. Results provide insight into the biological effects of an industrial settlement on the liver of an aboriginal species.

Organism:

Mus musculus; Mus spretus

Type:

Expression profiling by array, count, 5 other sets

Platform:

GPL4134

Series:

GSE33663

19 Samples

Download data: TXT

(Submitter supplied) The “CTCF code” hypothesis posits that CTCF pleotropic functions are driven by recognition of diverse DNA sequences through combinatorial use of its 11 zinc fingers (ZFs). This model however is supported by in vitro binding studies of a limited number of sequences. To directly test CTCF multivalency in vivo we here define ZF binding requirements at ~50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. more...

Organism:

Mus musculus; Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17106 GPL9250 GPL13112

45 Samples

Download data: WIG

(Submitter supplied) We used tiling arrays to compare the testicular expression of chromosomes 2, X, Y and the mitochondrial genome between Mus m. domesticus and Mus spretus. We found an excess of dysregulated non-coding RNAs on chromosome 2. This group consists of intronic antisense RNAs, intergenic RNAs and also premature forms of PIWI-interacting RNAs (piRNAs). The unique transcriptional regulation in spermatogenesis is a characteristic of chromosome X. more...

Organism:

Mus spretus; Mus musculus; Mus musculus domesticus

Type:

Expression profiling by genome tiling array

Platform:

GPL6445

6 Samples

Download data: BED, CEL

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

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL11047 GPL10992

81 Samples

Download data: PAIR

(Submitter supplied) This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. more...

Organism:

Mus musculus; Mus spretus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11047

17 Samples

Download data: PAIR

(Submitter supplied) Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs.

Organism:

Mus musculus; Mus spretus; Mus musculus domesticus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10992

64 Samples

Download data: PAIR

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

Organism:

Mus musculus; Mus spretus; Mus musculus x Mus spretus

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL1261 GPL11355

273 Samples

Download data: CEL, TXT