GEO DataSets

(Submitter supplied) In order to rule out the presence of random X inactivation in A. carolinensis females we generated scRNA-Seq from liver cells and genome sequence data from liver.

Organism:

Anolis carolinensis

Type:

Genome variation profiling by high throughput sequencing

Platforms:

GPL23678 GPL15001

7 Samples

Download data: VCF

(Submitter supplied) In order to study the green anole dosage compensation mechanism we generated strand-specific RNA-seq libraries for a total of 186 samples from the green anole and other representative amniotes (human, mouse, opossum, platypus, chicken and xenopus). Moreover, in order to understand the dosage compensation mechanism of A. carolinensis, we generated ChIP-Seq data for the histone modification H4K16ac and compared levels of acetylation between males and females. more...

Organism:

Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Mus musculus; Homo sapiens; Anolis carolinensis; Monodelphis domestica

Type:

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

8 related Platforms

197 Samples

Download data: BW, TXT

(Submitter supplied) As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore dosage balance between the X and autosomes, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. more...

Organism:

Ornithorhynchus anatinus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13798

3 Samples

Download data: TXT

(Submitter supplied) Sex chromosome dosage differences between males and females are a significant form of natural genetic variation in many species. Like many species with chromosomal sex determination, Drosophila females have two X chromosomes, while males have one X and one Y. The model species D. melanogaster has five roughly equally sized chromosome arms, one of which is the X chromosome. However, fusions of sex chromosomes with autosomes have occurred along the lineage leading to D. more...

Organism:

Drosophila miranda; Drosophila pseudoobscura

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18087 GPL13310

96 Samples

Download data: TXT

(Submitter supplied) To understand transcriptomic dynamics of PGC (primordial germ cells; pole cell) of fruit fly, we used fluorescence-activated cell sorting (FACS) to isolate PGC from the embryos carrying the transgene, EGFP-vasa, which expresses GFP specifically and continuously in the germline throughout the life cycle. The PGCs collected at 11 time points during the embryogenesis were subjected to microarray analyses.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL4336

44 Samples

Download data: TXT

(Submitter supplied) Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma. We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by array; Other

Platforms:

GPL20 GPL9058

17 Samples

Download data: GPR, TXT

(Submitter supplied) Data from whole-body, head, thorax, abdomen, ovaries, testes and accessory glands was used to assess possible causes of a non-random distribution of sex-biased genes (sexually dimorphic expression). All samples were derived from virgin adult flies.

Organism:

Drosophila serrata

Type:

Expression profiling by array

Platform:

GPL16969

176 Samples

Download data: PAIR

(Submitter supplied) Here, we show that doubling of the global expression level of the X chromosome achieves dosage compensation in somatic tissues from several mammalian species. X-linked genes are highly expressed in brain tissues, consistent with a role in cognitive functions. Keywords: Normal Tissue

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data

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

Organism:

Anopheles gambiae; Drosophila melanogaster

Type:

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

Platforms:

GPL25232 GPL23323

32 Samples

Download data: BW

(Submitter supplied) Heteromorphic sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies and mammals. The reason for these mechanistic differences remain unclear: Are they a consequence of distinct genomes and gene content, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. more...

Organism:

Anopheles gambiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25232

12 Samples

Download data: BW

(Submitter supplied) Heteromorphic sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies and mammals. The reason for these mechanistic differences remain unclear: Are they a consequence of distinct genomes and gene content, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. more...

Organism:

Anopheles gambiae; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25232 GPL23323

20 Samples

Download data: TXT

(Submitter supplied) Whole genome expression analyses reveal little evidence for X chromosome dosage compensation or meiotic inactivation in Drosophila testes, whereas testes-specific transgene reporters suggest a novel form of X chromosome-specific regulation.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL7300

3 Samples

Download data: TXT

(Submitter supplied) To measure the response to gene dose, we performed mRNA-Seq of fly heads with molecularly defined deletions constructed from DrosDel deficiency lines (Ryder et al. Genetics 2007, 177(1):615-29) on the Illumina HiSeq 2000 platform.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

249 Samples

Download data: TXT

(Submitter supplied) This track depicts high throughput sequencing of long RNAs (>200 nt) from RNA samples from tissues or subcellular compartments from ENCODE cell lines. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9052

3 Samples

Download data: BB

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

Organism:

Mus musculus x Mus spretus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

9 related Platforms

60 Samples

Download data: BED, BIGWIG, CEL, GFF, PAIR, TXT

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9185

1 Sample

Download data: TXT

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9833

2 Samples

Download data: GFF, PAIR

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Alex Dobin mailto:dobin@cshl.edu (computational), Felix Schlesinger mailto:schlesin@cshl.edu (computational), Tom Gingeras mailto:gingeras@cshl.edu (primary investigator), and Roderic Guigo's group mailto:rguigo@imim.es at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL9115 GPL11154

99 Samples

Download data: BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF, TXT

(Submitter supplied) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

4 related Platforms

84 Samples

Download data: BAM, BB, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF

(Submitter supplied) Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

32 Samples

Download data: CSV, TXT