GEO DataSets

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

Organism:

Drosophila melanogaster; Drosophila virilis; Drosophila busckii

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

17 Samples

Download data: BED, BW, H5

(Submitter supplied) We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. more...

Organism:

Drosophila virilis; Drosophila busckii; Drosophila melanogaster

Type:

Other; Third-party reanalysis

4 related Platforms

5 Samples

Download data: BED, FA, GTF, H5, TXT

(Submitter supplied) We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. more...

Organism:

Drosophila busckii; Drosophila virilis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25633 GPL25632

12 Samples

Download data: BW

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

Organism:

Mus musculus; Drosophila melanogaster

Type:

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

4 related Platforms

69 Samples

Download data: BW

(Submitter supplied) Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23323 GPL19132

6 Samples

Download data: BW

(Submitter supplied) Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

21 Samples

Download data: TXT

(Submitter supplied) Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23323 GPL19132

38 Samples

Download data: BED, BW

(Submitter supplied) Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21493

4 Samples

Download data: BW

(Submitter supplied) We identified orthologs of the roX lncRNAs across diverse Drosophilid species, and then mapped the genomic binding sites of roX1 and roX2 in four Drosophila species (D. melanogaster, D. willistoni, D. virilis, and D. busckii) using ChIRP-seq (chromatin isolation by RNA Purification and sequencing), thus revealing the interplay of the evolution of roX1 and roX2 and their genomic binding sites.

Organism:

Drosophila melanogaster; Drosophila busckii; Drosophila virilis; Drosophila willistoni

Type:

Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

35 Samples

Download data: BED, BEDGRAPH, BW, FA, RTF, XLSX

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

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19951

57 Samples

Download data: BEDGRAPH

(Submitter supplied) The rules according to which transcription factors selectively bind only a small subset of genomic sites from a vast pool of similar sequences are not understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the unequivocal distinction between a sex chromosome and all autosomes. In Drosophila melanogaster the male-specific-lethal dosage compensation complex (MSL-DCC) doubles the transcription output of most genes on the X chromosome via chromatin modification, but the nature of this selectivity is not known. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19951

12 Samples

Download data: BEDGRAPH

(Submitter supplied) The rules according to which transcription factors selectively bind only a small subset of genomic sites from a vast pool of similar sequences are not understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the unequivocal distinction between a sex chromosome and all autosomes. In Drosophila melanogaster the male-specific-lethal dosage compensation complex (MSL-DCC) doubles the transcription output of most genes on the X chromosome via chromatin modification, but the nature of this selectivity is not known. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19951

28 Samples

Download data: BEDGRAPH

(Submitter supplied) The rules according to which transcription factors selectively bind only a small subset of genomic sites from a vast pool of similar sequences are not understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the unequivocal distinction between a sex chromosome and all autosomes. In Drosophila melanogaster the male-specific-lethal dosage compensation complex (MSL-DCC) doubles the transcription output of most genes on the X chromosome via chromatin modification, but the nature of this selectivity is not known. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19951

17 Samples

Download data: BEDGRAPH

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

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL17275 GPL13304

6 Samples

Download data

(Submitter supplied) Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

2 Samples

Download data: TXT

(Submitter supplied) Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

2 Samples

Download data: TXT

(Submitter supplied) Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL17275

2 Samples

Download data: TXT

(Submitter supplied) During sexual dimorphism, the loss of one entire X chromosome in Drosophila males is achieved largely via a broad genome-wide aneuploid effect. Exploring how MSL proteins and two large non coding RNAs (roX1 and roX2) modulate trans-acting aneuploid effect for equality to females, we employ a system biology approach (microarray) to investigate the global aneuploid effect of maleless(mle) mutation by disrupting MSL binding. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL72

6 Samples

Download data: CEL, TXT

(Submitter supplied) Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bam∆86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL25244 GPL13304

14 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs), some of them being attached to the nuclear lamina (NL) in lamina-associated domains (LADs). Here, we identified LADs and TADs at two consecutive stages of Drosophila spermatogenesis – in spermatogonia (SpG) and spermatocytes (SpCs). We found that launching of SpC-specific transcription frequently correlates with promoters’ detachment from the NL accompanied by spatial insulation of adjacent regions. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL21306 GPL25244

5 Samples

Download data: COOL, MCOOL