GEO DataSets

(Submitter supplied) Comparing the transcriptome of wildtype and kdm5 mutant flies in normal conditions revealed a total of 4787 genes that were significantly downregulated and thus require KDM5 for their activation, and 3269 upregulated genes that are normally repressed by KDM5 (p<0.05, FDR <0.05). Because kdm5 mutants are sensitive to the oxidizer paraquat, we also carried out RNA-seq from wildtype and kdm5 mutant adults in oxidative stress conditions. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

4 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL13304

13 Samples

Download data: BED, TXT

(Submitter supplied) To determine which genes affected by loss of KDM5 in adults were direct targets, we carried out KDM5 ChIP-seq analyses. To valide this data, we utilized a previously generated fly strain in which the sole source of KDM5 is from a transgene expressing an HA tagged form of KDM5 expressed under the control of its endogenous promoter. Comparing genome-wide gene expression and KDM5 binding analyses in Drosophila adults, we demonstrate the primary function of KDM5 in adults is to activate gene expression KDM5. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: BED

(Submitter supplied) In order to determine which genes were affected by the complete loss of kdm5, we carried out RNA-seq analysis using wing discs from wildtype and kdm5 140, the new null mutant. Consistent with the phenotypes observed, transcriptome analyses of kdm5140 mutant wing imaginal discs revealed the dysregulation of a significant number of genes involved in cell cycle progression and DNA repair.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to generate a Drosophila model of intellectual disability caused by mutations in kdm5. RNA-seq was used to define the transcriptional defects of a mutation in Drosophila that is analogous to a human intellectual disability-associated allele, kdm5[A512p]. These data revealed a total of 1609 dysregulated genes, 778 of which were upregulated and 831 were downregulated. To determine whether these transcriptional defects were due to the loss of KDM5-induced histone demethylation, we also carried out RNA-seq from a enzymatic inactive strain, kdm5[Jmjc*]. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

9 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL25244 GPL32218

16 Samples

Download data

(Submitter supplied) kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. To profile KDM5 binding within these cells and this developmental stage, we performed Targeted DamID (TaDa). By profiling the nearest genes to significant TaDa peaks (FDR < 0.01), we identified 5815 candidate KDM5 target genes. Interestingly, 42% of these candidate KDM5 target genes appear to be conserved across multiple cellular contexts in Drosophila and span many cellular processes for future investigation.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32218

8 Samples

Download data: BEDGRAPH, XLSX

(Submitter supplied) kdm5 is an essential gene in Drosophila that has critical developmental roles in the prothoracic gland cells of the larval ring gland. We performed a bulk transcriptome analysis of the larval ring gland in w[1118] (wild type) and kdm5[140] (null mutant) in order to identify genes in the prothoracic gland involved in the lethality of kdm5 null mutants. We found that the absence of kdm5 causes dysregulation of genes involved in various metabolic pathways. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

8 Samples

Download data: TXT

(Submitter supplied) Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding the spatiotemporal requirements or neurodevelopmental contributions of KDM5 proteins. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is specifically required within ganglion mother cells and immature neurons for proper neurodevelopment. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26560

9 Samples

Download data: BEDGRAPH, GFF, XLSX

(Submitter supplied) We performed a transcriptome analysis of the larval VNC in kdm5 WT, kdm5[L854F] and enzymatically inactive kdm5[JmjC] in order to identify genes contributing to the phenotypes observed in the mutants' neuromuscular junction (NMJ). We found that inactivation of the catalytic activity in kdm5[JmjC] causes dysregulation of genes related to glutamate metabolism while the mutation L854F leads to dysregulation of genes involved in microtubule cytoskeleton dynamics. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

12 Samples

Download data: TXT

(Submitter supplied) Histone posttranslational modifications (HPTMs) are involved in regulating the synthesis of fungal bioactive compounds. The exact molecular mechanisms of the silencing/activation of secondary metabolism (SM) clusters by these epigenetic events however are not yet fully understood. This work applies a combined approach of quantitative mass spectrometry (LC-MS/MS) and chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) to identify the chromatin landscape in two metabolic states: primary and secondary metabolism. more...

Organism:

Aspergillus nidulans

Type:

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

Platform:

GPL19470

37 Samples

Download data: SGR, TXT

(Submitter supplied) A. nidulans kdmA encodes a member of the KDM4 family of jumonji histone demethylase proteins, highly similar to metazoan orthologues both within functional domains and in domain architecture. This family of proteins exhibits demethylase activity toward lysines 9 and 36 of histone H3 and plays a prominent role in gene expression and chromosome structure in many species. Mass spectrometry mapping of A. more...

Organism:

Aspergillus nidulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19470

8 Samples

Download data: TXT

(Submitter supplied) Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding their spatiotemporal requirements or neurodevelopmental contributions. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is required within ganglion mother cells and immature neurons for proper axogenesis. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL26560

32 Samples

Download data: XLSX

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16479 GPL17275 GPL21306

40 Samples

Download data

(Submitter supplied) To determine microbiota composition associated with loss of KDM5 in intestine, we carried out 16S rRNA seq analyses of dissected intestine from wildtype and kdm5 mutant. [GSM2628181-GSM2628190]. A total of 78 operational taxonomic units (OTUs) were identified in the sequence data. There were about 15 genera much less abundant in kdm5 mutant compared to wildtype. The kdm5 mutant were sensitive to pathogen. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL17275 GPL16479

36 Samples

Download data: FASTA, TXT, XLS

(Submitter supplied) To determine the gene expression changes associated with loss of KDM5 in drosophila intestine tissue, we performed RNA-seq analyses for these dissected intestine tissue from wildtype and kdm5 mutant. These analyses revealed different expressed genes between kdm5 mutant compared to wildtype in intestine tissue. These differentially expressed genes were enriched in the innate immune pathway through Gene ontology(GO) enrichment analysis.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

4 Samples

Download data: XLSX

(Submitter supplied) Mutations in PHF8 are associated with X-linked mental retardationand cleft lip/cleft palate. PHF8 contains a plant homeodomain(PHD) in its N-terminus and is member of a family of JmjC-domaincontaining proteins. While PHDs can act as methyl lysine recognitionmotifs, JmjC-domains can catalyze lysine demethylation. Here,we show that PHF8 is a histone demethylase that removes repressivehistone H3 dimethyl lysine 9 marks. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9115 GPL6480

16 Samples

Download data: BED, TXT, WIG

(Submitter supplied) PHF8 is an H3K9me2 demethylase, interacts with H3K4me3 and RNA Polymerase II, is enriched at thousands of transcription start sites and can act as a transcriptional co-activator.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

10 Samples

Download data: BED, WIG

(Submitter supplied) PHF8 is an H3K9me2 demethylase, interacts with H3K4me3 and RNA Polymerase II, is enriched at thousands of transcription start sites and can act as a transcriptional co-activator. In the following experiment we wanted to analyze the impact of PHF8-knockdown on transcript levels in HeLa cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

6 Samples

Download data: TXT

(Submitter supplied) Here we have characterized the role of KDM5 family during adipocyte differentiation of 3T3-L1 preadipocytes. Notably, our study represents the first to simultaneously knock down all the KDM5 family members thereby avoiding interference from redundancy between KDM5 subtypes. Using a combination of knockdown and genome-wide ChIP-seq and RNA-seq analyses we uncover the underlying mechanisms of the inhibition of adipogenesis as well as basic aspects of KDM5 function.

Organism:

Mus musculus

Type:

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

Platform:

GPL18480

34 Samples

Download data: BEDGRAPH, TXT