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Items: 1 to 20 of 1195

1.

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL19806 GPL19132 GPL16479
16 Samples
Download data: BW, TXT
Series
Accession:
GSE225980
ID:
200225980
2.

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila [ChIP LBF]

(Submitter supplied) Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16479
2 Samples
Download data: BW, TXT
Series
Accession:
GSE225970
ID:
200225970
3.

R7-dependent transcription in the developing Drosophila retina

(Submitter supplied) Color vision in Drosophila is mediated by photoreceptors R7 and R8, which express various combinations of opsins Rh3, Rh4, Rh5 and Rh6 depending on their cellular identity. Most ommatidia are classified as either “pale” or “yellow” subtypes with pale ommatidia coordinately expressing Rh3 and Rh5—in R7 and R8 cells respectively—while yellow express Rh4 and Rh6. Subtype identity is established initially in R7 photoreceptors via a stochastic mechanism then transmitted to the R8 via an inductive signal to ensure paired opsin expression. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
8 Samples
Download data: CSV
Series
Accession:
GSE220550
ID:
200220550
4.

Quantitative acetylomics reveals substrates of lysine acetyltransferase GCN5 in adult and aging Drosophila

(Submitter supplied) Drosophila GCN5 activity profoundly impacts gene expression.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19132 GPL16479
36 Samples
Download data: CSV, TXT
Series
Accession:
GSE221154
ID:
200221154
5.

Global Stable-isotope Tracing Metabolomics Reveals System-wide Metabolic Alternations in Aging Drosophila

(Submitter supplied) System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
6 Samples
Download data: CSV
Series
Accession:
GSE204740
ID:
200204740
6.

Despite its sequence identity with canonical H4, Drosophila H4r product is enriched at specific chromatin regions

(Submitter supplied) A single H4 variant gene (H4r) that is located outside of the histone cluster and gives rise to a polyA tailed messager RNA via replication-independent expression is preserved in Drosophila strains despite that its protein product is identical with canonical H4. In order to reveal information on the possible role of this alternative H4 we epitope tagged endogenous H4r and revealed its genome-wide localization to chromatin at the nucleosomal level. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16479
24 Samples
Download data: BW
Series
Accession:
GSE197256
ID:
200197256
7.

Protein-RNA-Chromatin Interactions Reveal Nuclear RNA Architecture Functions in Transcriptional Condensation and Chromatin Folding

(Submitter supplied) It has been proposed that nucleome organization and genome function involve interplays between protein, RNA and chromatin architectures. However, how chromatin interactions are cooperatively mediated by nuclear proteins and RNAs have not been fully explored. Here, we report the multivalent interplays in Drosophila cells involving RNA Polymerase II (RNAPII), nuclear RNAs and chromatin interactions. Using a novel genomic approach (pRChIA-PET) for protein-RNA-chromatin interactions, we discovered that extensive combination of nuclear RNAs cooperatively act in trans and co-localize with RNAPII and associated protein cofactors at chromatin interaction loci of active promoters and enhancers. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL16479 GPL19132
22 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE123455
ID:
200123455
8.

Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling.

(Submitter supplied) We report the 4C-seq data and ChIP-seq to study Shep regulation of chromatin looping. We also reported ATAC-seq and CUT&Tag data on sorted neurons that reveal chromatin accessibility and states during the neuronal remodeling of Drosophila melanogaster
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19132 GPL16479 GPL17275
23 Samples
Download data: BW
Series
Accession:
GSE154645
ID:
200154645
9.

RNA-Chromatin Interactome Reveals ncRNA Functions for Transcription Regulation in 3D Genome Organization

(Submitter supplied) Noncoding RNAs (ncRNAs) are an emerging class of regulatory molecules with a broad range of regulatory functions believed to be mediated by ncRNA-chromatin interactions. Genome-wide understanding of ncRNA functions requires precise mapping of all ncRNAs and their target loci. Current methods for studying chromatin-associated ncRNA lack specificity or are limited to singly assessing RNAs. We devised an unbiased strategy to identify all RNA Interactions with Chromatin by Paired-End-Taging (RICh-PET) and applied this approach to characterize the Drosophila RNA-chromatin interactome. more...
Organism:
Drosophila melanogaster; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL22339 GPL16479
19 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE85764
ID:
200085764
10.

Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are germline-specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes), and plays a critical role for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation, and increases H3K9me3 and histone H1. Additionally, Nxf2, a nuclear RNA export factor variant, has been identified as a co-factor. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL23702 GPL21306 GPL16479
36 Samples
Download data: BEDGRAPH, TSV, WIG
Series
Accession:
GSE158082
ID:
200158082
11.

Drosophila CRTC promotes starvation resistance by modulating one-carbon metabolism and insulin signaling

(Submitter supplied) CRTC modulates one-carbon metabolism and insulin signaling during fasting
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
21 Samples
Download data: DIFF, TXT
Series
Accession:
GSE156577
ID:
200156577
12.

Histone lysine methyltransferase Pr-set7/SETD8 promotes neural stem cell reactivation

(Submitter supplied) The ability of neural stem cells (NSCs) to switch between quiescence and proliferation is crucial for brain development and homeostasis. Increasing evidence suggest that variants of histone lysine methyltransferases including KMT5A are associated with neurodevelopmental disorders. However, the function of KMT5A/Pr-set7/SETD8 in the central nervous system is not well established. Here, we show that Drosophila Pr-Set7 is a novel regulator of NSC reactivation. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16479
4 Samples
Download data: BED
Series
Accession:
GSE158764
ID:
200158764
13.

Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells

(Submitter supplied) Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16479 GPL13304
18 Samples
Download data: BEDGRAPH, CSV, TXT
Series
Accession:
GSE108329
ID:
200108329
14.

Single-cell RNAsequencing of Drosophila PI Circadian Output Cells

(Submitter supplied) The circadian system produces ~24-hr oscillations in behavioral and physiological processes to ensure that they occur at optimal times of day and in the correct temporal order. At its core, the circadian system is composed of dedicated central clock neurons that keep time through a cell-autonomous molecular clock. To produce rhythmic behaviors, time-of-day information generated by clock neurons must be transmitted across output pathways to regulate the downstream neuronal populations that control the relevant behaviors. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
5 Samples
Download data: TXT
Series
Accession:
GSE162379
ID:
200162379
15.

Nucleosome assembly protein-1 (NAP-1) is regulator of histone H1 acetylation

(Submitter supplied) We identified NAP-1 as regulator of histone H1 acetyation.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
6 Samples
Download data: TXT
Series
Accession:
GSE159294
ID:
200159294
16.

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster

(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:
GPL16479
13 Samples
Download data
Series
Accession:
GSE155581
ID:
200155581
17.

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [RNA-seq]

(Submitter supplied) Three distinct enzymes are known to be capable of methylating lysine 9 residue of the histone H3 in Drosophila melanogaster: Su(var)3-9, SetDB1, and G9a. Here, we explored functional specialization of the two of them: SetDB1 and Su(var)3-9. Using DamID approach, we generated the binding profile for SetDB1 in salivary gland chromosomes, and matched it to the previously published profile of Su(var)3-9. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16479
3 Samples
Download data: TXT
Series
Accession:
GSE155580
ID:
200155580
18.

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster [DamID-seq]

(Submitter supplied) Three distinct enzymes are known to be capable of methylating lysine 9 residue of the histone H3 in Drosophila melanogaster: Su(var)3-9, SetDB1, and G9a. Here, we explored functional specialization of the two of them: SetDB1 and Su(var)3-9. Using DamID approach, we generated the binding profile for SetDB1 in salivary gland chromosomes, and matched it to the previously published profile of Su(var)3-9. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16479
10 Samples
Download data: WIG
Series
Accession:
GSE155579
ID:
200155579
19.

Comparison of mitochondrial transcription errors in wild type and mutant mitochondrial RNA polymerase overexpression flies

(Submitter supplied) To determine the error rate of mitochondrial transcription, we ananlyzed 33 and 37 million reads respectively for wild type (WT) and mutant (E423P) mitochondrial RNA polymerase (POLRMT) overexpression flies and found that the error frequency of mitochondrial transcripts were over 5 fold higher in E423P flies than that of WT. To gain more insight into the molecular mechanisms that drive the error rate of transcription by POLRMT, we examined its distribution of errors along the mitochondrial genome. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL16479 GPL23323
4 Samples
Download data: TXT
Series
Accession:
GSE154310
ID:
200154310
20.

Developmental regulation of Canonical and small ORF translation from mRNAs

(Submitter supplied) We present a genome-wide assessment of the translation of small open reading frames (smORF) in Drosophila melanogaster mRNAs, using ribosomal profiling of polysomal fractions in three contiguous temporal windows, which encopass all of embryogenesis. We also performed the same protocol using S2 cells. In this way, mRNAs bound by multiple ribosomes can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits.
Organism:
Drosophila melanogaster
Type:
Other
Platforms:
GPL19132 GPL16479
13 Samples
Download data: CSV
Series
Accession:
GSE147619
ID:
200147619
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