GEO DataSets

(Submitter supplied) The Piwi-piRNA pathway is well known for its germline function, yet its somatic role remains elusive. We show here that Piwi is required autonomously not only for germline stem cell (GSC) but also for somatic cyst stem cell (CySC) maintenance in the Drosophila testis. Reducing Piwi activity in the testis caused defects in CySC differentiation. Accompanying this, GSC daughters expanded beyond the vicinity of the hub but failed to differentiate further. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

1 Sample

Download data: TXT

(Submitter supplied) piRNAs function in silencing retrotransposons by associating with the PIWI proteins, AGO3, Aub, and Piwi, in Drosophila germlines. Bioinformatics analyses of piRNAs in Drosophila ovaries suggested that piRNAs are produced by two systems, the primary processing pathway and the amplification loop, from repetitive genes and piRNA clusters in the genome. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9333

1 Sample

Download data

(Submitter supplied) Despite exciting progress in understanding the Piwi-associ-ated RNA (piRNA) pathway in the germ line, less is known about this pathway in somatic cells. We showed previously that Piwi, a key component of the piRNA pathway in Drosophila, is regulated in somatic cells by Yb, a novel protein containing an RNA helicase-like motif and a Tudor-like domain. Yb is specifically expressed in gonadal somatic cells and regulates piwi in somatic niche cells to control germ line and somatic stem cell self-renewal. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

2 Samples

Download data: TXT

(Submitter supplied) This project aims to identify molecular effects of piwi mutations and c-Fos overexpression on the formation of Drosophila ovarian germline RNA-seq was utilized to compare transcript levels between wild type, piwi mutant, and c-Fos over-expressing ovarian tissues

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: TXT

(Submitter supplied) With the ChIP-seq experiment, we identified direct target genes of E(Pc) specifically in somatic gonadal cells. We found that the E(Pc)-binding genes are enriched with signaling pathway components, consistent with our functional data showing prevailing germline defects even when E(Pc) function is exclusively compromised in somatic gonadal cells. In addition, we also performed RNA-seq to compare transcriptomes between E(Pc) knockdown testes and control testes.

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL16479 GPL17275

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Heterochromatin, representing the silenced state of transcription, largely consists of transposon-enriched and highly repetitive sequences. Implicated in heterochromatin formation and transcriptional silencing in Drosophila are PIWI and repeat-associated small interfering RNAs (rasiRNAs). Despite this, the role of PIWI in rasiRNA expression and heterochromatic silencing remains unknown. Here we report the identification and characterization of 12,903 PIWI-interacting RNAs (piRNAs) in Drosophila, demonstrating that rasiRNAs represent a subset of piRNAs. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL5922

1 Sample

Download data: TXT

(Submitter supplied) PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposable elements in animal gonads. Here we demonstrate that in the mouse embryonic male germline, endonucleolytic cleavage (slicing) of a transcript by cytosolic MILI acts as a trigger to initiate its further 5??3? processing into non-overlapping fragments. These fragments accumulate as new piRNAs within the nuclear PIWI protein MIWI2. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: CSV, TXT

(Submitter supplied) Piwi in a complex with Piwi-interacting RNAs (piRNAs) triggers transcriptional silencing of Transposable Elements (TEs) in Drosophila ovaries, thus ensuring genome stability. To do this, Piwi must scan the nascent transcripts of genes and TEs for complementarity to piRNAs. The mechanism of this scanning is currently unknown. Here we report the DamID-seq mapping of multiple Piwi-interacting chromosomal domains in somatic cells of Drosophila ovaries. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL13304 GPL17275

7 Samples

Download data: BW, TXT

(Submitter supplied) The maintenance and differentiation of highly potent animal stem cells generates an epigenetic cycle that underlies development. Drosophila female germline stem cells (GSC) produce cystoblast daughters that differentiate into nurse cells and oocytes. Developmental chromatin analysis profiling the differentiation of GSCs into cystoblasts and NCs of increasing ploidy shows that cystoblasts start developing by forming heterochromatin while in a transient syncytial state, the germline cyst, reminiscent of early embryonic cells. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL19132

28 Samples

Download data: BEDGRAPH, BW, CSV, TXT

(Submitter supplied) Here we used laser cutting microdissection and RNA amplification to profile the gene expression in wildtype female germaria and male apex of the testes. These tissue contain germline stem cells and early dividing germ cells. Our goal was to identify genes expressed in these cell types.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL3880

4 Samples

Download data: GPR

(Submitter supplied) In many metazoans, germ cells are separated from somatic lineages early in development and maintain their identity throughout life. Here we show that a Polycomb group (PcG) component, Enhancer of Zeste [E(z)] H3K27me3-specific methyltransferase, maintains germline identity in Drosophila adult testes. We find excessive early-stage somatic gonadal cells in E(z) mutant testes, which originate from both over-proliferative cyst stem cells and germ cells turning on an early-stage somatic cell marker. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

3 Samples

Download data: TXT, WIG

(Submitter supplied) The importance of the niche to provide regulatory inputs to balance stem cell self-renewal and differentiation has become clear. However, the regulatory interplay between stem cells and their niche at the whole genome level is still poorly understood. To elucidate the mechanisms controlling stem cells and their progenies as they progress through development at the transcriptional level, we recorded the regulatory program of two independent cell lineages in the Drosophila testis. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

16 Samples

Download data: BEDGRAPH, CEL

(Submitter supplied) DEAD-box RNA helicases DDX3 are important developmental regulators of multiple aspects of RNA metabolism of eukaryotes. belle, a single DDX3 ortholog in Drosophila, is essential for fly viability, fertility, and germline stem cell maintenance. Here we showed that RNAi belle knockdown in testis cyst cells caused a disruption of adhesion between germ cells and cyst cells and a generation of tumor-like clusters of stem-like germ cells. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

2 Samples

Download data: XLSX

(Submitter supplied) Here we use DamID to identify Esg binding sites in Drosophila testes in order to investigate how it maintains somatic cyst stem cells.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15057

3 Samples

Download data: GFF, PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Abstract To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. Here, we show in the Drosophila male germline stem cell lineage that a spermatocyte-specific zinc finger protein, Kumgang (Kmg), working with the chromatin remodeler dMi-2 prevents transcription of genes normally expressed only in somatic lineages. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL1322 GPL19132

52 Samples

Download data: BW, CEL

(Submitter supplied) Genome wide localization of Kumgang, dMi-2, and Aly in Drosophila melanogaster testes were evaluated by ChIP-Seq in wild-type and kmg knock down testes. / Title: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression / Abstract: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

26 Samples

Download data: BW

(Submitter supplied) The effect of different spermatocyte-specific loss of functions; kumgang (kmg or CG5204), dMi-2 in the gene expression in fly testes was assessed by RNA-Seq. Gene expression in wild-type heads were also measured to have a reference expression profile of 'somatic tissues'. / Title: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression / Abstract: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

10 Samples

Download data: BW

(Submitter supplied) The effect of different loss of functions; kumgang (kmg or CG5204), dMi-2, and kmg and always early (aly) double on the gene expression in spermatocyte differentation was assessed by microarray. TITLE: Blocking promiscuous activation at cryptic promoters directs cell type–specific gene expression ABSTRACT: To selectively express cell type–specific transcripts during development, it is critical to maintain genes required for other lineages in a silent state. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

17 Samples

Download data: CEL, TXT

(Submitter supplied) We report the transcriptional profiles obtained by next-generation sequencing (NGS) of FACS-purified somatic cyst stem cells (CySCs) from adult testes of Drosophila melanogaster. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of wild type CySCs to those that have decreased Chinmo, increased Chinmo, elevated JAK/STAT signaling or elevated Hh signaling.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

15 Samples

Download data: CSV

(Submitter supplied) We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL9061

9 Samples

Download data: BED, BEDGRAPH, XLS