GEO DataSets

(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

(Submitter supplied) Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

4 Samples

Download data: GRAPH, TXT

(Submitter supplied) Transcriptional silencing of terminal differentiation genes by the Polycomb group (PcG) machinery is emerging as a key feature of precursor cells in stem cell lineages. How, then, is this epigenetic silencing reversed for proper cellular differentiation? Here we investigate how the developmental program reverses local PcG action to allow expression of terminal differentiation genes in the Drosophila male germline stem cell lineage. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

12 Samples

Download data: CEL

(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:

GPL19132 GPL1322

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) 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) 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; Other

Platforms:

GPL17275 GPL25244

63 Samples

Download data: BEDGRAPH, GFF, NARROWPEAK

(Submitter supplied) To investigate the chromatin state into an adult stem cell lineage, we generate cell-type specific chromatin state maps in the adult Drosophila intestine and identify principal chromatin state transitions during lineage determination. we profiled the binding sites of five chromatin-associated proteins from which the previously described five major types of chromatin.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL17275

51 Samples

Download data: BEDGRAPH, GFF

(Submitter supplied) To investigate the chromatin state into an adult stem cell lineage, we generate cell-type specific chromatin state maps in the adult Drosophila intestine and identify principal chromatin state transitions during lineage determination. we profiled the binding sites of five chromatin-associated proteins from which the previously described five major types of chromatin.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: NARROWPEAK

(Submitter supplied) To investigate the chromatin state into an adult stem cell lineage, we generate cell-type specific chromatin state maps in the adult Drosophila intestine and identify principal chromatin state transitions during lineage determination. we profiled the binding sites of five chromatin-associated proteins from which the previously described five major types of chromatin.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

12 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq to map enrichment of histone modifications and RNA polymerase II DNA occupancy in imaginal wing discs at 120 h of development.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: BEDGRAPH

(Submitter supplied) To study the antagonism between Esg and Sc, we compared their direct binding sites identified by 3HA-esg and 3HA-sc ChIP-Seq. Through ChIP-Seq analysis, 14347 binding sites of Sc and 2765 binding sites of Esg were identified through p-value cutoff 1.00e-05. Among Sc binding sites, 10675 were protein-coding genes and 2678 localized to promoter region. For Esg, 2036 were protein-coding genes and 846 localized to promoter region. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: BW, XLS

(Submitter supplied) [PROJECT] After fertilization the embryonic genome is inactive until transcription is initiated during the maternal-zygotic transition (MZT). This universal process coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem (ES) cells. To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency, we mapped the genomic locations of histone H3 modifications before and after MZT in zebrafish embryos. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9970

12 Samples

Download data: PAIR, WIG

(Submitter supplied) PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmD23-c4 cells by hybridization of ChIP products with tiling microarrays

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6016

9 Samples

Download data: CEL, SGR

(Submitter supplied) PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac, H3K9ac in cultured Drosophila Sg4 cells by hybridization of ChIP products with tiling microarrays.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6016 GPL5919

12 Samples

Download data: CEL, SGR