GEO DataSets

(Submitter supplied) We report the genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that proper absolute R-loop levels chage during embryogenesis and that resolution of R-loops is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq revealed that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL25244

15 Samples

Download data: BED

(Submitter supplied) We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL19290 GPL24468

10 Samples

Download data: BED, TXT

(Submitter supplied) We performed mRNA-seq on mouse embryonic stem cells, with four DEAD-box family proteins, DDX10, DDX24, DDX27, DDX54 being partially depleted using RNA interference. Knockdown of EGFP was carried out as a control. By comparing all four knockdowns, we observed misregulation of a highly-overlapping set of genes, indicating that they regulate mRNA levels through a shared pathway.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

15 Samples

Download data: TXT

(Submitter supplied) High-level H3K27me3 domains are required for proper gene repression mediated by Polycomb proteins. Genome-wide profiling of H3K27 methylation during developmental progression and in animals with reduced PRC2 levels illustrates how mass spectrometry-based normalization permits the quantitative analysis of changes in chromatin states.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17275 GPL19132

10 Samples

Download data: BEDGRAPH

(Submitter supplied) R-loops impact transcription and genome stability and are related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive RNase H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific KAS-seq (spKAS-seq) to map R-loops by taking advantage of the presence of a single-stranded DNA (ssDNA) in the triplex structure. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

46 Samples

Download data: BIGWIG

(Submitter supplied) We report the nuclear transcriptome of Drosophila photoreceptor neurons obtained using a tissue-specific approach at different time points after eclosion

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

19 Samples

Download data: TXT

(Submitter supplied) We report the nuclear transcriptome of Drosophila Top3beta-deficient photoreceptor neurons obtained using a tissue-specific approach to purify nuclei and express an siRNA against Top3beta or mCherry for negative control

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: TXT

(Submitter supplied) We report the application of R-loop mapping in a cell-type specific context using photoreceptor neurons at different ages, as measured by days post eclosion (Day 10, Day 30 and Day 50). To validate our approach, we also performed R-loop mapping in 10 day old nuclei that were treated with RNAse H1 for 3 hours prior to application of MapR.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL17275

10 Samples

Download data: BW

(Submitter supplied) The maternal to zygotic transition (MZT) involves the transfer of genome regulation from the oocyte to the embryo and is essential for the formation of totipotent embryos. However, regulatory mechanisms are still poorly understood despite recent progress in mapping the dynamics in RNA transcripts and DNA methylation1-9. Previous studies suggest that dynamic histone modifications may play important roles in MZT10-12, however direct measurements of chromatin states has been hindered by technical difficulties in profiling histone modifications from small quantities of cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL16791 GPL17021

65 Samples

Download data: BW, TXT

(Submitter supplied) Cell fate transitions involve integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of the genomic sequences that control the earliest steps of human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs) unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, and monomethylation of histone H3 at lysine 4 (H3K4me1). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9052

16 Samples

Download data: BED, TXT

(Submitter supplied) H3.3-mediated paternal chromatin remodeling is essential for the development of preimplantation embryos and the activation of the paternal genome during embryogenesis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Strand asymmetry in the distribution of guanines and cytosines, measured by GC skew, predisposes DNA sequences towards R-loop formation upon transcription. Previous work revealed that GC skew and R-loop formation associate with a core set of unmethylated CpG island (CGI) promoters in the human genome. Here, we show that GC skew can distinguish four classes of promoters, including three types of CGI promoters, each associated with unique epigenetic and gene ontology signatures. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

5 Samples

Download data: WIG

(Submitter supplied) Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL23157

5 Samples

Download data: BW, NARROWPEAK

(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

Platform:

GPL13304

7 Samples

Download data: FPKM_TRACKING, TAB, TDF

(Submitter supplied) Expression profiles of in after egg laying (AEL) 3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118)

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

1 Sample

Download data: FPKM_TRACKING

(Submitter supplied) H1 ChIP-seq profiling and nucleosome MNase-seq profiling were performed in after egg laying (AEL) 3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118).

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: TAB, TDF

(Submitter supplied) The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. more...

Organism:

Drosophila ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; Drosophila melanogaster; Drosophila yakuba; Drosophila mauritiana; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila willistoni; Drosophila persimilis; Drosophila santomea

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

14 related Platforms

119 Samples

Download data: TXT

(Submitter supplied) We mapped ssDNA formation in WT and hpr1delta cells at permissive (30C) and non-permissive (37C) temperature. We showed that hpr1 cells accumulate ssDNA show elevated levels of ssDNA at centromeric regions. Additionally, we show replication fork-associated ssDNA at origins of replication is more confined to the origins in hpr1 cells than WT cells, suggesting a defect in replication fork progression.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL10930

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Histone modifications play critical roles in regulating developmental genes expression during embryo development in mammals1,2. However, genome-wide analysis of histone modifications in pre-implantation embryos has been impeded by technical difficulties and the scarcity of required materials. Here, by using a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method3, for the first time, we mapped the genome-wide profile of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), associated with gene activation and repression respectively, in mouse pre-implantation embryos. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

67 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

191 Samples

Download data: BW, FPKM_TRACKING, TXT