GEO DataSets

(Submitter supplied) The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSS) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than RNA-seq. more...

Organism:

Neurospora crassa; Oryza sativa; Homo sapiens; Mus musculus; Capsaspora owczarzaki; Nematostella vectensis

Type:

Other

10 related Platforms

40 Samples

Download data: BIGWIG, BW, TXT

(Submitter supplied) Coccidioidomycosis (Valley Fever) is an emerging endemic fungal infection with a rising incidence and an expanding geographic range. It is caused by Coccidiodes, which are thermally dimorphic fungi that grow as mycelia in soil but transition in the lung to form pathogenic spherules. The regulatory mechanisms underlying this transition are not understood. Exploiting capped small (cs)RNA-seq, which identifies actively initiated stable and unstable transcripts and thereby detects acute changes in gene regulation with remarkable sensitivity, here we report the changes in architectural organization and key sequence features underlying phase transition of this highly pathogenic fungus. more...

Organism:

Agaricus bisporus; Coccidioides immitis; Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

7 related Platforms

27 Samples

Download data: GTF, TXT

(Submitter supplied) Coccidioides immitis and posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule. Genes that were highly up-regulated in young spherules include a spherule surface protein and iron and copper membrane transporters. Genes that are unique to Coccidioides spp. are also over-represented in this group, suggesting that they may be important for spherule differentiation. more...

Organism:

Coccidioides immitis RS

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29969

6 Samples

Download data: TXT

(Submitter supplied) BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5′-end of genes promoting the identification of transcription start sites (TSSs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) Here we describe a novel class of short RNAs that indicate widespread divergent transcription at mammalian promoters

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL7564

3 Samples

Download data

(Submitter supplied) Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

1 Sample

Download data

(Submitter supplied) To study the function of this residue independent from the enzymes that modify it, we used a “histone replacement” system in Drosophila to generate a non-modifiable H3K36 lysine-to-arginine (H3K36R) mutant. Post-translational modification of histone H3K36 is neither required to suppress cryptic transcription initiation nor to include alternative exons in Drosophila; instead it promotes expression of active genes by stimulating polyadenylation.

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL19132 GPL16479 GPL13304

52 Samples

Download data: BED, BW, DIFF

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

7 Samples

Download data: BIGWIG, BW

(Submitter supplied) Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: BW

(Submitter supplied) Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BIGWIG

(Submitter supplied) Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BIGWIG

(Submitter supplied) We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

6 Samples

Download data: BW, TSV

(Submitter supplied) Transcriptional regulation of gene expression is a major mechanism utilized by plants to confer phenotypic plasticity, yet compared to archaebacteria, eubacteria, and other eukaryotes, very little is known about the design principles of plant transcription. We generated an extensive catalog of nascent and steady state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq and RNA-seq and reanalyzed published maize data to capture the general characteristics of plant transcription. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

5 Samples

Download data: TXT

(Submitter supplied) MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL17021

8 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. more...

Organism:

Dictyostelium discoideum AX2

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24706 GPL24705

16 Samples

Download data: TXT

(Submitter supplied) Transcriptional regulation is a universal mechanism for a wide array of biological processes, and is driven in large part by genetic enhancer elements. These regulatory elements have been well-studied in animal species, yet their plant counterparts remain poorly characterized. While high-throughput profiling of animal genomes has yielded great success in identifying genetic enhancers through secondary characteristics – flanking histone posttranslational modifications (PTMs), chromatin accessibility, and the production of enhancer RNAs (eRNAs) – it is an active line of investigation as to whether these secondary characteristics can be used in a similar way to locate regulatory regions of plant genomes. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: BED, BW

(Submitter supplied) Recent high-throughput transcriptome analyses have revealed that >90% of all human DNA is transcribed. The vast majority of these transcripts are non-coding, thus challenging the classical definition of what constitutes a gene and, by association, a promoter. Adding to the complexity, short-lived transcripts have likely gone unnoticed. Here, we couple RNAi-depletion of one of the major RNA degradation activities, the human 3’-5’ exoribonucleolytic exosome with ENCODE microarrays tiling 1% of the human genome, to reveal a new class of short, polyadenylated and highly unstable transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL7161

1 Sample

Download data: TXT

(Submitter supplied) Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20219

4 Samples

Download data: WIG

(Submitter supplied) Steady-state gene expression across the cell cycle has been studied extensively. However, 2 transcriptional gene regulation and histone modification dynamics at different cell cycle stages is3 largely unknown. By applying a combination of GRO-seq, RNA-seq and histone modification 4 ChIP-seq, we depicted a comprehensive transcriptional landscape at G0/G1, G1/S and M phases 5 of breast cancer MCF-7 cells. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

13 Samples

Download data: BW, TXT