GEO DataSets

(Submitter supplied) Accelerating the design of synthetic biological circuits for biosensing requires expanding the currently available genetic toolkit. Although whole-cell biosensors have been successfully engineered and deployed, particularly in applications such as environmental and medical diagnostics, novel sensing applications necessitate the discovery and optimization of novel biosensors. Here we develop a data-driven approach that combines dynamic mode decomposition and observability analysis to extract salient, endogenous genetic sensors for analytes of interest from dynamic gene expression profiles. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31044

40 Samples

Download data: JSON, TSV

(Submitter supplied) HutC in Pseudomonas is a representative member of the HutC/GntR family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate binding domain. HutC is generally known to represses expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28231

2 Samples

Download data: CSV

(Submitter supplied) We report the expression levels of transcripts for two alleles of 6,211 genes in log-phase growing cells of the wild type SN148 and the crz1/crz1 with or without 0.2M CaCl2 treatment.We find that as compared to the wild type cells without 0.2M CaCl2 treatment, there are 828 genes upregulated in the wild type cells with 0.2M CaCl2 treatment.

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23041

4 Samples

Download data: XLSX

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

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11203 GPL13304

37 Samples

Download data: BED, BW

(Submitter supplied) Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11203 GPL13304

36 Samples

Download data: BED, BW, TXT

(Submitter supplied) 5'-complete cDNA sequencing on ribosome-depleted total RNA from the human K562 cell line. Provides high-quality, genome-wide single-base resolution profiling of transcription start sites and their expression levels.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

1 Sample

Download data: BED, BW

(Submitter supplied) We developed a computational framework to discover short DNA sequences that confer strong expression in non-model organisms. The framework relies solely on whole genome and RNA sequencing data types, which are easily accessible to a variety of research groups. The framework proceeds in three main stages: 1) identification of a group of highly expressed loci that maintain high transcript counts across a broad range of experimental conditions, 2) extraction of the corresponding upstream candidate promoter regions of these highly expressed loci while minding nearby annotations and avoiding those that may potentially reside in operons, and 3) application of the motif finding algorithm in BioProspector to these upstream regions to predict the location and sequence of the -35 and -10 hexamers that drive the strong expression of these loci. more...

Organism:

Methylotuvimicrobium buryatense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23841

56 Samples

Download data: TXT

(Submitter supplied) Functional validation of the genome-scale CRISPR-activation screen by transcriptomic profiling of MGT#4-reporter expressing IDH-wt human glioma initiating cells (hGICs) upon CRISPRa-mediated overexpression of the predicted pro-mesenchymal drivers.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

15 Samples

Download data: TXT

(Submitter supplied) Related surrogate species are often used to study the molecular basis of pathogenicity of a pathogen on the basis of a shared set of biological features generally attributable to a shared core genome consisting of orthologous genes. An important and understudied aspect, however, is the extent to which regulatory features affecting the expression of such shared genes are present in both species. Here we report on an analysis of whole transcriptome maps for an important member of the TB complex Mycobacterium bovis and a closely related model organism for studying mycobacterial pathogenicity Mycobacterium marinum.

Organism:

Mycobacterium tuberculosis variant bovis; Mycobacterium marinum

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17861 GPL17862

8 Samples

Download data: TXT

(Submitter supplied) Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL10570

12 Samples

Download data: TXT

(Submitter supplied) Promoters play a central role in controlling gene regulation; however, a small set of promoters is used for most genetic construct design in the yeast Saccharomyces cerevisiae. The ability to generate and utilize models that accurately predict protein expression from promoter sequence may enable rapid generation of novel useful promoters, facilitating synthetic biology efforts in this model organism. more...

Organism:

synthetic construct

Type:

Other

Platforms:

GPL17769 GPL19424

102 Samples

Download data: CSV, TXT