GEO DataSets

(Submitter supplied) Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

31 Samples

Download data: CSV

(Submitter supplied) The regulation of gene expression in Pichia pastoris has so far involved study of transcription factors. However, there are factors other than transcription factors affecting mRNA synthesis such as coactivators, enhancers, and chromatin modifiers. This study is a first ever report on epigenetic regulation in Pichia pastoris where, a histone acetyltransferase is reported to regulate transcription of genes involved in utilization of alternate carbon sources. more...

Organism:

Komagataella pastoris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25256

4 Samples

Download data: XLSX

(Submitter supplied) A histidine prototrophic strain achieves A600 three-four fold higher than a histidine auxotroph when cultured in nutrient rich media YPA, which is abundant in amino acids. This retaded growth of histidine auxotroph in YPA can also be rescued by supplementing media with exogenous histidine. Here, we aim to study the transcriptomic changes associated with culturing of histidine auxotroph and prototroph in YPA and also the effects of histidine addition to the culture medium of histidine auxotroph.

Organism:

Komagataella pastoris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25256

6 Samples

Download data: XLSX

(Submitter supplied) Neutrophil granulocytes are the major cells involved in the Chlamydia trachomatis (C.trachomatis)-mediated inflammation and histopathology. A key gene in human intracellular antichlamydial defense is the tryptophan degrading enzyme indoleamine 2,3-dioxygenase (IDO), which limits the growth of the tryptophan auxotroph Chlamydia. Despite its importance, the role of IDO in the intracellular defense against Chlamydia in neutrophils has not yet been characterized. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

6 Samples

Download data: CEL, CHP

(Submitter supplied) The role of transcription factor Mxr1p has so far been studied in methanol, amino acid and acetate metabolism. We have demonstrated a key role of Mxr1p in regulation of ethanol metabolism when cells are cultured in medium containing ethanol as sole carbon source. We employed RNA Seq to identify new targets of Mxr1p in medium containing ethanol.

Organism:

Komagataella pastoris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25256

4 Samples

Download data: XLSX

(Submitter supplied) Pichia pastoris (Komagataella phaffi) transcription factor Mxr1p is known to regulate multiple metabolic pathways by binding to Mxr1p response elements of target genes. Mxr1p possesses a transactivation domain within the N-terminal 400 amino acids (Mxr1N400) which is functional during methanol metabolism. (Parua et al; 2012) Studies from our lab have shown that delta_mxr1 complemented with Mxr1N400 fails to reverse the growth defect of delta_mxr1 cultured in a medium containing methanol suggesting that region beyond N-terminal 400 amino acids has an essential function. more...

Organism:

Komagataella pastoris

Type:

Expression profiling by array

Platform:

GPL28264

8 Samples

Download data: TXT

(Submitter supplied) Phosphatidylcholine (PC) is an abundant membrane lipid component in most eukaryotes including yeast. PC has been assigned a multitude of functions in addition to that of building block of the lipid bilayer. Here we show that PC is evolvable essential in yeast by isolating suppressor mutants devoid of PC that exhibit robust growth. The requirement for PC is suppressed by monosomy of chromosome XV, or by a point mutation in the ACC1 gene encoding acetyl-CoA carboxylase. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

10 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae, SEY6210a/KMY1006a cells were treated with a sphingolipid species, phytosphingosine and time course change was monitored to understand mediator function of phytosphingosine. Gene expression differences were monitored with DNA microarray. Transcriptomic analyses showed that systemic reduction of ribosome-related genes, leading to the new insight in the transcriptional regulation downstream of phytosphingosine.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1945

5 Samples

Download data: TXT, XLS

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We provide an insight to the DNA auxotrophy of P. aeruginosa PASS4 isolate. Better understanding of P. aeruginosa adaptations in the CF lung environment can have a great impact in the development of specialised treatment regimes aimed at the eradications of P. aeruginosa infections. Methods: P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

12 Samples

Download data: TXT

(Submitter supplied) Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrB during threonine starvation

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25498

8 Samples

Download data: TXT

(Submitter supplied) Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrA during methionine starvation

Organism:

Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL19545

12 Samples

Download data: MEV

(Submitter supplied) We conducted experimental evolution of E. coli a mutual cross-feeding coculture, composed of two genetically-engineered Escherichia coli populations, I- and L-, which lack genes for biosynthesis of Ile (ilvE gene) and Leu (leuB gene), respectively. These two populations grew in a coculture by complementing required nutrients each other. After 883 generations of evolution experiments, we measured evolutionary changes in transcriptome, and we found ABC transporters for the branched chain amino acids (Ile, Leu, and Val) were significantly increased in both I- and L-. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by genome tiling array

Platform:

GPL13336

20 Samples

Download data: CEL, XLSX

(Submitter supplied) The inducible innate immune response to infection requires a concerted process of gene expression that is regulated at multiple levels. Most global analyses of the innate immune response have focused on transcription induced by defined immunostimulatory ligands, such as lipopolysaccharide. However, the response to pathogens involves additional complexity, as pathogens interfere with virtually every step of gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

41 Samples

Download data: TXT

(Submitter supplied) The nematode C. elegans was exposed to TiO2 nanoparticles (NPs) to evaluate the ecotoxicity of TiO2 nanoparticles. We used the DNA microarray method to understand changes in gene expression after the exposure to TIO2 NPs. We identified various genes involved in metal detoxification as well as in regulating worm development.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

2 Samples

Download data: CEL

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL9134

30 Samples

Download data: TXT

(Submitter supplied) Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

13 Samples

Download data: TXT

(Submitter supplied) Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔmetA during methionine starvation

Organism:

Mycobacterium tuberculosis; Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL19545

9 Samples

Download data: TXT

(Submitter supplied) Differential gene expression was determined using yeast cDNA microarray mRNA were enriched from auxotroph-matched yeast cells; control WT vs fpk1/2∆ cells and transcriptomic difference was examined

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1945

1 Sample

Download data: TXT

(Submitter supplied) Whole genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var uvarum (henceforth referred to as S. more...

Organism:

Saccharomyces bayanus; Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by array

8 related Platforms

360 Samples

Download data: GPR

(Submitter supplied) The opportunistic yeast pathogen Candida glabrata is recognized for its ability to acquire resistance during prolonged treatment with azole antifungals. Resistance to azoles is largely mediated by the transcription factor PDR1, resulting in the upregulation of ATP-binding cassette (ABC) transporter proteins and drug efflux. Studies in the related yeast Saccharomyces cerevisiae have shown Pdr1p forms a heterodimer with another transcription factor, Stb5p. more...

Organism:

Nakaseomyces glabratus; Nakaseomyces glabratus CBS 138

Type:

Expression profiling by array

Platforms:

GPL8174 GPL10325

13 Samples

Download data: GPR, TXT