GEO DataSets

(Submitter supplied) Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. more...

Organism:

Mesocricetus auratus; synthetic construct; Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

65 Samples

Download data: CSV

(Submitter supplied) We determined lithium cobalt oxide LCO’s effects on pathways in the model organism Daphnia magna through RNA-Seq global gene expression analysis.

Organism:

Daphnia magna

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28557

20 Samples

Download data: TSV

(Submitter supplied) Human neuronal-like cells (NT2-N) were treated with either lamotrigine (50 µM), lithium (2.5 mM), quetiapine (50 µM), valproate (0.5 mM) or vehicle control for 24 hours. Genome wide mRNA expression was quantified by RNA-sequencing. Results offer insights on the mechanism(s) of action of bipolar disorder drugs at the transcriptional level.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) In this study, we demonstrated dysregulation of DNA transcription in H3K4me3 histone in circulating neutrophils of HIV-infected subjects. Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis revealed that the most spectacular abnormalities were observed in the exons, introns and promoter-TSS regions. Bioinformatic analysis of Gene Ontology, including biological processes, molecular function and cellular components, demonstrated that the main changes were related to the genes responsible for cell activation, cytokine production, adhesive molecule expression, histone remodeling via upregulation of methyltransferase process and downregulation of NF-kB transcription factor in canonical pathways. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: TAR

(Submitter supplied) Brain tumors are dynamic complex ecosystems with multiple cell types. To model the brain tumor microenvironment in a reproducible and scalable system, we developed a rapid three-dimensional (3D) bioprinting method to construct clinically relevant biomimetic tissue models. In recurrent glioblastoma, macrophages/microglia prominently contribute to the tumor mass. To parse the function of macrophages in 3D, we compared the growth of glioblastoma stem cells (GSCs) alone or with astrocytes and neural precursor cells (NPCs) in a hyaluronic acid (HA)-rich hydrogel, with or without macrophages. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

15 Samples

Download data: TXT, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL23159 GPL21145

128 Samples

Download data: CEL, CHP, IDAT

(Submitter supplied) Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells reveals long range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci range dysregulation of key inflammatory pathways mediated by disease-associated System sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

64 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells reveals long range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci range dysregulation of key inflammatory pathways mediated by disease-associated System sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

64 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens; Bos taurus; synthetic construct

Type:

Other

Platforms:

GPL26849 GPL26850 GPL26848

158 Samples

Download data: TXT

(Submitter supplied) Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). more...

Organism:

Homo sapiens; Bos taurus; synthetic construct

Type:

Other

Platform:

GPL26850

114 Samples

Download data: TXT

(Submitter supplied) Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26849

12 Samples

Download data: TXT

(Submitter supplied) Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26848

32 Samples

Download data: TXT

(Submitter supplied) Status Epilepticus (SE) is an abnormally prolonged seizure that results from either a failure of mechanisms that terminate seizures or from initiating mechanisms that inherently lead to prolonged seizures. Here we report an unbiased analysis of the hippocampal transcriptome of mice with targeted disruption of Dio2 in the astrocytes (Astro-D2KO mouse) undergoing 3 h SE.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

16 Samples

Download data: CEL, CHP

(Submitter supplied) Heterochromatin is a tightly packaged form of DNA that leads to permanent or temporal gene silencing. In P. falciparum heterochromatin is formed after trimethylation of lysine 9 on histone H3 and consequent binding of heterochromatin protein 1 (HP1). Genome-wide profiling studies established that in P. falciparum blood stage schizonts heterochromatin is formed at subtelomeres and some intra-chromosomal islands. more...

Organism:

Plasmodium vivax; Plasmodium berghei; Plasmodium chabaudi; Plasmodium yoelii; Plasmodium falciparum; Plasmodium knowlesi

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

26 Samples

Download data: BEDGRAPH

(Submitter supplied) Salmonella can survive for long periods under extreme desiccation conditions. This stress response poses a risk for food safety, but relatively little is known about the molecular and cellular regulation of this adaptation mechanism. To determine the genetic components involved in Salmonella’s cellular response to desiccation, we performed a global transcriptomic analysis comparing Salmonella Typhimurium cells equilibrated to low water activity (aw 0.11) and cells equilibrated to high water activity (aw 1.0). more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20792

2 Samples

Download data: TXT

(Submitter supplied) Huh7.5 cells, when grown in presence of 1-2mg/ml of Geneticin, generarated colonies with cells that were morphologically distinct from the parental cells. These cells were substantially smaller in size, had spindle like features and grew faster. They expressed mesenchymal markers and were named as Huh7.5M cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13252

4 Samples

Download data: TXT

(Submitter supplied) Huh7.5 cells, when grown in presence of 1-2mg/ml of Geneticin, generarated colonies with cells that were morphologically distinct from the parental cells. These cells were substantially smaller in size, had spindle like features and grew faster. They expressed mesenchymal markers and were named as Huh7.5M cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13252

4 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae is an established microbial host for the production of non-native compounds. The synthesis of these compounds typically demands energy and competes with growth for carbon and energy substrate. Uncoupling product formation form growth would benefit product yields and decrease formation of by-product biomass. Studying non-growing metabolically-active yeast cultures provides a first step towards developing S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

13 Samples

Download data: CEL

(Submitter supplied) Hepatitis C Virus protein NS5A was found to upregulate assembly of cap binding initiation complex eIF4F in Huh7.5 cells. NS5A also was found to associate with translation machinery. To understand consequences of NS5A mediation in host translation, we analyzed mRNA associated with polysome fractions of NS5A expressing Huh7.5 cells and compared them with the corresponding fractions from control cells.

Organism:

Homo sapiens

Type:

Expression profiling by array; Other

Platform:

GPL13252

8 Samples

Download data: TXT

(Submitter supplied) GSK3b signaling has been implicated in the pathophysiology of bipolar affective disorder based on the inhibitory effect of lithium salts on this pathway. This has been supported by a recent genome wide association study. In addition, GSK3b signaling may also play a role in schizophrenia, an idea that is based on the finding that the protein encoded by the schizophrenia candidate gene DISC1 inhibits GSK3b. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL6325 GPL6326

4 Samples

Download data: PAIR, TXT