GEO DataSets

(Submitter supplied) To investigate HCMV (and human host) gene expression profile during latency and reactivation, we infected THP-1 cells with the wildtype HCMV-TB40E or with recombinant viruses that cannot establish latency (UL138stop) or cannot reactivate (UL135stop). After the establishment of viral latency, we treated cells with TPA to induce cellular differentiation and viral reactivation. We then performed gene expression profiling analysis using data obtained from RNA-seq over a timecourse of undifferentiated and differentiated cells that are infected with each virus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

143 Samples

Download data: XLSX

(Submitter supplied) Purpose: There is a need for point-of-care diagnostics for future mass casualty events involving radiation exposure. The development of radiation exposure and dose prediction algorithms for biodosimetry is needed for screening of large populations during these scenarios, and exploration of the potential effects which sex, age, genetic heterogeneity, and physiological comorbidities may have on the utility of biodosimetry diagnostics is needed. more...

Organism:

Mus musculus; Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL34462

148 Samples

Download data: TXT

(Submitter supplied) Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling. Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, skeletal muscle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

481 Samples

Download data: CSV

(Submitter supplied) Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling. Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, skeletal muscle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

474 Samples

Download data: CSV

(Submitter supplied) Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling. Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, skeletal muscle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

468 Samples

Download data: CSV

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca mulatta; Macaca nemestrina

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL33261

116 Samples

Download data: TXT

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca nemestrina; Macaca mulatta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL33261 GPL27943

120 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.

Organism:

uncultured soil microorganism; soil metagenome

Type:

Other

Platform:

GPL29739

120 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL24247

109 Samples

Download data

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

179 Samples

Download data

(Submitter supplied) Although evidence indicates that the adult brain retains a considerable capacity for circuit formation, adult wiring has not been broadly considered and remains poorly understood. Here, we investigated wiring activation in adult neurons. Based on bioinformatic analyses on a previously published dataset (GSE161619), we identified the basic-helix-loop-helix (bHLH) transcription factor Ascl4 as a potential regulator of adult wiring and show that the AAV-mediated overexpression of Ascl4 can cell autonomously induce wiring in different types of hippocampal neurons of adult mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

228 Samples

Download data: TSV

(Submitter supplied) Using murine models that exclude variation in host genetics, environmental factors and tumour mutation burden, limiting variation between animals to naturally diverse TCRβ repertoires, we applied bulk TCRseq to study TCRβ repertoire dynamics in ICT responders and non-responders

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

225 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Protein profiling by protein array; Expression profiling by array

Platforms:

GPL32055 GPL18573 GPL32054

300 Samples

Download data: BW, RCC, SF

(Submitter supplied) A 122-epigenetic gene signature distinguished low- versus high-risk early stage melanomas. We sought to validate the signature, examined clinical correlates in a cohort of primary melanomas of the skin, and studied the underlying transcriptomic aberrations and changes in chromatin in cell lines representing these two groups.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL32055

124 Samples

Download data: RCC

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20795 GPL24676 GPL20301

105 Samples

Download data: BED, HIC, TAB, TSV, TXT

(Submitter supplied) Huntington’s disease (HD) and juvenile-onset schizophrenia (SCZ) have long been regarded as distinct disorders. However, both manifest cell-intrinsic abnormalities in glial differentiation, with resultant astrocytic dysfunction and hypomyelination. To assess whether a common mechanism might underlie the similar glial pathology of these otherwise disparate conditions, we utilized comparative correlation network approaches to analyze RNA-seq data from human glial progenitor cells (hGPCs) produced from disease-derived pluripotent stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL18573 GPL16791

139 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Huntington’s disease (HD) and juvenile-onset schizophrenia (SCZ) have long been regarded as distinct disorders. However, both manifest cell-intrinsic abnormalities in glial differentiation, with resultant astrocytic dysfunction and hypomyelination. To assess whether a common mechanism might underlie the similar glial pathology of these otherwise disparate conditions, we utilized comparative correlation network approaches to analyze RNA-seq data from human glial progenitor cells (hGPCs) produced from disease-derived pluripotent stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

137 Samples

Download data: TXT

(Submitter supplied) How different histone methyltransferases (HMT) cooperate to progressively catalyze different methylation states of the same residue as well the functional consequences of the different methylation states are not well known. Here, we address in the context of Drosophila H3K36 methylation by using single and combinatorial RNAi of HMTs along with genome-wide MNase-ChIPseq analyses. Our study reveals that K36me1/2/3 each mark distinct chromatin compartments. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL33093 GPL19951

107 Samples

Download data: BED, BW, TXT

(Submitter supplied) Coordination of cell activity trough Ca2+ waves enables pancreatic β-cells to secrete precise quantities of insulin in response to blood sugar. However, how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single-molecule RNA detection, we reveal a gene-signature depicting a molecularly and metabolically distinct state of first responder β-cells. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

191 Samples

Download data: CSV

(Submitter supplied) We report the development of a method (nanoSPLITS) capable of performing global proteome and transcriptome measurements from the same single-cell.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

192 Samples

Download data: TXT