GEO DataSets

(Submitter supplied) The human polyomavirus, JCPyV, establishes a lifelong persistent infection in the peripheral organs of a majority of the human population worldwide. Patients who are immunocompromised due to underlying infections, cancer, or to immunomodulatory treatments for autoimmune disease are at risk for developing progressive multifocal leukoencephalopathy (PML) when the virus invades the CNS and infects macroglial cells in the brain parenchyma. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

6 Samples

Download data: CEL

(Submitter supplied) We investigated the root growth of several knockout mutants of heat shock protein family genes and found that heat stress response was compromised in these mutants compared to wild type plants. It suggested that heat shock protein genes including heat shock protein genes including HSP17s, HSP23s, HSP101, and HSFA2 proteins are deployed upon exposure to Cs for plant stress tolerance. Our study provided novel insights into the molecular events occurring in Cs-stressed plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(Submitter supplied) Cesium (Cs) is known to exert toxicity in plants by competition and interference with the transport of potassium (K). However, the precise mechanism of how Cs mediates its damaging effect is still unclear. To identify putative genes that are functionally involved in this response, RNA-seq was conducted on Arabidopsis roots grown in low K and Cs medium conditions. Comparison of both stress condition reveals Cs alters ABA signaling during seed germination and induced expression of thiamine biosnynthesis genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28290

9 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to investigate mechanisms leading to changes in epigenetics and chromatin organization during irradiation. Purpose: Use of next-generation sequencing (NGS) to investigate the changes in transcriptional (RNAseq) profiles in mouse oocyte after irradiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: TXT

(Submitter supplied) Acute exposure to high-dose gamma radiation can result in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium (Lung Alveolus Chip) is used to model acute, early stage RILI in vitro. Both lung epithelium and endothelium exhibit DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure, and greater damage is observed in the endothelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

32 Samples

Download data: TXT

(Submitter supplied) Acute exposure to high-dose gamma radiation often results in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip device consisting of human lung alveolar epithelium and pulmonary endothelium (Lung Alveolus Chip) is used to recapitulate acute, early stage RILI in vitro. This RNA-seq data captures that both the lung epithelium and endothelium in this model capture key hallmarks of this disease particularly, DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

24 Samples

Download data: TXT

(Submitter supplied) To identify new potential therapeutic targets for the treatment of GB we performed ribosome profiling of glioblastoma sphere cultures (GSCs) under normal and radiotherapeutic conditions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

32 Samples

Download data: RDS

(Submitter supplied) Sequencing of chromatin associated with H3K4me3 histone marks in live c-kit+ cells isolated by CUT&RUN from chimeras after transplantation with Ctrl-BM, MSC-BM and CpG-BM.

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

7 Samples

Download data: BW

(Submitter supplied) We studied the effect of social environment (presence of conspecific males and/or females) and gamma irradiation on gene expression in the male reproductive tract (aedeagus, ejaculatory bulb, 2 bilobed testes and 3 pairs of smaller accessory glands; the two pairs of larger accessory glands were removed) in a full factorial design.

Organism:

Callosobruchus maculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28770

32 Samples

Download data: TXT

(Submitter supplied) The thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

5 Samples

Download data: CEL

(Submitter supplied) In the current study, we investigated the gene expression response of blood cells of mice that were injected with variable amounts of 137Cs We isolated total RNA from peripheral blood from mice with 0 (control), 158, 191, 215 and 259 uCi cesium source amount on days 2, 3, 5, 7 and 14 days after injection. Using Agilent Mouse Whole Genome microarrays, we identified x genes that were significantly differentially expressed across the 14-day time course of this study. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

152 Samples

Download data: TXT

(Submitter supplied) Safeguards against excess DNA replication are often dysregulated in cancer, and driving cancer cells towards over-replication is a promising therapeutic strategy. We determined DNA synthesis patterns in cancer cells undergoing partial genome re-replication due to perturbed regulatory interactions ("re-replicating cells"). These cells exhibited slow replication, increased frequency of replication initiation events and a skewed initiation pattern that preferentially reactivated early-replicating origins. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL24676 GPL20301

38 Samples

Download data: BED, BROADPEAK, BW

(Submitter supplied) Transcriptomic profiling of breast cancer cells incubated in vitro with surgical wound fluids from patients with breast cancer reveals similarities in the biological response induced by intraoperative radiation therapy and the radiation-induced bystander effect In patients with breast cancer who undergo breast-conserving surgery (BCS), more than 90% of local recurrences occur in the same quadrant as the primary cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

15 Samples

Download data: CEL

(Submitter supplied) Lung adenocarcinoma (ADC) is the most prevalent subtype of lung cancer and characterized by considerable morphological and mutational heterogeneity. However, little is known about the epigenomic intratumor variability between spatially separated histological growth patterns of ADC. In order to reconstruct the clonal evolution of histomorphological growth patterns, we performed global DNA methylation profiling of 27 primary tumor regions, seven matched normal tissues, and six lymph node metastases from seven ADC cases. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

40 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Epigenetic modifications have been shown to play an important role in the classification and pathogenesis of the pediatric brain tumor ependymoma, suggesting they are a potential therapeutic target. Methods: The effects of agents targeting epigenetic modifications on the growth and death of a panel of ependymoma cell lines was investigated, as well as toxicity to normal fetal neural stem cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

16 Samples

Download data: IDAT, TXT

(Submitter supplied) We report a novel method to quantify bulk changes of chromatin associated proteins in different cellular states and apply it to the mammalian cell cycle

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL16791

13 Samples

Download data: TXT, WIG

(Submitter supplied) Ependymomas are neuroepithelial tumors of the central nervous system (CNS), presenting in both adults and children but accounting for almost 10% of all pediatric CNS tumors and up to 30% of CNS tumors in children under 3 years (Bouffet et al., 2009; McGuire et al., 2009; Rodriguez et al., 2009). In children, most ependymomas arise in the posterior fossa, while most adult ependymomas present around the lower spinal cord and spinal nerve roots. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL13534 GPL21145

675 Samples

Download data: IDAT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL8321 GPL1261

13 Samples

Download data: CEL

(Submitter supplied) The thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

9 Samples

Download data: CEL

(Submitter supplied) Purpose: Breeding for gibberella ear rot resistance have been challenging due to the high complexity of the trait. The current study attempts to characterize defence responses to Fusarium graminearum infection in two maize inbred lines with different levels of resistance to the pathogen. Methods: RNA was extracted from developing kernels of two inbred lines, which had been either fungal (F. graminearum DAOM180378) or mock inoculated 11 days post sibcrossing, using a guanidine isothiocyanate method and ultra-centrifugation with cesium chloride. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

16 Samples

Download data: XLSX