GEO DataSets

(Submitter supplied) Background: Arteriosclerosis (AS) involves arterial inflammation. Using macrophage-based drug delivery system, we aim to enhance local drug concentration, especially for short-lived anti-inflammatory molecules like interleukin-10. Our study intervenes in plaque progression by boosting IL-10 expression in macrophages lentiviral transfection and introducing these anti-inflammatory cells into Apoe-/- mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: XLSX

(Submitter supplied) Traumatic brain injury (TBI) is a risk factor for neurodegeneration, however little is known about how different neuron types respond to this kind of injury. In this study, we follow neuronal populations over several months after a single mild TBI (mTBI) to assess long ranging consequences of injury at the level of single, transcriptionally defined neuronal classes. We find that the stress responsive Activating Transcription Factor 3 (ATF3) defines a population of cortical neurons after mTBI. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: CSV, MTX, RDS, TSV

(Submitter supplied) Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres during aging in human cells. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells, in a p53-dependent manner. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: RESULTS

(Submitter supplied) Aging and chronic inflammation are associated with overabundant myeloid-primed multipotent progenitors (MPPs) amongst hematopoietic stem and progenitor cells (HSPCs). While HSC differentiation bias has been considered a primary cause of myeloid bias, whether it is sufficient has not been quantitatively evaluated. Here, we analyzed bone marrow data from the IκB– (Nfkbia+/-Nfkbib-/-Nfkbie-/-) mouse model of inflammation with elevated NFκB activity, which shows increased myeloid-biased MPPs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) We report long-term outcomes up to 18 years of a clinical trial treating children with neuroblastoma with EBV-specific T lymphocytes and CD3-activated T cells – each expressing chimeric antigen receptors (CAR) targeting GD2 but without an embedded costimulatory sequence (1st generation CARs). These CARs incorporated barcoded sequences to track each infused population. Of 11 patients with active disease at infusion, three patients achieved a complete response that was sustained in 2, one for 8 years until lost to follow up and one for 18+ years. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV, MTX, RDS, TSV

(Submitter supplied) Tissue and microbial cues regulate the abundance and function of CD8+ T cells at barrier sites, yet the impact of specific microbes on their long-term durability remains unclear. Here, we show that the commensal protist Tritrichomonas musculus (T. mu) depletes intestinal CD8+ T cells, particularly tissue resident memory (TRM) cells, through activation of localized type 2 immunity. Colonization with T. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: H5

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

15 Samples

Download data

(Submitter supplied) Parkinson’s disease (PD) is an age-related neurodegenerative disorder characterized by the degeneration of the nigrostriatal dopaminergic neurons, and by intraneuronal accumulation of aggregated α-synuclein (aSyn). Environmental factors contribute significantly to neurodegeneration in patients, and non-pharmacological interventions are increasingly explored. Among these, caloric restriction and time-restricted feeding have demonstrated beneficial effects in animal models of neurodegenerative diseases. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: CSV

(Submitter supplied) Parkinson’s disease (PD) is an age-related neurodegenerative disorder characterized by the degeneration of the nigrostriatal dopaminergic neurons, and by intraneuronal accumulation of aggregated α-synuclein (aSyn). Environmental factors contribute significantly to neurodegeneration in patients, and non-pharmacological interventions are increasingly explored. Among these, caloric restriction and time-restricted feeding have demonstrated beneficial effects in animal models of neurodegenerative diseases. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: CSV

(Submitter supplied) To explore the early steps in glioma formation, we utilized conditional gene deletion and lineage tracing in tumour mouse models, coupled with serial magnetic resonance imaging to initiate and then closely track tumour formation. We isolated labeled and unlabeled cells at multiple stages -- before the first visible abnormality, at the time of the first visible lesion, and then through the stages of tumour growth -- and subjected each stage to single-cell profiling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

40 Samples

Download data: RDATA

(Submitter supplied) Current approaches to track stem cell clones through differentiation require genetic engineering or rely on sparse somatic DNA variants. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a method for transgene-free lineage tracing based on microfluidic, targeted single-cell DNA methylation analysis. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TSV

(Submitter supplied) Recent research has indicated the presence of heterochromatin-like regions of extended protein occupancy and transcriptional silencing of bacterial genomes. We utilized an integrative approach to track chromatin structure and transcription in E. coli K-12 across a wide range of nutrient conditions. In the process, we identified multiple loci which act similarly to facultative heterochromatin in eukaryotes, normally silenced but permitting expression of genes under specific conditions. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

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

Platform:

GPL21117

64 Samples

Download data: BEDGRAPH

(Submitter supplied) Regulation of gene expression during development and stress response requires the concerted action of transcription factors and chromatin-binding proteins. Because this process is cell-type specific and varies with cellular conditions, mapping of chromatin factors at individual regulatory loci is crucial for understanding cis-regulatory control. Previous methods only characterize static protein binding. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

111 Samples

Download data: BW

(Submitter supplied) Regulation of gene expression during development and stress response requires the concerted action of transcription factors and chromatin-binding proteins. Because this process is cell-type specific and varies with cellular conditions, mapping of chromatin factors at individual regulatory loci is crucial for understanding cis-regulatory control. Previous methods only characterize static protein binding. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL24676

52 Samples

Download data: BW

(Submitter supplied) The combination of immune checkpoint blockade and tyrosine kinase inhibitors has shown promising clinical benefits, but the underlying mechanisms driving response and resistance are poorly understood. Here, we performed single-cell RNA- and TCR-sequencing, together with a HBV-peptide-barcoded single-cell RNA-sequencing approach, on paired tumor and blood samples to track the dynamic changes of T cells in HBV+ hepatocellular carcinoma (HCC) patients before or after anti-PD-1 plus lenvatinib combination therapy.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

69 Samples

Download data: CSV, H5AD, TXT

(Submitter supplied) Over half of BRAF-mutant melanoma patients with initial response to targeted therapy will recur with resistant disease. It is thought that resistance can arise from the ability of cells to enter and exit a slow cycling persister state, evade treatment with relative dormancy, and repopulate the tumor when reactivated. However, the expression states of persister and resistant cells, their spatial relationships in the tumor environment, and the evolutionary progression among these populations are not well understood. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

24 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Understanding the pulmonary adaptive immune system of pigs is of importance as respiratory pathogens present a major challenge for swine producers and pigs are increasingly used to model human pulmonary diseases. Single-cell RNA sequencing (scRNAseq) has accelerated the characterization of cellular phenotypes in the pig respiratory tract under both healthy and diseased conditions. However, combining scRNAseq with recovery of paired VJ and VDJ T cell receptor (TCR) as well as heavy (IGH) and light (IGL) chains of B cell receptors (BCR) to interrogate receptor repertoires has not to our knowledge been demonstrated for pigs. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26351

48 Samples

Download data: FASTA, MTX, TSV

(Submitter supplied) The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

13 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30821

22 Samples

Download data: TSV

(Submitter supplied) The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL30821

4 Samples

Download data: BED, NARROWPEAK, TDF, TSV, TXT