GEO DataSets

(Submitter supplied) Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal (GI) malignancies and a major cause of death worldwide, with limited therapeutic options. Although Mixed Lineage Kinase 3 (MLK3), a MAPKKK, has emerged as a key regulator of acute liver injury, inflammation, and non-alcoholic steatohepatitis (NASH), its role in HCC remains unclear. TCGA databases suggest an elevated expression of MAP3K11 (gene of MLK3) and TMA studies show higher MLK3 activation in human HCCs compared to the normal livers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) The data in the present study suggested the possibility of using UV and γ-radiation to enhance lipid accumulation along with detailed insights at the molecular level.The transcriptomic data at 24 h post UV (1 J/cm2) and γ-radiation (1 kGy) revealed foremost effect of UV on photosynthetic machinery while in γ-, DNA damage, repair and replication at a global level. In addition, the key fatty acid biosynthesis related genes were also found to be upregulated which coincided with 1.56- and 1.73-fold increase in lipid content

Organism:

Chlorella sorokiniana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30017

6 Samples

Download data: FASTA, TXT

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: BED, BIGWIG

(Submitter supplied) We profiled MEG-DNA interactions using gluteraldehyde assisted chromatin immunoprecipitation by RNA purification (ChIRP-seq) in primary human ECs. Genome-wide MEG3-associated loci were obtained.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

8 Samples

Download data: BIGWIG

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

62 Samples

Download data

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

15 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL24676

117 Samples

Download data: ZIP

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

16 Samples

Download data: ZIP

(Submitter supplied) Active DNA demethylation in mammals involves Ten-eleven translocation (TET) family proteins-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC, an oxidized derivative of 5mC) at the single-cell level remains unexplored. Here we present “CLEVER-seq”, which is a single-cell, single-base resolution 5fC sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL17021 GPL16791

30 Samples

Download data: BIGWIG

(Submitter supplied) The gastrointestinal (GI) tract consists of highly specialized organs from the proximal esophagus to the distal colon, each with unique functions. Rare congenital malformations of the GI tract, including organ atresia, agenesis or mispatterning are linked to gene mutations although the molecular basis of these malformations has been poorly studied due to lack of model systems to study human development. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

55 Samples

Download data: TXT

(Submitter supplied) Precision medicine's potential to transform complex autoimmune-disease treatment is often challenged by limited data availability and inadequate sample size when compared to the number of molecular features found in high-throughput multi-omics datasets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein–protein interaction network to reverse disease states. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) The embryonic loss during early stage of gestation is one of the major causes of infertility for domestic ruminants, causing huge economic losses to pasture. Maternal recognition of pregnancy and implantation are the crucial process for determining the successful establishment and development of pregnancy in cattle. The research on molecular mechanisms of pregnancy recognition will facilitate illustrating the complex process of pregnancy establishment and help to improve pregnancy outcomes. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

9 Samples

Download data: TXT

(Submitter supplied) Candida albicansis a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously,C. albicanscolonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about howC. albicansresponds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. more...

Organism:

Candida albicans SC5314

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33778

24 Samples

Download data: TXT

(Submitter supplied) Polyploid Giant Cancer Cells (PGCC) are increasingly being studied for their role in cancer recurrence and mortality. PGCC arise from cancer cells in response to stress such as radiation, chemotherapy, or hypoxia. PGCC remain viable but do not divide by mitosis. However, upon cessation of stress, PGCC are capable of progeny formation via primitive, amitotic mechanisms akin to budding or bursting. In this study, the initial PGCC offspring are referred to as “early progeny”. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: TXT

(Submitter supplied) Agouti-related peptide (AgRP)- and proopiomelanocortin (POMC)-expressing neurons reciprocally regulate food intake. Here, we combined non-interacting recombinases to simultaneously express functionally opposing chemogenetic receptors in AgRP and POMC neurons allowing to compare metabolic responses in mice with simultaneous activation of AgRP and inhibition of POMC neurons with isolated activation of AgRP neurons or isolated inhibition of POMC neurons. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) Homology Directed Repair (HDR) enables precise genome editing and holds great promise in the gene therapy field. However, the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we demonstrate the development of a functional, pooled screening platform utilizing an HDR-based readout to identify protein-based reagents that improve HDR outcomes in human hematopoietic stem and progenitor cells (HSPCs), a clinically relevant cell type for gene therapy. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

43 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520

1545 Samples

Download data: H5

(Submitter supplied) Traumatic brain injury (TBI) initiates not only complex neurovascular and glial changes within the brain but also pathophysiological responses that extend beyond the central nervous system. The peripheral response to TBI has become an intensive area of research, as these systemic perturbations can induce dysfunction in multiple organ systems. As there are no approved therapeutics for TBI, it is imperative that we investigate the peripheral response to TBI to identify targets for future intervention. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

89 Samples

Download data: CSV, XLSX

(Submitter supplied) We report the differential expression of circRNAs between T-BEAS-2B cells (cadmium-transformed BEAS-2B cells) and C-BEAS-2B cells (passage-matched control BEAS-2B cells) by high-throughput sequencing. T-BEAS-2B cells are BEAS-2B cells transformed by cadmium at 2.0 μM for twenty weeks, and C-BEAS-2B cells are their passage-matched control. RNAs were sequenced on Illumina HiSeq Xten platform in triplicates, and expressions of circRNAs were calculated by TPM (transcripts per kilobase of exon model per million mapped reads). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) mRNA-based immunotherapeutics have garnered widespread interest for their potential to revolutionize cancer treatment. In this study, we have established a personalized and customizable mRNA-therapeutic approach that effectively targets a plurality of tumor antigens and demonstrated potent anti-tumor response in preclinical brain tumor models. Our platform uniquely addresses the challenge of tumor heterogeneity and low antigen burden, two key deficiencies in targeting classically immunotherapy-resistant CNS malignancies.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

20 Samples

Download data: TXT