GEO DataSets

(Submitter supplied) We demonstrate that dsRNA is significantly accumulated in cancer cells following pharmacologic induction of micronuclei, stimulating MAVS-mediated dsRNA sensing in conjunction with the cGAS/STING pathway. Activation of cytosolic dsRNA sensing co-operates with dsDNA sensing to up-regulate immune cell migration and antigen-presenting machinery. Tracing of dsRNA-sequence identity revealed that dsRNA-forming transcripts are predominantly generated from non-exonic regions, particularly in locations proximal to genes exhibiting high chromatin accessibility. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) We demonstrate that dsRNA is significantly accumulated in cancer cells following pharmacologic induction of micronuclei, stimulating MAVS-mediated dsRNA sensing in conjunction with the cGAS/STING pathway. Activation of cytosolic dsRNA sensing co-operates with dsDNA sensing to up-regulate immune cell migration and antigen-presenting machinery. Tracing of dsRNA-sequence identity revealed that dsRNA-forming transcripts are predominantly generated from non-exonic regions, particularly in locations proximal to genes exhibiting high chromatin accessibility. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL28038

8 Samples

Download data: TXT

(Submitter supplied) EM-Seq of DNA derived from freshly sorted AT2 cells from aged (24-30 months old) and young (3-4 months old) C57BL6/J mice

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

44 Samples

Download data: BW, RDS

(Submitter supplied) Although mutations in human patatin-like phospholipase PNPLA6 are associated with hereditary retinal degenerative diseases, its mechanistic action in the retina is poorly understood. Here, we uncover the molecular mechanism by which PNPLA6 dysfunction disturbs retinal homeostasis and visual function. PNPLA6, by acting as a phospholipase B, regulates choline mobilization from phosphatidylcholine and subsequent choline turnover for phosphatidylcholine regeneration in retinal pigment epithelial (RPE) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

2 Samples

Download data: TXT

(Submitter supplied) Adeno-associated virus (AAV) vectors generated with five different capsids were intravenously injected into human livers undergoing normothermic machine perfusion (NMP). To assess the tropism of the five AAV vectors in the human livers, single-cell suspensions of hepatocytes and non-parenchymal cells (NPCs) were analyzed by single-cell RNA sequencing (scRNAseq). Differentially expressed genes were identified in AAV vector-transduced hepatocytes and unique cell populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

34 Samples

Download data: TXT

(Submitter supplied) We examined how glyceolin I, a phytoalexin from soybeands, affects gene expression in breast cancer cells. mRNA was collected at time points of 0, 6, 12, and 24 hours, and mRNA-seqs were performed.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: TXT

(Submitter supplied) CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies have reported that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. Here, we investigated the role RNA plays on CTCF’s transcription factor function through its chromatin occupancy. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: BW

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive skin cancer with high propensity for metastasis, caused by Merkel cell polyomavirus (MCPyV), or chronic UV-light-exposure. How MCPyV modulates immune responses within the tumor microenvironment and how such are linked to patient outcomes remain unknown partly due to technical barriers to understanding the spatial organization of the tumor microenvironment at single-cell resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

146 Samples

Download data: CSV

(Submitter supplied) The gene expression profling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

8 Samples

Download data: TXT

(Submitter supplied) The gene expression profiling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice transplanted with commercially available human hepatocytes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

9 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

64 Samples

Download data

(Submitter supplied) Oncogenic KRAS mutations frequently detected in non-small cell lung cancer (NSCLC)1,2, have been considered undruggable until recent development of inhibitors, e.g., sortorasib, adagrasib or divarasib, specifically targeting KRASG12C 3-6. However, it still remains as a big challenge to target all the KRAS mutants besides KRASG12C 2,7,8. We here found that MEK inhibitor trametinib treatment results in the feedback activation of multiple receptor tyrosine kinases (RTKs) in NSCLC, and combined treatments with trametinib and anlotinib, a pan-RTK inhibitor, effectively inhibited KRAS-mutant lung cancer progression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

48 Samples

Download data: CSV, TXT

(Submitter supplied) Neuropathic pain (NP) is a complex chronic pain due to the nervous system damage or diseases.Yuan-Hu Zhi Tong Prescription (YZP) is a well-known Traditional Chinese Medicine (TCM) formula for pain relief, which is composed of Corydalis Rhizoma (Yuanhu, YH) and Angelicae Dahuricae Radix (Baizhi, BZ). However, understanding of the analgesic and compatibility mechanisms of YZP remains limited. The present study found that YZP was more effective in relieving mechanical allodynia and thermal hypersensitivity than YH and BZ administered alone. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

15 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional processing and modification of messenger RNA (mRNA) regulates gene expression in eukaryotes by dictating the stability, localisation and translation of newly synthesised transcripts 1. These epitranscriptomic events are coordinated by an extensive network of RNA-binding proteins 2,3. Here we observed that the bacterial pathogen, Legionella pneumophila, caused the selective degradation of host cellular mRNAs encoding factors involved in glycolysis and related metabolic pathways. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

8 Samples

Download data: BED

(Submitter supplied) Our study investigated the therapeutic potential of OKN-007 in the SOD1 G93A mouse model of amyotrophic lateral sclerosis (ALS). The impact of OKN-007, known for its antioxidant, anti-inflammatory, and neuroprotective properties, was tested at two doses (150 mg/kg and 300 mg/kg) at onset and late-stage disease. Results demonstrated a significant delay in disease progression at both doses, with treated mice showing a slower advance to severe disease stages compared to untreated controls. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

32 Samples

Download data: TXT

(Submitter supplied) The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. more...

Organism:

Erythranthe guttata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23162

80 Samples

Download data: CSV

(Submitter supplied) Alveolar macrophages (AMs) are crucial for pulmonary defense and immune regulation. Exosomes from adipose-derived mesenchymal stem cells (ADSC-Exos) have emerged as a promising therapy for inflammatory lung diseases by modulating immune responses. This study investigates the ability of ADSC-Exos to alleviate inflammation in acute lunag injury (ALI), a condition often triggered by sepsis and characterized by lung permeability and respiratory failure.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: XLS

(Submitter supplied) Meniscus injuries are common and while surgical strategies have improved, there is a need for alternative therapeutics to improve long-term outcomes and prevent post-traumatic osteoarthritis. Current research efforts in regenerative therapies and tissue engineering are hindered by a lack of understanding of meniscus cell biology and a poorly defined meniscus cell phenotype. This study utilized bulk RNA-sequencing to identify unique and overlapping transcriptomic profiles in cartilage, inner and outer zone meniscus tissue, and passaged inner and outer zone meniscus cells. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22475

14 Samples

Download data: XLSX

(Submitter supplied) Maternal ketosis during pregnancy can impact fetal development, yet its effects on kidney development are not well understood. This study investigates the impact of maternal ketosis on offspring nephrogenesis using two mouse models: a ketogenic diet and β-hydroxybutyrate supplementation. Pregnant mice were subjected to either intervention from conception until birth. Offspring kidneys were analyzed at birth and in adulthood for nephron number, glomerular density, and renal function. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: XLSX

(Submitter supplied) RNA-seq analysis was performed in a T-ALL cell line (Jurkat) with FKBP tag knock-in at the MYB locus to analyze gene expression changes after dTAG-mediated MYB depletion.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

36 Samples

Download data: SF, TSV