GEO DataSets

(Submitter supplied) Age-related macular degeneration (AMD) is a leading cause of blindness. Metabolic disorders and diets are risk factors. We compared lipid profiles and retinal phenotypes with long-term feeding of four diets in male Chinchilla rabbits. Animals were fed with normal diet (ND), high fat diet (HFD), high sucrose diet (HSD), or high-fat and high-sucrose diet (HFSD) for six months. The eyes were examined using multimodal imaging modalities and electroretinogram (ERG). more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21255

8 Samples

Download data: TXT

(Submitter supplied) Hypertrophic scars, which result from aberrant fibrosis and disorganized collagen synthesis by skin fibroblasts, emerge due to disrupted wound healing processes. These scars present significant psychosocial and functional challenges to affected individuals. The current treatment limitations largely arise from an incomplete understanding of the underlying mechanisms of hypertrophic scar development. Recent studies, however, have shed light on the potential of exosomal non-coding RNAs interventions to mitigate hypertrophic scar proliferation. This research assesses the impact of exosomes derived from adipose-derived stem cells (ADSCs-Exos) on hypertrophic scar formation using a rabbit ear model. We employed Hematoxylin and Eosin staining, Masson’s Trichrome staining, and Immunohistochemical staining techniques to track scar progression. Our comprehensive analysis encompassed the differential expression of non-coding RNAs, enrichment analyses of functional pathways, protein-protein interaction studies, and miRNA-mRNA interaction investigations. The results reveal a marked alteration in the expression levels of long non-coding RNAs and microRNAs following ADSCs-Exos treatment, with little changes observed in circular RNAs. Notably, miR-194 emerges as a critical regulator within the signaling pathways that govern hypertrophic scar formation. Dual-luciferase assays indicated a significant reduction in the promoter activity of TGF-β1 after miR-194 overexpression. Quantitative reverse transcription PCR and Western blotting assays further validated the decrease in TGF-β1 expression in the treated samples. Moreover, the treatment resulted in diminished levels of inflammatory markers IL-1β, TNF-α, and IL-10. In vivo evidence strongly supports the role of miR-194 in attenuating hypertrophic scar formation through the suppression of TGF-β1. Our findings endorse the strategic use of ADSCs-Exos, particularly through miR-194 modulation, as an effective strategy for reducing scar formation and lowering pro-inflammatory and fibrotic indicators like TGF-β1. Therefore, this study advocates for the targeted application of ADSCs-Exos, with an emphasis on miR-194 modulation, as a promising approach to managing proliferative scarring.

Organism:

Oryctolagus cuniculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26786

6 Samples

Download data: XLS

(Submitter supplied) Hypertrophic scars, which result from aberrant fibrosis and disorganized collagen synthesis by skin fibroblasts, emerge due to disrupted wound healing processes. These scars present significant psychosocial and functional challenges to affected individuals. The current treatment limitations largely arise from an incomplete understanding of the underlying mechanisms of hypertrophic scar development. Recent studies, however, have shed light on the potential of exosomal non-coding RNAs interventions to mitigate hypertrophic scar proliferation. This research assesses the impact of exosomes derived from adipose-derived stem cells (ADSCs-Exos) on hypertrophic scar formation using a rabbit ear model. We employed Hematoxylin and Eosin staining, Masson’s Trichrome staining, and Immunohistochemical staining techniques to track scar progression. Our comprehensive analysis encompassed the differential expression of non-coding RNAs, enrichment analyses of functional pathways, protein-protein interaction studies, and miRNA-mRNA interaction investigations. The results reveal a marked alteration in the expression levels of long non-coding RNAs and microRNAs following ADSCs-Exos treatment, with little changes observed in circular RNAs. Notably, miR-194 emerges as a critical regulator within the signaling pathways that govern hypertrophic scar formation. Dual-luciferase assays indicated a significant reduction in the promoter activity of TGF-β1 after miR-194 overexpression. Quantitative reverse transcription PCR and Western blotting assays further validated the decrease in TGF-β1 expression in the treated samples. Moreover, the treatment resulted in diminished levels of inflammatory markers IL-1β, TNF-α, and IL-10. In vivo evidence strongly supports the role of miR-194 in attenuating hypertrophic scar formation through the suppression of TGF-β1. Our findings endorse the strategic use of ADSCs-Exos, particularly through miR-194 modulation, as an effective strategy for reducing scar formation and lowering pro-inflammatory and fibrotic indicators like TGF-β1. Therefore, this study advocates for the targeted application of ADSCs-Exos, with an emphasis on miR-194 modulation, as a promising approach to managing proliferative scarring.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26786

6 Samples

Download data: XLSX

(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Capra hircus; Rattus norvegicus; Danio rerio; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus; Cavia porcellus; Macaca fascicularis; Oryctolagus cuniculus; Cricetulus griseus; Mesocricetus auratus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

12 related Platforms

138 Samples

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(Submitter supplied) Hypertrophic scar (HS) considerably affects the appearance and causes tissue dysfunction in patients. Here we show a separating microneedle (MN) consisting of photo-crosslinked GelMA and 5-FuA-Pep-MA prodrug in response to high reactive oxygen species (ROS) levels and overexpression of matrix metalloproteinases (MMPs) in the HS pathological microenvironment. Bulk and single cell RNA sequencing analyses confirm that drug-loaded MNs could reverse skin fibrosis through down-regulation of BCL-2-associated death promoter (BAD), insulin-like growth factor 1 receptor (IGF1R) pathways, simultaneously regulate inflammatory response and keratinocyte differentiation via up-regulation of toll-like receptors (TOLL), interleukin-1 receptor (IL1R) and keratinocyte pathways, and promote the interactions between fibroblasts and keratinocytes via ligand-receptor pair of proteoglycans 2 (HSPG2)-dystroglycan 1(DAG1). more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24886

4 Samples

Download data: TXT

(Submitter supplied) Translation termination is an essential cellular process that is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins fom ribosomes, and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26786

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Objective: A model of infectious mandibular defect (IMD) caused by infection with Staphylococcus aureus and Pseudomonas aeruginosa was established to explore the occurrence and development of IMD and identify key genes by transcriptome sequencing and bioinformatics analysis. Methods: S. aureus and P. aeruginosa were diluted to 3×108 CFU/ml, and 6×3×3 mm defects lateral to the Mandibular Symphysis were induced in 28 New Zealand rabbits. more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33967

7 Samples

Download data: TXT

(Submitter supplied) MAF from pika Epas1-3FLAG knock-in mice were extracted and immortalized. After 12h DMOG treatment, cells were conducted for the ChIP-seq (Bmal1,Flag). We found that in knock-in mice fibroblasts, EPAS1-3FLAG can bind to similar E-box locus compared with BMAL1. Fibroblasts from mouse, rat, rabbit and Tibetan pika were extracted (and Tibetan pika fibroblasts were immortalized). RNA was extracted at 90% confluency. more...

Organism:

Mus musculus; Oryctolagus cuniculus; Rattus norvegicus; Ochotona curzoniae

Type:

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

5 related Platforms

18 Samples

Download data: BW, TXT

(Submitter supplied) Adenomyosis is an estrogen-dependent disease in which endometrial glands and stroma are pathologically demonstrated in the myometrium. Despite its prevalence and severity of symptoms, the precise etiology and physiopathology of adenomyosis is not well understood.Vitamin defciency increase in women with adenomyosis. Much less is known about the mechanism of their relationship. We found the retinol-binding protein receptor STRA6 upregulation in uterinespiral arteries from adenomyosis patients. more...

Organism:

Oryctolagus cuniculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21255

9 Samples

Download data: TXT

(Submitter supplied) Adenomyosis is an estrogen-dependent disease in which endometrial glands and stroma are pathologically demonstrated in the myometrium. Despite its prevalence and severity of symptoms, the precise etiology and physiopathology of adenomyosis is not well understood.Vitamin defciency increase in women with adenomyosis. Much less is known about the mechanism of their relationship. We found the retinol-binding protein receptor STRA6 upregulation in uterinespiral arteries from adenomyosis patients. more...

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21255

9 Samples

Download data: TXT

(Submitter supplied) As a polyphenolic herbal extract, Gallic acid (GA) is known for its antioxidant and anti-inflammatory properties. However, its application in parathyroid ischemia-reperfusion injury (IRI) has not been well examined. This study aimed to elucidate the protective effects of GA pretreatment in a parathyroid IRI model and explore the underlying mechanisms.Hypoxia and hypoxia/reoxygenation models were established with primary parathyroid cells to explore the protective effect of GA.The results from sequencing and bioinformatic analyses indicated that GA might regulate MMP1, MMP9, FOSB, GSY2, DUSP5, TRPV1/3, TIAM1 and multiple signaling pathways in this process such as IL-17, AMPK, MAPK, Transient Receptor Potential (TRP) channels, cAMP and Rap1.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21255

9 Samples

Download data: TXT

(Submitter supplied) We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells from post-traumatic temporomandibular joint osteoarthritis model to investigate the signaling pathways critical for cellular functions during temporomandibular joint osteoarthritis pathology.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25392

12 Samples

Download data: XLSX

(Submitter supplied) Construction of ceRNA network based on an RNA‑seq shows prognostic lncRNA biomarkers in Perthes’ disease

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL25392 GPL21255

16 Samples

Download data: TXT

(Submitter supplied) In this study, we collected rabbit supraspinatus muscle tissue with higher temporal resolution (1, 2, 4, 8 weeks)after 8 wk tear followed by repair (n=4/group), to determine time-depenet transcriptional changes after repair. RNA sequencing and analyses were performed using standard techniques to identify a transcriptional timeline of rotator cuff muscle changes and related morphological sequelae.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25392

34 Samples

Download data: CSV

(Submitter supplied) To investigate the effect of mechanical ventilation and mechanical ventilationon with PEEP application on diaphragmatic dysfunction, we established a model of mechanical ventilation on New Zealand rabbit, in which rabbits in the experimental group were ventilated with/without PEEP application for 48 hours continuously

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25392

9 Samples

Download data: XLSX

(Submitter supplied) We investigate the Inner Cell mass and the Trophectoderm specific response to the presence of insulin, glucose or both in media culture from 1 cell to blatsocyst stage in rabbit embryo

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24886

24 Samples

Download data: TXT

(Submitter supplied) The regenerative capacity of corneal endothelial cells (CECs) differs between species; in bigger mammals such as humans and sheep, CECs are arrested in a non-proliferative state. Damage to these cells can compromise its function leading to corneal opacity and impaired vision. Corneal transplantation is the current treatment for the recovery of a clear eyesight, but the donor tissue demand is higher than the offer and there is the need to develop novel treatment modalities. more...

Organism:

Homo sapiens; Ovis aries; Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24886 GPL22509 GPL18573

15 Samples

Download data: TSV

(Submitter supplied) We present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. This approach enabled the identification of three multiple myeloma cell surface antigens, and cognate monoclonal antibody probes.

Organism:

Oryctolagus cuniculus

Type:

Other

Platform:

GPL28443

21 Samples

Download data: TXT

(Submitter supplied) Intraventricular hemorrhage (IVH) remains a major neurological complication of prematurity that results in cerebral palsy, hydrocephalus, and cognitive deficits. No effective therapy exists to prevent these disorders in infants with IVH. IVH triggers inflammation, cellular infiltration and white matter injury following neurobehavioural deficits.

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29005

8 Samples

Download data: CSV

(Submitter supplied) To evaluate decellularized skeletal muscle extracellular matrix hydrogel effectiveness in treating shoulder cuff tears using a rabbit (RI) model. Male New Zealand white rabbits had supraspinatus tendon severed and were housed for 12 weeks, after which they had tendon reattached and half of rabbits also received an extracellular matrix gel injection. We then performed gene expression profiling analysis using data obtained from RNA-seq from rabbit supraspinatus muscles (n=5 for repair+gel treatment, n=5 for repair only treatment , n=4 for injured control) at 2 weeks post and (n=5 for repair+gel treatment, n=5 for repair only treatment , n=5 for uninjured control) at 12 weeks post treatment

Organism:

Oryctolagus cuniculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28431

34 Samples

Download data: TAB