F821137e-05a3-41d7-82ed-c268008e6382 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006873 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:BAM files (aligned against the hg38 genome) from a shallow whole-genome sequencing experiment (median depth 0.5X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.
| EGAD00001006881 | EGA
Project description:The uni- and bilateral excision models allow comparison of the combined effects of ocular desiccation and neuroinflammation on trigeminal gene expression vs the isolated effects of neuroinflammation propagated from the other side. Also, the transient receptor potential vanilloid 1 (Trpv1)-deficient mice allow the assessment of the role of this channel. In the unilateral excision model, only the left trigeminal ganglia were analyzed, which were contralateral to the desiccated eyes (right eyes) secondary to excision of the right-side extraorbital lacrimal glands, as the left-side lacrimal glands were left untouched. Eight-week-old female mice of both strains were either operated on day 1 (either bilateral or unilateral -right-side- extraorbital lacrimal gland excision or sham surgery) and allowed to develop a dry eye state until day 10, when they were euthanized and the trigeminal ganglia were excised for RNA extraction. The two trigeminal ganglia of each mouse were pooled in one sample for the bilateral excision or sham groups whereas only the left trigeminal ganglion of each mouse was harvested for the contralateral (unilateral) group. There were 18 samples in total (2 x 3 design, 2 strains, 3 treatments) including 3 replicates/group.
2025-07-01 | E-MTAB-15193 | biostudies-arrayexpress
Project description:Bilateral renal cell carcinoma (RCC) is a rare type of this disease and includes familial bilateral and sporadic bilateral RCCs. Studying the cellular molecular characteristics of sporadic bilateral is important to provide a direct guide for clinical treatment. These cellular molecular characteristics can be expressed at the RNA level, especially at the single-cell RNA level. Single-cell RNA sequencing (scRNA-seq) was performed on bilateral clear cell RCC (ccRCC). A total of 3,575 and 3,568 high-quality single-cell transcriptome data were captured from the left and right tumour tissues, respectively. Gene characteristics were identified by comparing left and right tumours at the scRNA level. This work presented the complex cellular environment of bilateral ccRCC by scRNA-seq. Single-cell transcriptome analysis revealed high similarity in gene expression among most cell types of bilateral RCCs but significant differences in gene expression among different site tumour cells. Additionally, the potential biological function of different tumour cell types was determined by gene ontology (GO) analysis. The transcriptome characteristics of tumour tissues in different locations at the single-cell transcriptome level were revealed through the scRNA-seq of bilateral sporadic ccRCC. This work provides new insights into the diagnosis and treatment of bilateral RCC.
2021-05-05 | GSE171306 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung condition with an unpredictable disease course. The pathology of IPF starts in the lung bases such that a patient’s lung apices are comparatively less fibrotic at the time of transplantation. We hypothesized that RNA sequencing of the lung apices and bases may identify differentially expressed genes that better reflect disease progression in IPF. Samples were derived from both right and left lungs when available and RNA Seq was performed on a total of 139 samples.
2022-11-02 | GSE213001 | GEO
Project description:Rats were subjected to bilateral rotator cuff tears of the right and left supraspinatus muscle. Muscles were harvested from each shoulder at 0, 10, 30, or 60 days post surgery.
2018-08-02 | MSV000082718 | GNPS
Project description:Alterations in glycosylation are seen in many types of cancer, including colorectal cancer (CRC). CRC is known to display glycosylation alterations. Glycans, the sugar moieties of glycoconjugates, are involved in many important functions relevant to cancer, such as cell signaling and adhesion, and may can be of value as biomarkers. In this study, we have used mass spectrometry to analyze the N-glycan profiles of 35 CRC tissue samples from patients with tumors in the right or left colon and 10 healthy tissue samples from non-CRC patients who underwent operations for other reasons. The tumor samples were divided into groups depending on tumor location (right or left colon) and stage (II or III), while the healthy samples were divided into right or left side of the colon. The levels of neutral and acidic N-glycan compositions and glycan classes were analyzed in a total of ten different groups. Surprisingly, there were no significant differences in glycan levels when all right- and left-sided CRC samples were compared, and few differences (such as in the abundance of the neutral N-glycan H3N5) were seen when the samples were divided according to both location and stage. Multiple significant differences were found in the levels of glycans and glycan classes when stage II and III samples were compared, and these glycans could be of value as candidates for new markers of cancer progression. In order to validate our findings, we analyzed healthy tissue samples from the right and left colon and found no significant differences in the levels of any of the glycans analyzed, confirming that our findings when comparing CRC samples from the right and left colon are not due to normal variations in the levels of glycans between the healthy right and left colon. Additionally, the levels of the acidic glycans H4N3F1P1, H5N4F1P1, and S1H5N4F1 were found to change in a cancer-specific but colon location-nonspecific manner, indicating that CRC affects glycan levels in similar ways, regardless of tumor location.
2020-06-10 | PXD018673 | Pride
Project description:<p>Colorectal cancer (CRC) exhibits profound molecular heterogeneity based on primary tumor location. A comprehensive understanding of the spatially resolved metabolic differences between right-sided (RCC) and left-sided (LCC) carcinomas remains elusive. Here, to eliminate the influence of inter-individual heterogeneity on metabolic differences, we performed spatial metabolomics using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) on synchronous bilateral tumors from the same patient. This was complemented by untargeted metabolomic profiling via ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) on tumor and matched normal tissues from 30 CRC patients with different locations and histologies. Our analysis identified 345 metabolites and revealed distinct, location-specific metabolic reprogramming. Among these, 72 altered metabolites between left- (Ltu) and right-sided colon tubular adenocarcinomas (Rtu) indicated disruptions in ether lipid and phosphatidylcholine metabolism of Ltu and nucleotide, amino sugar, and fatty acid metabolism of Rtu. Furthermore, right-sided mucinous adenocarcinomas (Rmu) were characterized by unique sphingolipid metabolism reprogramming, shifting from an 'apoptosis-promoting signaling' to a 'structural construction' function, compared to Rtu. N-Acetylneuraminic acid, oleoyl-l-carnitine and 12-Hydroxystearic acid are representative DEMs in the aforementioned pathway. Spatial analysis delineated metabolic profiles varied spatially from the tumor center to the periphery. Collectively, our findings underscore the influence of primary tumor location on metabolism and suggest subtype-specific metabolic adaptation mechanisms associated with histology and spatial architecture.</p>
2026-03-24 | MTBLS13729 | MetaboLights
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.
2021-11-25 | GSE174767 | GEO
Project description:This research aimed to identify protein biomarkers of right ventricular dysfunction in patients with advanced heart failure with reduced ejection fraction (HFrEF). Samples of myocardium from both, right and left ventricles (RV, LV) were obtained from 10 HFrEF patients with right ventricular dysfunction (RVD), 10 HFrEF patients without RVD (noRVD) undergoing heart transplantation, and 10 non-failing unused donor hearts (Control). Tissue samples were homogenized and extracted using mild Triton X-100 detergent and processed by SP3 extraction to remove the detergent prior the analysis, (LFQ) proteomic analysis identified a total of 4 032 proteins in the left ventricle and 3 788 proteins in the right ventricle.
2025-02-11 | PXD043768 | Pride
Project description:Left-right asymmetry is a basic character of aging brain; however, the molecular foundation of the left-right asymmetry remains unclear. The morphology, physiology and behavior of rhesus aging are obviously similar to human aging, but the aging-rate of rhesus is roughly three times as fast as human, in which the underlying mechanism needs further investigation. By using of 6-plex tandem mass tag (TMT) labeling, we presented a high throughput quantitative proteomics analysis to 6 group hippocampal samples including left and right hippocampus from 3 years, 6 years and 20 years old rhesus. Our data identified 3391 high-confidence proteins. After screening, we found 340 aging-related proteins of left hippocampus and 334 aging-related proteins of right hippocampus, in which there were 114 overlap proteins. Furthermore, the aging-related proteome of left rhesus hippocampus aging was compared with human aging-related proteome of left hippocampus that was reported by our lab previously. As the results show, we discovered 446 aging-related proteins in rhesus and 830 aging-related proteins in human with an overlap of 106 proteins.
2020-01-23 | PXD011398 | Pride