Similar Datasets
Project description:Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis with very frequent post-surgical local recurrence. The combination of adjuvant chemotherapy with radiotherapy is under consideration to achieve a prolonged disease-free survival (DFS). To date, few studies have determined protein profiles that are associated with responsiveness to adjuvant chemoradiation. Here, we analyzed the proteomes of primary, surgically resected PDAC tumors subjected to adjuvant chemoradiation and achieving short DFS (median DFS of 6 months, n = 6) or a prolonged DFS (median DFS of 28 months, n = 6) using liquid chromatography tandem mass spectrometry.
2018-09-11 | PXD009254 | Pride
Project description:Interleukin-1 (IL-1) is produced from immune-activated cells upon infection and tissue injury, and stimulates a variety of cells expressing its receptor. IL-1 receptor activation results in intracellular signaling cascades that culminate in the activation of transcription factors such as NF-kappaB, AP-1, and C/EBPbeta. To identify genes whose expression is induced in response to IL-1, we performed DNA microarray analysis of IL-1-treated murine dermal fibroblasts (DFs). The gene expression patterns in control, untreated DFs and in DFs treated with IL-1 were compared. Experiment Overall Design: Total RNAs from untreated DFs (0 h) vs. IL-1-treated DFs (1 h, 2 h, or 4 h after IL-1 treatment) were isolated and analyzed using an Agilent DNA microarray platform. Hybridization was performed in duplicate for dye swapping.
2009-01-14 | E-GEOD-12285 | biostudies-arrayexpress
Project description:Expression profiles of colorectal liver metastasis samples collected from Paul Brousse Hospital (France) and University Hospital Utrecht (The Netherlands). Patients are divided into a high-risk (DFS < 1 year) and a low-risk group (DFS < 1 year).
2012-11-29 | E-TABM-1112 | biostudies-arrayexpress
Project description:The understanding of metastatic spread is limited and molecular mechanisms causing particular characteristics of metastasis are largely unknown. This comprises the extremely varying dormancy periods of tumor cells in the secondary organ after metastatic spread, represented by the disease-free survival (DFS) of the patients, or differing numbers of metastases in different patients. Knowing the molecular fundamentals of these phenomena would support the individual prediction of patients´ outcome and facilitate the decision for an appropriate monitoring and therapy regime. In a first study (PMID 19391132) we analyzed the transcriptome-wide expression profiles of 20 pulmonary metastases of renal cell carcinoma (Met1-9, Met11-18, Met20, Met23, Met25) to identify expression patterns associated with the dormancy period and the number of metastases per patient. Pre-processed and analyzed data for this study are available in GEO Series GSE14378. In this second study, we validated the DFS-associated expression pattern from the first study on four further metastases and also included primary ccRCC with different DFS. For this, the microarray data of all metastases and primary tumors were pre-processed together. The aim of this second study was to identify those genes, which are differentially expressed in metastases developed after different dormancy periods and which are already deregulated in primary tumors. Genes differentially expressed in synchronously vs. metachronously metastases might contribute functionally to the dormancy period. Genes already deregulated in primary ccRCC might be suitable for prognostic purposes. metastases manifested synchronously or metachronously (DFS less than or equal to 9 months compared with DFS greater than or equal to 60 months); primary ccRCC which developed synchronous or metachronous metastases (DFS less than or equal to 6 months compared with DFS greater than or equal to 45 months)
2010-07-30 | E-GEOD-22541 | biostudies-arrayexpress
Project description:Interleukin-1 (IL-1) is produced from immune-activated cells upon infection and tissue injury, and stimulates a variety of cells expressing its receptor. IL-1 receptor activation results in intracellular signaling cascades that culminate in the activation of transcription factors such as NF-kappaB, AP-1, and C/EBPbeta. To identify genes whose expression is induced in response to IL-1, we performed DNA microarray analysis of IL-1-treated murine dermal fibroblasts (DFs). The gene expression patterns in control, untreated DFs and in DFs treated with IL-1 were compared. Keywords: Time course
2009-01-01 | GSE12285 | GEO
Project description:Stenotrophomonas sp. DFS-20110405 Genome sequencing
| PRJNA756010 | ENA
Project description:Diabetes Mellitus (DM) is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU) that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS) and healthy non-diabetic foot skin (NFS). MicroRNA (miR) profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05). Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy, vascular complications, or duration of DM, may further compromise tissue’s healing ability leading to development of DFUs.
2015-05-01 | GSE68185 | GEO
Project description:Neisseria meningitidis strain:DFS-1910310016 Genome sequencing
| PRJNA828430 | ENA
Project description:DC DFS SARS-CoV-2 Raw Sequencing Reads
| PRJNA717017 | ENA
Project description:Chemoradiation therapy (CRT) is a treatment for muscle invasive bladder cancer (MIBC). Using a novel transcriptomic profiling panel, we validated prognostic immune biomarkers for response to CRT on 70 pre-treatment tumor samples from NRG/RTOG 0524 and 0712, two prospective trials of MIBC. Disease-free survival (DFS) and overall survival (OS) was estimated by Kaplan-Meier method and stratified by genes correlated with immune cell proportions and activation. Cox proportional hazards models were used to assess group differences. Sample clustering based on gene expression profiles driven by immune cell proportions demonstrated cluster 2 with a high percentage of immune cell content with significantly longer DFS (Hazard Ratio (HR): 0.53 (95% CI: 0.26 – 1.10), p=0.071) and OS (HR: 0.48 (95% CI: 0.24 – 0.97), p=0.040) than cluster 1 with a low percentage of immune cell content. Higher expression of T cell infiltration genes (CD8A and ICOS ) showed longer DFS (HR: 0.40 (95% CI: 0.21 – 0.75), p=0.005) and OS (HR: 0.49 (95% CI: 0.25 – 0.94), p=0.033). Higher expression of interferon gamma signaling (IDO1) also showed longer DFS (HR: 0.44 (95% CI: 0.24 – 0.88), p=0.021) and OS (HR: 0.49 (95% CI: 0.24 – 0.99), p=0.048). These findings have treatment implications that should be validated in CRT MIBC trials particularly those that integrate immunotherapy.
2023-12-31 | GSE245748 | GEO