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ABSTRACT:
PROVIDER: PRJNA984449 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis.
2014-05-27 | GSE57969 | GEO
Project description:Input control for ChIP-seq on transgenic flies expressing stc-eGFP fusion proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2024-02-27 | GSE256989 | GEO
Project description:To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis. The samples were obtained and washed with cold PBS, transported in liquid nitrogen and immediately stored in liquid nitrogen after removal. Total RNA was isolated from frozen histologic specimens using a mirVana™ RNA isolation Kit.
2014-05-27 | E-GEOD-57969 | biostudies-arrayexpress
Project description:The goal of this study is to compare the differently expressed genes in colon tissue of Control and loperamide (LOP) induced slow transit constipation (STC) rat model with or without Golden Bifid (Jin Shuang Qi, JSQ) or positive control group (Prukapril Succinate Tablet, PST) treatment. The loperamide induced STC rat model were randomly divided into 3 groups: LOP, LOP + JSQ and LOP + PST groups (n=6 for each group). Control rats (n=6) were set as control. The STC rat model was induced by administering loperamide intraperitoneally at a dose of 3 mg/kg body weight twice daily for 21 days in all groups except the Control group. On the 8th day, the LOP + JSQ group was intragastrically with 0.540 g/kg/d 1 h after each loperamide administration for 14 days. The LOP + PST group was given prucalopride succinate tablets at a dose of 0.18 mg/kg/d by oral gavage 1 h after each loperamide administration for 14 days. Then the colon tissues were used to identify differentially expressed genes among different groups.
2025-09-25 | GSE273280 | GEO
Project description:ChIP-seq on transgenic flies expressing stc-eGFP fusion proteins. The IP was performed using an anti-GFP antibody. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2024-02-27 | GSE257253 | GEO
Project description:Senescent tumor cells (STCs) play a crucial role for radiotherapy-induced immunosuppressive tumor microenvironments (ITM). However, current senolytic strategies lack specificity for STCs and often cause off-target toxicity. Here, we first identified the antigen presenting potential of STCs in patient-derived tumor tissues and demonstrated their capacity for directly priming and inducing STC-specific CD8+ T cells. We thereafter engineered STC-derived nanovesicles for directly priming CD8+ T cells through their upregulated antigen-presenting machinery (termed as nano-APM). Upon systemic administration, nano-APMs specifically accumulated in the spleen and directly primed CD8⁺ T cell, thereby establishing STC-specific T cell pool. Based on these finding, we sequentially combining nano-APM with RT to achieve spatiotemporally-confined activation of anti-senescence immunity via RT-controlled tumor senescence induction. In preclinical mouse models of pancreatic ductal adenocarcinoma and bladder cancer, the sequential combination of the nano-APM with RT effectively eliminated STCs, reprogramed RT-induced ITM (e.g., 21.5-folds higher CD8+ T cell to Tregs ratio than the control group), and induced durable antitumor response. Overall, this study pioneered a STC-derived nanovesicle platform to directly prime splenic T cells and achieve spatiotemporally-confined senolysis for potentiating RT.
2026-01-14 | GSE306978 | GEO
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:meiose non oriented RNA-Seq data
| PRJEB5029 | ENA
Project description:Cold stimulation not only activates the thermogenesis activity of brown adipose tissue (BAT) but also induces browning of white adipose tissue (WAT). To elucidate the mechanisms underlying cold-induced thermogenesis and adipose tissue remodeling, we used RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to examine the transcriptomic and proteomic profiles, respectively, of adipose tissue from mice exposed to cold or thermoneutral temperature. The male C57BL/6J mice were divided into three groups (5 mice/group), two groups were kept at 6 ˚C for 6 h and 24 h, respectively, and the control group were kept at 22 ˚C for 24 h. Subsequently, the BAT and inguinal WAT of each mouse were dissected and subjected to RNA-seq and data-independent acquisition (DIA)-based LC-MS/MS.
2026-01-09 | PXD067973 | Pride
Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.
2024-04-09 | GSE263135 | GEO