GNPS - Arterio-venous metabolomics for postprandial inter-organ flux analysis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive Plus
ORGANISM(S): Sus Scrofa (ncbitaxon:9823)
SUBMITTER: 
Cholsoon Jang
PROVIDER: MSV000095381 | GNPS | Thu Jul 18 16:26:00 BST 2024
REPOSITORIES: GNPS
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Project description:Yucatan minipigs, fasted overnight, were previously fed either a control or a Western diet (high-fat, high-sucrose). They received 23.7ml/kg of their body weight in liquid diet via intra-gastric tubing, with blood samples collected 120 minutes post-administration.
For sampling, catheters were inserted into the femoral artery and vein. Blood was drawn from the hepatic, portal, renal, splenic, and inferior mesenteric veins, the lateral auricular vein, the aorta, and the coronary sinus using a 23G butterfly needle attached to a 1 mL syringe. The external jugular vein and the left and right ventricles were sampled using a 27G needle connected to a 1 mL syringe. All organ blood samples were taken within 5-10 minutes of the initial sampling. Tissue samples were collected post-terminal surgery.
2024-07-16 | MSV000095352 | MassIVE
Project description:Yucatan minipigs, fasted overnight, were previously fed either a control or a Western diet (high-fat, high-sucrose). They received 23.7ml/kg of their body weight in liquid diet via intra-gastric tubing, with blood samples collected 120 minutes post-administration. For sampling, catheters were inserted into the femoral artery and vein. Blood was drawn from the hepatic, portal, renal, splenic, and inferior mesenteric veins, the lateral auricular vein, the aorta, and the coronary sinus using a 23G butterfly needle attached to a 1 mL syringe. The external jugular vein and the left and right ventricles were sampled using a 27G needle connected to a 1 mL syringe. All organ blood samples were taken within 5-10 minutes of the initial sampling. Tissue samples were collected post-terminal surgery.
2024-07-18 | MSV000095381 | MassIVE
Project description:Yucatan minipigs, fasted overnight, were previously fed either a control or a Western diet (high-fat, high-sucrose). They received 23.7ml/kg of their body weight in liquid diet via intra-gastric tubing, with blood samples collected 120 minutes post-administration.
For sampling, catheters were inserted into the femoral artery and vein. Blood was drawn from the hepatic, portal, renal, splenic, and inferior mesenteric veins, the lateral auricular vein, the aorta, and the coronary sinus using a 23G butterfly needle attached to a 1 mL syringe. The external jugular vein and the left and right ventricles were sampled using a 27G needle connected to a 1 mL syringe. All organ blood samples were taken within 5-10 minutes of the initial sampling. Tissue samples were collected post-terminal surgery.
2024-07-16 | MSV000095352 | GNPS
Project description:Interventions: The only intervention will be to take five ml of blood will be taken from a vein in the patient’s arm (this will be from a intravenous cannula as part of the patient’s general anaesthetic such that there will be no additional venepuncture burden) as well as another 5 ml of blood from the ileocolic / appendicular vein (a blood vessel that drains blood from the appendix or right colon that is located in the right lower side of the abdomen) during the initial stages of your peritonectomy surgery (total number of blood tests: 2; total volume: 10ml; NB: 5-10mL is equivalent to 1-2 teaspoons). The blood sampling would take less than one minute during surgery by the anaesthetist (peripheral sample) and the surgeon (portal vein sample). Assessment of the fidelity of this intervention will be in part by testing for albumin of these specimens for comparison.
Primary outcome(s): Carcinoembryonic antigen (CEA) levels determined from the portal vein[Blood samples to be collected during surgery];Carcinoembryonic antigen (CEA) levels determined from the peripheral vein[Blood samples to be collected during surgery];Albumin levels determined from the peripheral and portal vein as a composite primary outcome for correlation..[Blood samples to be collected during surgery]
Study Design: Purpose: Prevention; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Parallel;Type of endpoint: Efficacy
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Project description:Gene expression studies in peripheral blood mononuclear cells (PBMC) can provide knowledge that would be difficult to obtain using other types of biological samples, as these cells can reflect overall response of the body to a specific stimulus, such as diet. Here, we aimed to study the impact of sustained intake of isocaloric diets with an unbalanced macronutrient proportion (rich in fat or protein) on PBMC gene expression in rats using transcriptomics, to better understand the effects of these diets on metabolism and health. Macronutrient diet composition (especially increased protein content) affected PBMC gene expression. An important effect was observed in immune response-related genes. High protein (HP) diet produced an activation of genes mainly related to antigen recognition/presentation, whereas the high fat (HF) diet was more related to a decreased expression of these genes. Key energy homeostasis genes (mainly involved in lipid metabolism) were also affected, reflecting a nutritional adaptive response to the diets. Decreased Dhrs3 and increased Pref-1/Dlk1 expression observed in HP-fed animals reflects a lower lipogenic capacity. In addition, HF diet affected the expression of genes related to insulin resistance/signaling (Msra/Slc9a6, Asb6), hypoxia (Akap12), cardiovascular problems (Ethe1, Lr11), cognitive impairment (Tmcc2) and tumorigenesis (Ddx17, Phb, Rnasen/Drosha, and Tsc2). HP diet also impaired the expression of genes related to glucose metabolism and insulinemia (Glut-4/Slc2a4, Sfxn5, Slc16a1), but positively affected genes involved in liver function (Clec4f and St6galnac3) and cardiovascular protection (Sort1). In conclusion, gene expression analysis in PBMC can provide information that could be useful to detect metabolic deviations and health consequences of diets with an unbalanced macronutrient composition. 2 months-old male Wistar rats received a low fat control diet, or a high fat (HF) diet, or a high protein (HP) diet for 4 months, respectively. At the end of the intervention, prior to the sacrifice of the animals, peripheral blood samples (1.5-2.5 mL) were collected from the safena vein, using heparin in NaCl (0.9%) as anticoagulant. Immediately after blood collection, peripheral blood mononuclear cells (PBMC) were isolated by Ficoll gradient separation. Total RNA was isolated from PBMC, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 4x44K microarrays.
2015-12-07 | E-GEOD-54897 | biostudies-arrayexpress
Project description:Acute pulmonary thromboembolism (PTE) refers to the obstruction of the pulmonary artery or its branches by thrombus. Recent studies suggest that PTE-induced endothelium injury is the major physiological consequence of PTE, and PTE-induced endothelium injury can be used to stratify disease severity. Several plasma biomarkers have been identified in PTE patients, but genome-wide gene expression has not been attempted in PTE. In this study, using rabbit autologous thrombus PTE model, we applied gene expression array to identify genes and proteins changes in pulmonary arteries under PTE. Twenty healthy China big-ear rabbits, specific-pathogen-free (SPF) grade and weighing between 2.5 and 3 kg, were purchased from the Center of experimental animals of the Nantong University. These rabbits were randomly divided into control (n=10) and experimental group (n=10). One hour before the experiment, thrombi were generated by collecting 0.5 ml blood from the marginal ear vein and placing into a sterile petri dish for 45 minutes at room temperature. The autologous blood clot was subsequently cut into 5 mm sized aliquots and suspended in sterile saline. After anesthesia, a venous catheter was placed in the exposed and isolated femoral vein. In the experimental group, the blood clot in 10 mL of saline was injected into the femoral vein. An additional 5 mL of saline were used to flush the catheter. In the control group, 15 mL of saline were injected into the femoral vein. Afterwards, the animals were placed back in the cage.
2016-07-23 | E-GEOD-84738 | biostudies-arrayexpress
Project description:For the blood contamination studies a CSF pool was made with 1mL CSF free of blood from n=4 patients. The pool was divided into four aliquots. One aliquot was kept as reference CSF without added blood (named “neat” in the raw files), one was spiked with 20 µL blood/mL CSF (2%) (“20S”) and two were spiked with 5 µL blood/mL CSF (0.5%) (named “5S” and “5U”, S=centrifuged, U=not centrifuged). The sample spiked with 2% blood and one of the samples spiked with 0.5% blood were centrifuged at 4C at 400 x g for 10 minutes. In one experiment (BloodContamination_GeLC-MS_comb1-10) the reference CSF (neat), and 0.5% centrifuged (5S) and 2% centrifuged (20S) were protein depleted using the MARS Hu-14 column, separated by SDS-PAGE into ten fractions and in-gel digested. The samples (30 in total) were analysed by LC-MS on an OrbiTrap Velos Pro online coupled to a Dionex Ultimate 3000 nano RSLC system. The data was analysed by the Progenesis LC MS software 2.7 (Nonlinear Dynamics), and the MS/MS spectra were searched against UniProt/SwissProt using the open-source graphical user interface SearchGUI (version 1.7.3), with search engines OMSSA and X!Tandem. PeptideShaker (version 0.14.7) was used to assemble the peptides into proteins. The raw files were named according to sample and fraction, e.g. the first fraction of the reference CSF was called “BK_GeLC_neat_F1”, and the second fraction was called “BK_GeLC_neat_F2”. In the second blood contamination study the reference CSF (neat), and the 0.5% blood spiked samples centrifuged (5S) and not centrifuged (5U) were trypsin digested by in solution protocol and analysed using the same instruments as in the first study. (In the search output file are also the results for 2% blood spiked with and without centrifugation, 20S and 20U, but since the data was not used, the raw files are not distributed). The raw files were named “BK_Insol_FD_X” (X = neat, 5S or 5U). In the third experiment we examined the rostro-caudal gradient (RCG) on CSF in the spinal cord by sampling the 1st, 10th, 16th, 24th, 31st, 38th and 44th mL CSF in volumes of approximately 1 mL of a PSP patient during lumbar puncture. The CSF was centrifuged at 2000 x g for 10 min. We did an iTRAQ discovery study, and to be able to compare all seven RCG points, three related iTRAQ experiments (RCG exp 1, 2 and 3) were done. In each related experiment we included an identical reference which we labeled with the iTRAQ 114 reagent. The reference sample contained equal volumes of the seven RCG points, and was used as the reference in the data analysis. In the experiment we had twelve samples (equal volume) that were digested and labeled with iTRAQ reagents according to the vendor’s manual. The samples were combined into three related experiments as follows: Exp. 1 (common reference, 44th mL, 24th mL and 1st mL), Exp. 2 (common reference, 1st mL, 38th mL and 16th mL), and Exp. 3 (common reference, 10th mL, 44th mL and the 31st mL). The 1st and 44th mL were included twice, since they were expected to be the most different samples. The three combined samples (RCG exp 1, 2 and 3) were fractionated into 21 fractions using mixed mode reversed phase-anion chromatography (MM (RP-AX)). Fractions 1-4 were excluded from LC-MS analysis and the two latest fractions were combined before analysis on an Orbitrap Velos Pro, resulting in 16 fractions per combined sample. The raw files were named according to experiment (RCG 1, 2 or 3) and number of fraction (F4-F19), e.g. the raw file by the name EA_RCG3_F15 is fraction 15 from RCG experiment 3.
2014-02-13 | PXD000401 | Pride
Project description:Interventions: Group 1: Blood and sputum samples as well as paraffin embedded tumour tissue from patients with microsatellite stable colorectal cancer shall be analysed before therapy and over time to establish and validate hotspot mutation and somatic copy number variant (SCNAs) analysis. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
- One sputum tube (only at study inclusion).
- FFPE tissue samples from the primary tumor (from initial surgery)
Group 2: Blood samples of tumor-free control persons shall be tested for hotspot mutations and somatic copy number variants (SCNAs) to identify technical artefacts and improve our protocols. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
Primary outcome(s): Identification of tumorspecific SCNAs in plasma samples of colorectal cancer patients
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other
| 2433407 | ecrin-mdr-crc
Project description:We injected adenovirus overexpressing Chrna4 as well as vehicle via tail vein (1× 10^9 pfu per mouse). Mice were fed with high-fat diet at the same time. After two weeks from virius injection, mice were sacrificed and samples were collected
2022-07-08 | GSE133944 | GEO
Project description:Background: The transcriptome of peripheral white blood cells (PWBCs) contains valuable physiological information, thus making them a prime biological sample for investigating mRNA-based biomarkers. However, prolonged storage of whole blood samples can alter gene transcript abundance in PWBCs, compromising the results of biomarker discovery. Here, we designed an experiment to interrogate the impacts of delayed processing of whole blood samples on gene transcript abundance in PWBCs. We hypothesized that storing blood samples for 24 hours at 4°C would cause RNA degradation resulting in altered transcriptome profiles. Results: We produced RNA-sequencing data for 30 samples collected from five estrus synchronized heifers (Bos taurus). We quantified transcript abundance for 12,414 protein-coding genes in PWBCs. Analysis of parameters of RNA quality revealed no statistically significant differences (P>0.05) between samples collected from the jugular vein and coccygeal vein, as well as among samples processed after 1, 3, 6, or 8 hours. However, samples processed after 24 hours of storage had a significantly lower RNA integrity number value (P=0.03) in comparison to those processed after one hour of storage. Next, we analyzed RNA-sequencing data between samples using those processed after one hour of storage as the baseline for comparison. Interestingly, evaluation of 3’/5’ bias revealed no statistically significant differences between genes with lower transcript abundance in samples stored for 24 hours relative to one hour. In addition, sequencing coverage of transcripts was similar between samples from the 24 hours and one-hour groups. We identified four and 515 genes with differential transcript abundance in samples processed after storage for eight and 24 hours, respectively, relative to samples processed after one hour. Conclusions: The PWBCs respond to prolonged cold storage by increasing genes related to active chromatin compaction which in turn reduces gene transcription. This alteration in transcriptome profiles can impair accuracy of mRNA-based biomarkers. Therefore, blood samples collected for mRNA-based biomarker discovery should be refrigerated immediately and processed within six hours post sampling.
2021-12-30 | GSE192530 | GEO