Browse
Submit Data
Databases
API
Help

Dataset Information

195 Views

1 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1060

T cell metabolism during graft-versus-host disease(CAB 311)

ABSTRACT: T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis.

INSTRUMENT(S): QTOF

ORGANISM(S): Mouse Mus Musculus

TISSUE(S): T-cells

SUBMITTER: Maureen Kachman

PROVIDER: ST000181 | MetabolomicsWorkbench | Sun Jun 07 00:00:00 BST 2015

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Similar Datasets

T cell metabolism during graft-versus-host disease (CAB 307)-PART I

Project description:T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis. Several mice lines were used in this study.

2015-06-06 | ST000178 | MetabolomicsWorkbench

RNA-seq data from PBMC of M.tb-infected and M.tb-uninfected infants in MVA85A clinical trial

Project description:Frozen PBMC from infants 7 days before randomization (PBMC from two infant were 28 days after randomization) were stimulated in RPMI with 10% Feotal calf serum (FCS) at 5 million/ml with 1 million CFU/ml BCG (SII) or left unstimulated in a total volumn of 200ul/well in 96-well plates. Cells were incubated for 12 hours (37C, 5% CO2). Plates were centrifuged and 200ul supernatant was removed without disrupting the pellet and transferred into clean U-bottom plates. The plates were centrifuged again, the supernatant were flicked-out and the cells were resuspended in 200ul RLT buffer with beta-mercaptoethanol (10ul/ml). The samples were mixed with the buffer to lyse the cells and the plates were sealed and stored at -20C. At the time of RNA-extraction, plates were thawed at 37% for 10 mins. RNA extraction was performed using the Qiagen RNeasy kit following manufacturer's instructions (including optional DNase digestion) and RNA was eluted twice, 30 ul per elution. RNA was quantified by nanodrop and samples were stored at -80C.

2022-05-24 | GSE203395 | GEO

Expression data from mouse Nuocytes

Project description:Nuocytes are a recently described cell that responds to both IL-25 and IL-33 and produce high levels of IL-13 and IL-5 Mice were administered with 3 daily doses of IL-25 (400 ng/dose). Nuocytes were purified by flow cytometry. Spleen cells prepared from IL-25-treated mice were depleted of lineage+ cells before cell sorting by incubation with biotin-conjugated anti-CD3, anti-CD19, anti-CD11b and anti-FcεRI antibodies before removal of antibody-bound cells by magnetic separation using Dynabeads (Invitrogen). Lineage-depleted cells were stained with PE-conjugated antibodies against CD4, CD8, B220, TER-119 and CD11b, a FITC-conjugated antibody against CD45, and an APC-conjugated antibody against ICOS. PE−, FITC+, APC+ cells were collected using a Mo-flo cell sorter, and purity was checked by staining with lineage antibodies and antibodies against IL-17BR and T1/ST2. Following purification nuocytes were prepared directly for microarray gene expression analysis or cultured with IL-33 and IL-7 (both at 10 nanograms/ml) for 9 days before being prepared for microarray gene expression analysis.

2010-12-09 | E-GEOD-25890 | biostudies-arrayexpress

Maytansinoid DM4-Conjugated Humanized Monoclonal Antibody huC242 in Treating Patients With Solid Tumors

Project description:RATIONALE: Monoclonal antibodies, such as maytansinoid DM4-conjugated humanized monoclonal antibody huC242, can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. PURPOSE: This phase I trial is studying the side effects and best dose of maytansinoid DM4-conjugated humanized monoclonal antibody huC242 in treating patients with solid tumors that cannot be removed by surgery or have spread to other parts of the body.

| 2030868 | ecrin-mdr-crc

IL1β-dependent extravasation of pre-existing lung-restricted autoantibodies activates complement to promote primary graft dysfunction

Project description:Pre-existing lung restricted autoantibodies (LRA) are associated with a higher incidence of primary graft dysfunction (PGD) although it remains unclear whether LRA can drive its pathogenesis. In syngeneic murine left lung transplant recipients, pre-existing LRA worsened graft dysfunction, which was evident by impaired gas exchange, increased pulmonary edema, and activation of damage-associated pathways in lung epithelial cells. LRA-mediated injury was distinct from ischemia-reperfusion injury since deletion of donor non-classical monocytes as well as host neutrophils could not prevent graft dysfunction in LRA-pretreated recipients. Whole LRA IgG molecule was necessary for lung injury which was mediated by the classical and alternative complement pathways and reversed by complement inhibition. However, deletion of Fc receptors in donor macrophages or mannose-binding lectin proteins failed to rescue lung function. LRA- mediated injury was localized to the transplanted lung and dependent on IL1β-mediated permeabilization of pulmonary vascular endothelium which allowed extravasation of antibodies. Genetic deletion or pharmacological inhibition of IL1R in the donor lungs prevented LRA-induced graft injury. In humans, pre-existing LRA was an independent risk factor for severe PGD and could be treated with plasmapheresis and complement blockade. We conclude that pre-existing LRA can compound ischemia-reperfusion injury to worsen PGD for which complement inhibition may be effective.

2022-10-19 | GSE211501 | GEO

CD8 in vitro CD2-costimulation

Project description:Purified primary human CD8 T cells were stimulated in vitro in parallel using a magnetic bead conjugated to either anti-CD3/28 or anti-CD2/3/28 antibodies. Cells were cultured for 6 days in complete RPMI1640 and 10ng/ml IL2 and were harvested on day 6 and RNA was isolated for further labelling and hybridisation.

2015-08-12 | E-MTAB-3470 | biostudies-arrayexpress

RNA-seq of bronchoalveolar lavage samples of lung transplant primary graft dysfunction

Project description:This is an RNA-seq study of human lung transplant recipients. Bronchoalveolar lavage cells were collected on the first day after lung transplant. We performed bulk RNA-sequencing on 19 lung transplant recipients with severe primary graft dysfunction (PGD) and 19 lung transplant recipients without primary graft dysfunction. As this data is human identifiable, raw data are not included in this record.

2023-02-15 | E-MTAB-12282 | biostudies-arrayexpress

Influence of murine norovirus on cell metabolism

Project description:6.5 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of medium containing either Murine Norovirus-1 (MNV) at an MOI=5 or medium containing a v/v match of mock lysate was added to the cells. Plates were rocked on ice for 1 hour, then cells were washed 3X with cold DPBS++, and plain medium as added to cells. Plates were then incubated for 7.5 hours at 37 degrees and 5% CO2. Cells were washed with 12 mL of 150 mM Ammonium Acetate, swirled 8 times, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.

2017-08-02 | ST000833 | MetabolomicsWorkbench

Transcriptional analysis for cell-cell communication during graft union development in Arabidopsis

Project description:Grafting is an ancient cloning method that has been used widely for thousands of years in agricultural practices. However, the molecular mechanisms for graft union development are still largely unknown. The developmental stage of graft union was characterized based on micrografting method. Microarray data revealed a signal exchange process between cells of scion and stock at 1dag, which reestablished the communication network in graft union. This process was concomitant with the cleaning of cell debris, and both of the processes were initiated by a wound-induced program. The results demonstrate the feasibility and potential power of investigating various plant developmental processes by this method and represent a primary and significant step in interpretation of the molecular mechanisms underlying graft union development. WT/WT seedling grafts of 22-26 hours after grafting were collected for microarray, intact WT seedlings and ungrafted scions and stocks were as control. All three types of sample, grafts (marked as A: whole graft), ungrafted scions and stocks (marked as B: mixture of ungrafted scions and stocks) and intact seedlings (marked as C: whole seedling), were collected at the same time of 22-26 hours after grafting. For sample B, scions and stocks were cut at the same time during grafting. For sample C, intact seedlings were also reserved during grafting. Data were firstly compared between sample A and C, differential expressed probe sets were than tested based on A and B to obtain graft-specific probes.

2012-05-02 | E-GEOD-36447 | biostudies-arrayexpress

A Machine Learning Tool Integrating Circulating Cell-Free DNA Methylation with Clinical Variables for Non-Invasive Diagnosis of Liver Graft Pathology

Project description:Liver Transplant Recipients (LTRs) with elevated liver enzymes can develop graft injury due to various etiologies, such as T-cell mediated rejection (TCMR) and NASH (NASH-LT). While liver biopsy is the gold standard method for diagnosis of graft pathology, it is invasive and is associated with risks. The goal of our study was to develop a Machine Learning (ML) tool integrating clinical variables with methylation patterns on circulating DNA in plasma as a non-invasive diagnostic tool of graft injury. We generated methylation profiles of circulating DNA in a pilot study of 43 LTRs (11 NASH-LT, 19 TCMR, and 13 Control-LT), and developed an L2 multinomial logistic regression ML approach across 101 bootstrapped models to distinguish between the graft conditions. NASH was associated with distinctive methylation patterns on genes involved in fatty acid metabolism, while methylation of platelet-derived growth factors was identified in patients with TCMR. Our ML model achieved a mean multi-classification accuracy of 0.91, with mean specificity and sensitivity of 0.94 and 0.91, respectively. The model was found to be particularly adept at detecting TCMR and Control-LT, with true positive rates (TPRs) of 95% and 90%, and areas under the curve (AUROC) of 0.992 and 0.985, respectively. For NASH-LT, the models achieved a performance with a TPR of 82% and an AUROC of 0.991. These preliminary results suggest that our newly developed ML tool, leveraging cell-free DNA methylation and clinical variables, is a promising non-invasive classifier of graft pathology.

| EGAS00001007171 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data