Human spinal cord injury plasma LC-MSMS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Blood Plasma
DISEASE(S): Spinal Cord
SUBMITTER: 
Mateus Harrington
LAB HEAD: Karina Wright
PROVIDER: PXD035072 | Pride | 2022-07-14
REPOSITORIES: Pride
Similar Datasets
Project description:50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of H2O2 for 30 minutes, cultures were spun down and pellets were resuspended in same volume of GN101 media. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 exposed to H2O2 and 8 non-exposed controls) were each hybridized on duplicate arrays (as dye-flips) against the same standard control sample.
2010-05-27 | E-GEOD-7610 | biostudies-arrayexpress
Project description:100mM EMS was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of EMS for 30 minutes, cultures were spun down and pellets were re-suspended in same volume of GN101 media. Cultures were then harvested by centrifugation and pellets were snap frozen on a dry-ice ethanol bath. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 samples from EMS perturbed and 8 non-perturbed controls) were analyzed on replicate arrays (dye-flips) all against the same standard reference sample.
2010-05-27 | E-GEOD-7609 | biostudies-arrayexpress
Project description:The aim of this study was to understand how autotrophic (CO2-fixing) bacteria balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment.To this end, the proteome of the model chemolithoautotroph Ralstonia eutropha a.k.a. Cupriavidus necator was studied in different environmental conditions (four limiting substrates, and five different growth rates). Cupriavidus was cultivated in substrate-limited chemostats with fructose, formate, succinate and ammonium limitation to obtain steady state cell samples. The dilution rate/growth rate was increased step-wise from 0.05 to 0.25 1/h in 0.05 steps. Protein quantity was determined by LC-MS, and enzyme utilization was investigated by resource balance analysis modeling.
2022-02-17 | PXD024819 | Pride
Project description:To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. The results of the following two subset comparisons are linked to the Series record below: CpG loci differentially methylated (q<0.04) between AIS and male controls (primary human genital fibroblasts): To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. Cell culture of primary fibroblasts from scrotum/ labia majora from donors with PAIS (n=13), MAIS (n=1) or CAIS (n=13) and 9 controls were analyzed using the HumanMethylation27 Bead Chip. 13 AIS samples and all controls were analyzed in duplicates. Samples with gene call rates <95% as analyzed with BeadStudio software (Illumina, Inc.) and CpGs with detection p-values >0.05 in at least one experiment were excluded from analyses. 54 hybridizations with 25,988 CpGs entered the analysis. Differential methylation analysis (DMA) was performed based on average beta-values were performed using OMICS Explorer (v.2.1(25); Qlucore, Sweden). This file contains CpG loci found differentially methylated (q<0.04) by this approach. CpG loci characterized by a high varibility in their DNA methylation value in AIS compared to male controls (primary human genital fibroblasts): To decipher hormonal from chromosomal factors we compared DNA-methylation of 27,568 CpG-loci in genital fibroblasts from 46,XY feminized individuals (AIS) with inactivating androgen receptor mutations to those of normal males. Cell culture of primary fibroblasts from scrotum/ labia majora from donors with PAIS (n=13), MAIS (n=1) or CAIS (n=13) and 9 controls were analyzed using the HumanMethylation27 Bead Chip. 13 AIS samples and all controls were analyzed in duplicates. Samples with gene call rates <95% as analyzed with BeadStudio software (Illumina, Inc.) and CpGs with detection p-values >0.05 in at least one experiment were excluded from analyses. 54 hybridizations with 25,988 CpGs entered the analysis. CpG loci with beta-values ranged in control samples up to 0.34 and a difference of the interquartiles between controls and AIS samples above 0.16 were considered as being variably methylated in AIS and are included in this file.
2012-08-12 | GSE31362 | GEO
Project description:To understand the role of exosome miRNAs in AIS disease and to explore the miRNAs and the potential mechanisms related to the occurrence and development of the disease. This research collected serum samples from AIS patients and healthy volunteers and extracted exosome miRNA. The exosome miRNA associated with AIS was screened by illumina high-throughput sequencing . The differentially expressed target genes related to miRNAs were analyzed using bioinformatics analysis including GO functional enrichment analysis, KEGG pathway enrichment analysis, and the screening of key genes via PPI diagram. These differentially expressed mRNAs were indicated an important role in a variety of biological processes and multiple pathways of AIS disease.
2023-03-21 | GSE169353 | GEO
Project description:Benchmark of FeatureFinderIdentification (FFId), a targeted feature detection algorithm for use in label-free quantification, developed in the OpenMS software framework. The dataset used for the evaluation comes from the iPRG-2015 study ("Differential abundance analysis in label-free quantitative proteomics"), created by the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF); see https://abrf.org/research-group/proteome-informatics-research-group-iprg. The samples contain yeast protein digest spiked with six digested proteins in varying, known concentrations.
2017-07-07 | PXD006336 | Pride
Project description:Adenocarcinoma in situ (AIS) is considered an intermediate step in the progression of normal lung tissue to invasive adenocarcinoma. However, the molecular mechanisms underlying this progression remain to be fully elucidated due to difficulties in obtaining and preserving clinical samples for downstream analyses. Formalin fixation and paraffin embedding (FFPE) is a tissue preservation system that is widely used as a means for long-term storage. Until now, challenges in working with FFPE have precluded using new RNA sequencing technologies (RNA-seq), which would help clarify some of the key pathways affected in the transition from normal to AIS to invasive adenocarcinoma. Recent technological advances have made it possible to sequence RNA from archival tissues. Also, isolation techniques including laser-capture micro-dissection provide the ability to select histopathologically distinct tissues, allowing researchers to study transcriptional variations between tightly juxtaposed cell and tissue types. Utilizing these technologies and new alignment tools we examined differential expression of long intergenic non-coding RNAs and mRNAs across normal, AIS and invasive adenocarcinoma samples from six patients to identify possible markers of lung cancer progression. RNA extracted and sequenced from these 18 samples generated an average of 198 million reads per sample. After alignment and filtering, uniquely aligned reads represented an average 35% of the total reads. We detected differential expression of a number of lincRNAs and mRNAs when comparing normal to AIS, or AIS to invasive adenocarcinoma. Of these, 5 lincRNAs and 31 mRNAs were consistently up- or down-regulated from normal to AIS and more so to invasive carcinoma. We validated the up-regulation of two mRNAs and one lincRNA by RT-qPCR as proof of principle. Our findings indicate a potential role of not only mRNAs, but also lincRNAs in invasive adenocarcinoma. We anticipate that our current findings will lay the groundwork for future experimental studies of candidate RNAs from FFPE samples to identify their functional roles in lung cancer.
2014-12-01 | GSE52248 | GEO
Project description:Inhibition of the anaerobic digestion process through accumulation of volatile fatty acids (VFA) is a recurring problem which is the result of unbalanced growth between acidogenic bacteria and methanogens. A speedy recovery is essential for an establishment of a feasible economical biogas productions. Yet, little is known regarding the organisms participating in the recovery. In this study the organisms involved in the recovery were studied using protein-stable isotope probing (Protein-SIP) and mapping this data onto a binned metagenome. Under acetate-accumulated simulating conditions a formation of 13C-labeled CO2 and CH4 was detected immediately after the addition of [U-13C]acetate, indicative of a high turnover rate of acetate. Several labeled peptides were detected in protein-SIP analysis. These 13C-labeled peptides were mapped onto a binned metagenome for improved taxanomical classification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia and one Bacteroidetes. The organisms affiliating with Clostridia and Bacteroidetes all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis; indicating that these organisms are possible syntrophic acetate-oxidizing bacteria (SAOB) that can facilitate acetate consumption via syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms involved in specific pathways.
2016-05-11 | PXD002996 | Pride
Project description:In the US, the majority of cancer samples analyzed are from white people, leading to biases in racial and ethnic treatment outcomes. Colorectal cancer (CRC) incidence and mortality rates are high in Alabama African Americans (AAs) and Oklahoma American Indians (AIs). We hypothesized that differences between racial groups may partially explain these disparities. Thus, we compared transcriptomic profiles of CRCs of Alabama AAs, Oklahoma AIs, and white people from both states. Compared to CRCs of white people, CRCs of AAs showed (a) higher expression of cytokines and vesicle trafficking toward modulated antitumor-immune activity, and (b) lower expression of the ID1/BMP/SMAD axis, IL22RA1, APOBEC3, and Mucins; and AIs had (c) higher expression of PTGS2/COX2 (an NSAID target/pro-oncogenic inflammation) and splicing regulators, and (d) lower tumor suppressor activities (e.g., TOB2, PCGF2, BAP1). Therefore, targeting strategies designed for white CRC patients may be less effective for AAs/AIs. These findings illustrate needs to develop optimized interventions to overcome racial CRC disparities.
2023-08-23 | GSE237684 | GEO
Project description:Background: Despite recent studies investigating the involvement of single cells in regional differences of the small intestine (SI), the metabolic contribution of the duodenum, jejunum, and ileum to the overall intestinal metabolism is still unclear. Basic procedures and main findings: Using an untargeted proteomics approach, we identified similarities and differences between the three intestinal tracts of C57BL/6J mice and found that proteins highly abundant in the mouse ileum correlated with high ileal expression of the corresponding genes in humans. Consistent with human data, we detected increasing abundance of lysosomal acid lipase (LAL) in C57BL/6J mice from the duodenum to ileum. LAL is the only enzyme known to degrade triacylglycerols and cholesteryl esters within the lysosome. Lipid accumulation in various organs along with gastrointestinal disturbances and malabsorption are typical features of patients and mice with LAL deficiency. We previously demonstrated that macrophages massively infiltrate the SI of Lal-deficient (KO) mice, especially the duodenum. To identify potential mechanisms behind the intestinal lipid accumulation and infiltration of immune cells, we used untargeted proteomics. Our results revealed a general inflammatory response and a common lipid-associated macrophage phenotype in all three intestinal segments of Lal KO mice, accompanied by higher expression of GPNMB and increased concentrations of circulating sTREM2. However, only duodenal macrophages activated a metabolic switch from lipids to other pathways such as glycolysis, TCA cycle, and oxidative phosphorylation to meet their high energy demand. Unexpectedly, these pathways were downregulated in the jejunum and ileum of Lal KO mice. Conclusion: Our results provide new insights into the process of absorption in control mice and the basis for novel markers of LAL-D and/or systemic inflammation in LAL-D.
2024-02-20 | PXD048378 | Pride