GNPS - SEED Grant - Sanjay
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116)
SUBMITTER: 
Kevin Bush
PROVIDER: MSV000081077 | GNPS | Thu May 11 13:47:00 BST 2017
REPOSITORIES: GNPS
Similar Datasets
Project description:An experiment looking OATs (organic anion transporters) as the main microbiome pathway for renal elimination of many gut microbiome metabolites of clinical importance in children, pregnant mothers and other adults. Data was acquired using a Thermo Q-Exative and C18 RP-UHPLC. Negative polarity acquisition of LC-MS/MS.
2017-07-18 | MSV000081346 | GNPS
Project description:An experiment looking at how long leptospira must be cultivated to see sufficient molecules in mass spectrometry. Data was acquired using a Thermo Q-Exative and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS.
2017-05-09 | MSV000081068 | GNPS
Project description:Renal obstruction is a common cause of renal failure in adults and children and is suspected when hydronephrosis is detected on imaging. Since not all cases of hydronephrosis are associated with renal damage, biomarkers are needed to guide intervention to relieve obstruction. We performed gene expression profiling on the kidneys from adult mice over a detailed time course after obstruction and compared these data to a neonatal model of bilateral high grade obstruction induced by conditional deletion of the calcineurin ß1 (Cnb1) gene. Using a model of short term (non-damaging) and long term (damaging) temporary obstruction, we identified which of the transcripts common to the adult and neonatal models were induced early and associated with renal damage. Using QPCR, elevated levels of several candidate RNA biomarkers of renal damage were detected in urine from obstructed mice and children undergoing surgery for ureteropelvic junction obstruction (UPJO). This SuperSeries is composed of the SubSeries listed below.
2018-02-22 | GSE96571 | GEO
Project description:Contact lens-related ocular surface complications occur more often in teenagers and young adults. The purpose of this study was to determine changes in tear proteome of young patients wearing glasses (GL), orthokeratology lenses (OK), and soft contact lenses (SCL). Twenty-two young patients (10-26 years of age) who were established (> 3 years) GL (n=10), OK (n=6), and SCL (n=6) wearers were recruited. Tears were collected via Schirmer strips. Proteomic data were collected using a data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) workflow. Tear proteome composition and abundance were compared across different correction groups and between the children (age <18 years) and young adults (age 18 years) GL wearers. We identified 3406 protein groups in tears. Among proteins identified in 80% of tear samples, 8 proteins were upregulated, and 11 proteins were down-regulated in the SCL group compared to the OK group. Eighty-two proteins were differentially expressed in children and young adults GL wearers, among which 67 proteins were upregulated, and 15 proteins were downregulated in children. These 82 proteins were involved in 1 inflammation, 9 immune, and 1 glycoprotein metabolic biological processes. As teenagers and young adults have the highest risk of developing contact lens-related complications, this work highlights the importance of understanding ocular responses to contact lens wear across different ages.
2022-11-07 | PXD029188 | Pride
Project description:BACKGROUND. Coronavirus disease 2019 (COVID-19) is more benign in children compared with adults for unknown reasons. This contrasts with other respiratory viruses where disease manifestations are often more severe in children. We hypothesize that a more robust early innate immune response to SARS coronavirus 2 (SARS-CoV-2) protects against severe disease. METHODS. Clinical outcomes, SARS-CoV-2 viral copies, and cellular gene expression were compared in nasopharyngeal swabs obtained at the time of presentation to the emergency department from 12 children and 27 adults using bulk RNA sequencing and quantitative reverse-transcription PCR. Total protein, cytokines, and anti–SARS-CoV-2 IgG and IgA were quantified in nasal fluid. We used a subset of 21 samples for RNAseq analysis. RESULTS. SARS-CoV-2 copies, angiotensin-converting enzyme 2 (ACE2), and TMPRSS2 gene expression were similar in children and adults, but children displayed higher expression of genes associated with IFN signaling, NLRP3 inflammasome, and other innate pathways. Higher levels of IFN-α2, IFN-γ, IP-10, IL-8, and IL-1β protein were detected in nasal fluid in children versus adults. Children also expressed higher levels of genes associated with immune cells, whereas expression of those associated with epithelial cells did not differ in children versus adults. Anti–SARS-CoV-2 IgA and IgG were detected at similar levels in nasal fluid from both groups. None of the children required supplemental oxygen, whereas 7 adults did (P = 0.03); 4 adults died. CONCLUSION. These findings provide direct evidence of a more vigorous early mucosal immune response in children compared with adults and suggest that this contributes to favorable clinical outcomes.
2021-05-11 | GSE172274 | GEO
Project description:The ovarian cortical reserve of follicles is vital for fertility. Some medical treatments are toxic to follicles, leading to premature ovarian insufficiency. Ovarian tissue cryopreservation is an established method to preserve fertility in adults and even applied in prepuberty despite unproven efficacy. Here, we analyze transcriptomes of 120 cortical follicles from children and adults for detailed comparison. We discover heterogeneity with two main types of follicles in both age groups: one with expected oocyte-granulosa profiles and another with predicted role in signaling. Transcriptional changes during growth to the secondary stage are similar overall in children and adults, but variations related to extracellular matrix, theca cells, and miRNA profiles are found. Notably, cyclophosphamide dose correlates with interferon signaling in child follicles. Additionally, morphology alone is insufficient for follicle categorization suggesting a need for additional markers. Marker genes for early follicle activation are determined. These findings will help refine follicular classification and fertility preservation techniques across critical ages.
2024-06-26 | GSE241983 | GEO
Project description:The ovarian cortical reserve of follicles is vital for fertility. Some medical treatments are toxic to follicles, leading to premature ovarian insufficiency. Ovarian tissue cryopreservation is an established method to preserve fertility in adults and even applied in prepuberty despite unproven efficacy. Here, we analyze transcriptomes of 120 cortical follicles from children and adults for detailed comparison. We discover heterogeneity with two main types of follicles in both age groups: one with expected oocyte-granulosa profiles and another with predicted role in signaling. Transcriptional changes during growth to the secondary stage are similar overall in children and adults, but variations related to extracellular matrix, theca cells, and miRNA profiles are found. Notably, cyclophosphamide dose correlates with interferon signaling in child follicles. Additionally, morphology alone is insufficient for follicle categorization suggesting a need for additional markers. Marker genes for early follicle activation are determined. These findings will help refine follicular classification and fertility preservation techniques across critical ages.
2024-06-26 | GSE241982 | GEO
Project description:The ovarian cortical reserve of follicles is vital for fertility. Some medical treatments are toxic to follicles, leading to premature ovarian insufficiency. Ovarian tissue cryopreservation is an established method to preserve fertility in adults and even applied in prepuberty despite unproven efficacy. Here, we analyze transcriptomes of 120 cortical follicles from children and adults for detailed comparison. We discover heterogeneity with two main types of follicles in both age groups: one with expected oocyte-granulosa profiles and another with predicted role in signaling. Transcriptional changes during growth to the secondary stage are similar overall in children and adults, but variations related to extracellular matrix, theca cells, and miRNA profiles are found. Notably, cyclophosphamide dose correlates with interferon signaling in child follicles. Additionally, morphology alone is insufficient for follicle categorization suggesting a need for additional markers. Marker genes for early follicle activation are determined. These findings will help refine follicular classification and fertility preservation techniques across critical ages.
2024-06-26 | GSE241981 | GEO
Project description:While insulin replacement therapy restores the health and prevents the onset of diabetic complications (DC) for many decades, some T1D patients have elevated hemoglobin A1c values suggesting poor glycemic control, a risk factor of DC. We surveyed the stool microbiome and urinary proteome of a cohort of 220 adolescents and children, half of which had lived with T1D for an average of 7 years and half of which were healthy siblings. Phylogenetic analysis of the 16S rRNA gene did not reveal significant differences in gut microbial alpha-diversity comparing the two cohorts. The urinary proteome of T1D patients revealed increased abundances of several lysosomal proteins that correlated with elevated HbA1c values. In silico protein network analysis linked such proteins to extracellular matrix components and the glycoprotein LRG1. LRG1 is a prominent inflammation and neovascularization biomarker. We hypothesize that these changes implicate aberrant glycation of macromolecules that alter lysosomal function and metabolism in renal tubular epithelial cells, cells that line part of the upper urinary tract.
2019-03-28 | PXD012413 | Pride