Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

ABSTRACT: In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively. A total of seven astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)).RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. For expression analysis, Human Transcriptome Array 2.0 (HTA) (Santa Clara, CA, USA) was employed. in this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

ORGANISM(S): Homo sapiens

SUBMITTER: Ruth Ruiz-Esparza

PROVIDER: E-GEOD-72269 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

Project description:In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

2015-08-25 | GSE72269 | GEO

Transcriptional profiling by array in rat of age-dependent gene expression in sensorimotor cortex following spinal cord injury

Project description:In this study, we investigated the extent and nature of the difference between the dynamic cortical gene expression profiles of aged (22-month-old) and young (2-month-old) rats following thoracic corticospinal tract (CST) transection and whether the anti-scarring-treatment (AST)-induced regeneration program can be activated in aged animals. GeneChip analysis was performed on layers V/VI of the rat sensorimotor cortex at 1, 7 and 35 days post operation (dpo), which represented the acute, subacute and chronic stages of SCI, respectively. Anti-scarring treatment (AST) includes local injections of an iron chelator and cAMP immediately after SCI. For our purpose we used the Affymetrix GeneChip Rat Gene 1.0 ST Array (A-AFFY-160) which contains approximately 27,000 genes.

2012-01-15 | E-MTAB-794 | biostudies-arrayexpress

The effect of Nebulin-Deficiency on Skeletal Muscle

Project description:Nebulin is a giant filamentous protein that is coextensive with the actin filaments of the skeletal muscle sarcomere. Nebulin mutations are the main cause of nemaline myopathy (NEM), with typical NEM adult patients having low expression of nebulin, yet the roles of nebulin in adult muscle remain poorly understood. To establish nebulin’s functional roles in adult muscle we performed studies on a novel conditional nebulin KO (Neb cKO) mouse model in which nebulin deletion was driven by the muscle creatine kinase (MCK) promotor. Neb cKO mice are born with high nebulin levels in their skeletal muscle but within weeks after birth nebulin expression rapidly falls to barely detectable levels Surprisingly, a large fraction of the mice survives to adulthood with low nebulin levels (<5% of control), contain nemaline rods, and undergo fiber-type switching towards oxidative types. These microarrays investigate the changes in gene expression when nebulin is deficient. Two skeletal muscle groups were studied: Quadriceps (which is markedly smaller in the Neb cKO mice relative to control) and Soleus (which is not significantly smaller in the Neb cKO relative to control). Six biological replicates for each muscle group were selected; all are age-matched males.

2015-06-25 | E-GEOD-70213 | biostudies-arrayexpress

RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-31 | E-GEOD-65721 | biostudies-arrayexpress

RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (expression)

Project description:A study to define the binding loci of RelA-containing NF-kappaB dimers and subsequent correlation with gene expression in a human myometrial smooth muscle cell line after exposure to TNF. Monolayers of PHM1-31 cells were exposed to TNF (10ng/ml) for 1 hour or left unstimulated. Total RNA was isolated, prepared and used to probe AffymetrixU133Plus2 expression arrays. Both datasets were subsequently analysed in Partek Genomics Suite V6.6 and correlations between promoter occupancy (promoter arrays) and gene expression (expression arrays) were made.

2015-03-31 | E-GEOD-65707 | biostudies-arrayexpress

From Volcanos to the Bench: Advantages of Novel Hyperthermoacidic Archaeal Proteases for Proteomics Workflows

Project description:Here we introduce novel hyperthermoacidic archaeal proteases (HTA-Proteases) isolated from organisms that thrive in nearly boiling acidic volcanic springs and investigate their use for bottom-up proteomic experiments. We find that HTA-Proteases have novel cleavage specificities, show no autolysis, function in dilute formic acid, and store at ambient temperature for years. HTA-Proteases function optimally at 70-90°C and pH of 2-4 with rapid digestion kinetics. The extreme reaction conditions actively denature sample proteins, obviate the use of chaotropes, and allow for a one-step/five-minute sample preparation protocol without sample manipulation, dilution, or additional cleanup. We find that brief one-step HTA-Protease protocols significantly increase proteome and protein sequence coverage with datasets orthogonal to trypsin. Importantly, HTA-Protease digests markedly increase coverage and identifications for ribonucleoproteins, histones, and mitochondrial membrane proteins as compared to tryptic digests. In addition to increased coverage in these classes, HTA-Proteases and simplified one-step protocols are expected to reduce technical variability and advance the fields of clinical and high-throughput proteomics. This work reveals significant utility of heretofore unavailable HTA-Proteases for proteomic workflows. We discuss some of the potential for these remarkable enzymes to empower new proteomics methods, approaches, and biological insights.

2023-10-18 | PXD041226 | Pride

Expression Data from Memory P14 Tg CD8 T cells after either saline mock-infection, Pichinde Virus Infection (bystander infection) or Pichinde Virus infection with daily treatment with anti-CD122 (clone TM-b1)

Project description:Exposure to inflammatory cytokines driven by bystander cytokines can have profound effects on the function of memory CD8 T cells. Here we transferred a 1-5X10^4 of P14 TCR-tg T cells (specific for gp33-41 of LCMV) on day -1 followed by infection with 2X10^5 PFU of LCMV Armstrong ip to generate memory P14 populations. Mice were rested for >50 days before further challenge. Mice containing memory P14 populations were either mock-infected with saline, infected with 2X10^6 Pichinde Virus ip (no cross-reactivity wtih LCMV gp33-41) or infected with 2X10^6 Pichinde Virus ip together with daily injections of 200 micrograms of anti-CD122 antibody (clone TM-b1). On day 4 following indicated treatments P14s were flow sorted and RNA was extracted from 1X10^6 cells using an RNeasy kit (Qiagen). Each group had 3 biological replicates. Transcriptomes were compared by DAVID analysis (p<0.01, Fold-Change > 1.5) 3 biological replicates per group. Groups included P14 from mock-infected mice, P14 from Pichinde virus infected mice and P14 from Pichinde virus and anti-cd122 treated mice.

2015-09-01 | E-GEOD-69791 | biostudies-arrayexpress

Proteomics Indicates Lactate Dehydrogenase is Prognostic in Acetaminophen-induced Acute Liver Failure Patients and Reveals a Role for LKB1-AMPK Signaling

Project description:Better biomarkers to predict death early in acute liver failure (ALF) are needed. To that end, we obtained early (study day 1) and later (day 3) serum samples from transplant-free survivors (n=28) and non-survivors (n=30) of acetaminophen (APAP)-induced ALF from the NIH-sponsored Acute Liver Failure Study Group, and from control volunteers (n=10). To identify proteins that increase early in serum during ALF, we selected individuals from this cohort for whom ALT was lower on day 1 than day 3, indicating a time point before the peak of injury (n=10/group). We then performed untargeted proteomics on their day 1 samples. Out of 1,682 quantifiable proteins, 79 were elevated ≥4-fold in ALF patients vs. controls and 23 of those were further elevated ≥4-fold in non-survivors vs. survivors, indicating potential to predict death. Interestingly, the biomarker with best performance was LDH. To confirm the prognostic potential of LDH, we measured activity in all day 1 and 3 samples from all 58 ALF patients. LDH was elevated in the non-survivors vs. survivors on both days. In addition, receiver operating characteristic (ROC) curve analyses revealed that LDH alone performed similarly to the model for end-stage liver disease (MELD), while a combination of MELD and LDH outperformed either alone. Finally, Upstream Analysis of our proteomics data indicated activation of LKB1-AMPK signaling in liver regeneration after APAP overdose and we confirmed that in mice. Overall, we conclude LDH can predict death in APAP-induced ALF and that LKB1-AMPK signaling may be a promising therapeutic target to improve survival.

2022-08-12 | PXD029576 | Pride

Circulating Y-RNAs, a predicted function mainly in controlling the Immune System, Cell Signaling, and DNA Replication in Pediatric Patients with Pilocytic and Diffuse Astrocytoma

Project description:Y-RNAs are small noncoding RNAs firstly identified in patients suffering the Sjögren’s syndrome and lupus erythematosus, having different predicted cellular functions. Y-RNAs are very abundant ncRNAs present in serum and only a few is known respect their molecular roles. The aim of the study was to determine the circulating Y-RNAs expression from blood serum of pediatric patients with pilocytic or diffuse astrocytoma. Y-RNAs expression was determined by means of the HTA 2.0 arrays. In addition, a bioinformatic approximation of the possible biological functions of Y-RNAs was determined with the “Random Forest” (RF) and “Vector Support Machine” (VSM) algorithms. Results. Data showed a differential expression of RNY-3, RNY-4, and RNY-5 in pediatric patients with astrocytoma, relative to the control. Meanwhile, RNY-1 was shown to be upregulated in the Diffuse condition versus the Pilocytic. The bioinformatic analysis showed that RNY-4 and RNY-5 had the highest scores of interaction with Claudin, Toll-like receptors, and Hyaluronidase-1. In addition, the Y-RNAs loop domain by itself had the highest score of interaction with B cell receptor CD22 (RNY-3) and Toll-like receptor 7 and 3 (RNY-4). Conclusions. Our results showed, for the first time a differential expression of circulating Y-RNAs in pediatric astrocytoma, allowing to distinguish pediatric subjects without cancer from patients with pediatric diffuse or pilocytic astrocytoma and their potential involvement in regulating diverse biological processes, such as immune activation-suppression, cell signaling, selective transcription, and cell proliferation through activation of DNA replication.

2022-10-31 | GSE216815 | GEO

DosS Is Required for the Complete Virulence of Mycobacterium tuberculosis in Mice with Classical Granulomatous Lesions

Project description:Here we are including replicate mouse microarray data from Kramnik mice infected over the course of different time points with M. tuberculosis H37Rv and its isogenic mutants in dosR, dosS and dosT genes. Mice from day 1 infection universally served as controls and RNA derived from these was always labeled with Cy3. RNA derived from mice at 4, 8 and 16 weeks was labeled with Cy5

2014-12-11 | E-GEOD-64045 | biostudies-arrayexpress

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