Impact of pre-analytical handling on neuroblastoma cells mRNA gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE63294 | GEO | 2015/12/01
SECONDARY ACCESSION(S): PRJNA267205
REPOSITORIES: GEO
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Project description:Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays (24 and 48h) between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48h after aspiration. However, storage of BM has dramatic effects on mRNA expression of individual transcripts. Keywords: time-course
2004-04-28 | GSE1347 | GEO
Project description:Gene expression profiling has been used as a tool to gain mechanistic understanding of adverse effects in response to compound exposure. However, little is known about how the common handling procedures of experimental animals during a preclinical study alter their baseline gene expression. We report on gene expression changes in the livers of female Sprague-Dawley rats following common handling procedures. Insight on baseline gene expression changes obtained in this study will allow us to evaluate how these changes may affect interpretation of gene expression profiles following compound exposure. Rats were divided into three groups (n = 10 per group): one group was not subjected to handling procedures, euthanized on day 2, and served as controls for both handled groups. Animals in the other two groups were weighed, subjected to restraint in Broome restrainers, and administered water via oral gavage daily for 1 or 4 days with tail vein blood collections at 1, 2, 4, and 8 hours postdose on days 1 and 4 followed by euthanasia on day 2 or 5. Significantly altered genes were identified in livers of animals following 1 or 4 days of handling when compared to the unhandled animals. Gene changes in animals handled for 4 days were similar to those handled for 1 day, suggesting a lack of habituation. The altered genes were primarily immune function related genes. These findings, along with a correlating increase in corticosterone levels suggest that common handling procedures may cause a minor immune system perturbance.
2016-05-05 | GSE46702 | GEO
Project description:<p>The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. Data from this study will be used to develop evidence-based biospecimen standard operating procedures and best practices for fit-for-purpose collection, processing, and storage of biospecimens.</p> <p>The BPV Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following sub-studies below or in the "Substudies" box located on the right hand side of this top-level study page phs001304 BPV Cohort. The substudy links will be active once they are released by dbGaP.</p> <p> <ol> <li>Preanalytical Impacts on Global Metabolite Profiling - plasma (MassSpec by Metabolon) This study was to evaluate the impact of the storage temperature (s) (-80°C and LN2 vapor) and the length of storage on human plasma quality using LC-MS/MS (liquid-chromatography-mass spectrometry/mass spectrometry) based global metabolite profiling. The study includes 240 plasma samples collected from 40 donors.</li> <li>Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors.</li> <li>Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors.</li> <li>Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors.</li> <li>Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. The study includes 235 samples from 40 donors.</li> <li>Evaluation of frozen conditions on mRNA profiling by TaqMan assay (mRNA expression by Georgetown University). This study was to utilize gene expression profiling, using custom TaqMan arrays, to compare the molecular profiles of RNA from frozen tumor samples collected using two freezing methods (dry ice or LN2), two storage temperatures (-80°C or LN2 vapor), as well as Optimal Cutting Temperature (OCT) compound and non-OCT embedded. The study includes 100 samples from 20 donors.</li> <li>mRNA signature for stratification by cold ischemia time (mRNA expression by IBBL). The study was to determine the effects of cold ischemic time (delay-to-fixation) and formalin preservation (FFPE) on mRNA detection by Taqman assay using tumor tissue specimens from kidney, colon and ovarian cancer patients. There are160 samples from 40 donors.</li> </ol> </p> <p><b>The Biospecimen PV cohort is utilized in the following dbGaP individual studies.</b> To view molecular data, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page <a href="study.cgi?study_id=phs001304">phs001304</a> Biospecimen PV cohort. <ul> <li><a href="study.cgi?study_id=phs001634">phs001634</a> CIT mRNA</li> <li><a href="study.cgi?study_id=phs001635">phs001635</a> CNV aCGH</li> <li><a href="study.cgi?study_id=phs001636">phs001636</a> Fixation Delay</li> <li><a href="study.cgi?study_id=phs001637">phs001637</a> Global Metabolite Profiling</li> <li><a href="study.cgi?study_id=phs001638">phs001638</a> mRNA TaqMan</li> <li><a href="study.cgi?study_id=phs001639">phs001639</a> NGS</li> <li><a href="study.cgi?study_id=phs001640">phs001640</a> Tumor Storage</li> </ul> </p>
| phs001304 | dbGaP
Project description:Postnatal handling in rodents leads to decreased anxiety-like behavior in adulthood. We used microarrays to look at gene expression differences in the CA1 region of the hippocampus in female mice subjected to postnatal handling compared to controls.
2008-10-08 | GSE11679 | GEO
Project description:Handling of spurious sequences dictates the outcome of high-throughput 16S rRNA gene amplicon profiling
| PRJEB34431 | ENA
Project description:We constructed a targeted cDNA microarray consisting of 147 rainbow trout (Oncorhynchus mykiss) genes with known function to examine the transcriptional response to a standardized handling stress.
2006-01-31 | E-MEXP-622 | biostudies-arrayexpress
Project description:Postnatal handling in rodents leads to decreased anxiety-like behavior in adulthood. We used microarrays to look at gene expression differences in the CA1 region of the hippocampus in female mice subjected to postnatal handling compared to controls. Experiment Overall Design: Balb c/J offspring were briefly separated from mothers for 15 minutes each morning on postnatal days 1-14 (handled group) or left undisturbed. At 8 weeks of age mice were tested in the open-field and light-dark behavioral paradigms to verify a handling-induced behavioral phenotype. 2 weeks after behavioral testing, animals were sacrificed and the CA1 region was microdissected. CA1 regions were stored at -20C in RNA later. RNA was extracted from 8 samples (4 handled and 4 non-handled) using Trizol. RNA was extracted from second group of animals (7 handled and 10 non-handled) using Qiagen RNA/DNA columns. All total RNA samples were double round amplied and labeled using standard Affymetrix protocols and hybridized to Mouse 430_2.0 arrays in parallel.
2008-10-26 | E-GEOD-11679 | biostudies-arrayexpress
Project description:Biospecimen Pre-analytical Variables (BPV)
| PRJNA376469 | ENA
Project description:Biospecimen Pre-analytical Variables (BPV)
| PRJNA932917 | ENA
Project description:Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays (24 and 48h) between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48h after aspiration. However, storage of BM has dramatic effects on mRNA expression of individual transcripts.
2007-07-28 | E-GEOD-1347 | biostudies-arrayexpress