Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of rat mixed-tissue RNA samples over 8.5 months to monitor processing drift

ABSTRACT: Process drift at one site was monitored by assaying the rat Mixed Tissue RNA Reference Material (see E-TABM-16) multiple times a week for 8.5 months.

ORGANISM(S): Rattus norvegicus

SUBMITTER: P Scott Pine

PROVIDER: E-MEXP-1565 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

Pine P S PS Boedigheimer M M Rosenzweig B A BA Turpaz Y Y He Y D YD Delenstarr G G Ganter B B Jarnagin K K Jones W D WD Reid L H LH Thompson K L KL

Pharmacogenomics 20081101 11

Effective use of microarray technology in clinical and regulatory settings is contingent on the adoption of standard methods for assessing performance. The MicroArray Quality Control project evaluated the repeatability and comparability of microarray data on the major commercial platforms and laid the groundwork for the application of microarray technology to regulatory assessments. However, methods for assessing performance that are commonly applied to diagnostic assays used in laboratory medic ...[more]

PMID: 19018728

Similar Datasets

Transcription profiling of rat mixed-tissue RNA samples using different labeling protocols

Project description:At one site (#10), three different batches of MTRRM (see E-TABM-16), were labeled with two different kits (Enzo and Affymetrix) and hybridized to two different Affymetrix Arrays (RAE230A and RAE230_2).

2008-04-16 | E-MEXP-1563 | biostudies-arrayexpress

Transcription profiling of rat heart from a spontaneously hypertensive strain treated with doxorubicin or dexrazoxane and then doxorubicin

Project description:This study was initiated to characterize early DOX-induced changes in cardiac gene expression in order to identify potential additional areas for clinical intervention. Male spontaneously hypertensive rats (SHR) received 3 mg/kg DOX or vehicle (iv) 30 minutes following pretreatment with 50 mg/kg DZR or saline (ip) weekly for 1, 2 or 3 weeks.

2009-06-01 | E-MEXP-2071 | biostudies-arrayexpress

Platform comparison and transcription profiling of mixed tissue RNA samples formulated to contain different ratios of RNA for each of four rat tissues (brain, liver, kidney, and testes) on Affymetrix RAE230A, CodeLink UniSet Rat I, and Agilent G4130A rat oligonucleotide arrays

Project description:This experiment is a test of a reagent that can provide a basis for performance assessments on Affymetrix RAE230A, CodeLink UniSet Rat I, and Agilent G4130A rat oligonucleotide arrays. The reagent is a set of two mixed tissue RNA samples formulated to contain different ratios of RNA for each of four rat tissues (brain, liver, kidney, and testes). The analytes in this assay bind to a subset of gene probes that were matched across platforms to the same UniGene cluster or GenBank accession number, were determined to be tissue-selective on each of the 3 platforms using average baseline expression levels in single tissue samples from control animals, and have signal intensities that span the dynamic range of each platform. This reagent forms the basis of a ratiometric assay in a complex biological background that can be used to objectively assess the effect of different array processing methods and conditions on microarray data comparability within and across platforms, and could be a paradigm for similar performance standards for mouse and human arrays.

2010-03-30 | E-TABM-16 | biostudies-arrayexpress

Transcription profiling of fresh and frozen rat liver RNA samples to explore how RNA quality affects microarray results

Project description:To systemically explore how RNA quality affects microarray assay results, a set of rat liver RNA samples with a progressive change in RNA quality was generated either by thawing frozen tissue or by ex vivo incubation of fresh tissue.

2007-09-01 | E-MEXP-1069 | biostudies-arrayexpress

Transcription profiling of hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius to UV irradiation

Project description:Analysis of transcriptional response to UV irradiation in two related crenarchaea, Sulfolobus solfataricus and Sulfolobus acidocaldarius.

2007-11-21 | E-MEXP-1252 | biostudies-arrayexpress

Transcription profiling of synchronized Sulfolobus acidocaldarius populations as they progress through the cell cycle

Project description:Exponentially growing Sulfolobus acidocaldarius were treated with NaAc to generate replication runout and arrest in G2 phase. The cells were then resuspended in fresh acetate-free media which generates a synchronous population. Samples for investigation of gene expression change were taken during the synchronised populations progress through the cell cycle.

2007-12-08 | E-MEXP-936 | biostudies-arrayexpress

Transcription profiling of tissues of Arabidopsis plants overexpressing artificial microRNAs vs wild_type and respective target gene mutants

Project description:Tissues of Arabidopsis plants overexpressing artificial microRNAs were compared to wild_type and respective target gene mutants (duplicate arrays)

2006-04-01 | E-TABM-63 | biostudies-arrayexpress

Transcription profiling of matching human primary head and neck squamous cell carcinomas and cervical lymph node metastases.

Project description:An experiment was performed to investigate the perservation of gene expression upon metastasis of primary head and neck squamous cell carcinomas to the cervical lymph node.

2006-10-23 | E-TABM-114 | biostudies-arrayexpress

Transcription profiling of human primary B-cell vs monocyte-derived dendritic cells

Project description:Genome-wide RNAi screen reveals new pathways for MHC class II antigen presentation

2010-12-18 | E-MTAB-192 | biostudies-arrayexpress

Transcription profiling of kidney in rats exposed to different doses of Puromycin - ILSI-HESI NephroToxicity Study: Compound Puromycin

Project description:Evaluation and comparison of biological responses of rats and gene expression responses of the kidney in rats exposed to different doses of Puromycin [CAS:53-79-2;CHEBI:17939]

2004-09-01 | E-TOXM-12 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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