Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Serum Starvation/Refeeding RNA vs. RAP

ABSTRACT: Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics, signal-to-noise ratios, and interference between signals from mRNA isoforms. Individual sequences in LCRs are more highly represented than in the mRNA population from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo dT priming for target synthesis. An oligo dT-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo dT-primed target alone, as serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of spotted cDNA microarrays. Keywords: parallel sample

ORGANISM(S): Homo sapiens

PROVIDER: GSE2655 | GEO | 2005/05/17

SECONDARY ACCESSION(S): PRJNA92121

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Serum Starvation/Refeeding RNA vs. RAP

Project description:Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics, signal-to-noise ratios, and interference between signals from mRNA isoforms. Individual sequences in LCRs are more highly represented than in the mRNA population from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo dT priming for target synthesis. An oligo dT-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo dT-primed target alone, as serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of spotted cDNA microarrays.

2010-06-10 | E-GEOD-2655 | biostudies-arrayexpress

Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation

Project description:oligo-dT and random primed RNA-seq libraries were used to test an improved annotation of the zebrafish transcriptome

2020-07-28 | GSE152759 | GEO

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

Project description:Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

| PRJNA613041 | ENA

tiling hen2 and mtr4-HEN2 is a cofactor of the nuclear exosome in Arabidopsis

Project description:til-ath-2011_3 - tiling hen2 and mtr4 - Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants. Total RNA extracted from WT, hen2 and mtr4 mutants was used for oligo-dT primed cDNA preparation. Samples were hybridised to NimbleGen whole genome tiling arrays.

2013-06-30 | GSE48178 | GEO

CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

Project description:To more understand the poly(A) tail-tuned regulation in eukaryotic cells, we describe central limit theorem (CLT)-managed RNA-seq (CLT-seq) as a universal homopolymer-sequencing concept that features unbiased RNA-seq and facilitates accurate homopolymer base-calling. We then performed transcriptome-wide poly(A)-tail profiling analysis using data obtained from oligo(dT)-primed RNA-seq of HEK293T and A549 cell lines.

2022-05-09 | GSE202256 | GEO

Drosophila melanogaster short read RNA

Project description:Drosophila melanogaster RNA sequencing with Illumina Genome Analyzer. High-throughput sequencing of Drosophila melanogaster RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 5 Samples: Single Stranded cDNA, Oligo-DT Primed, run using a 1, 2 and 4 p-mol concentration, no replicates. Double Stranded cDNA, Random Primed, run using a 2 p-mol concentration, 2 replicates.

2008-11-04 | E-GEOD-13441 | biostudies-arrayexpress

tiling hen2 and mtr4-HEN2 is a cofactor of the nuclear exosome in Arabidopsis

2013-06-30 | E-GEOD-48178 | biostudies-arrayexpress

Single cell RNA sequencing analysis of in vitro DENV1 infected cells

Project description:CEM.NKR.DC-SIGN cells were infected in vitro with DENV1 (strain WestPac74) for 18 hours, after which either total viable cells or viable cells expressing surface DENV1 NS1 were isolated by flow cytometric sorting. Sorted cells were processed for scRNAseq analysis using either a standard Oligo(dT) primer, or an Oligo(dT) primer supplemented with a DENV-specific RT primer

2020-05-17 | GSE147103 | GEO

yeast hsf1-R206S/F256S mutant

Project description:Effect of hsf1-R206S/F256S mutation on heat-induced transcription of genes is analyzed. Total RNA was isolated from HSF1 wild type and hsf1-R206S/F256S cells grown at 39oC for 15 min. Probe cDNA was primed by oligo(dT) and was synthesized in the presence of 33P-dCTP. Hybridization was carried out using the same GF100 GeneFilter. Value higher than 30 in HSF1 wild type cells is confident. Values from duplicate experiments were averaged, and the average fold changes were calculated. Keywords = yeast Keywords = HSF1 Keywords: other

2004-12-24 | GSE2103 | GEO

Neurospora crassa early sexual development with MTP priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)

2010-07-03 | E-GEOD-22658 | 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