Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Use of an Isothermal Linear Amplification Method with Small Samples on DNA Microarrays

ABSTRACT: Experiment 1: U133A arrays (2) hybridized to duplicate sscDNA samples prepared from 20 ng Clontech UHR RNA Experiment 2: Mu6500A arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 5 ng mouse liver RNA and 3 x 100 ng mouse liver RNA Experiment 3: U95Av2 arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 10 ng K562 RNA and 3 x 10 ng Stratagene UHR RNA Experiment 4: U95Av2 array (1) hybridized to sscDNA sample prepared from template minus reaction (negative control) Keywords: parallel sample

ORGANISM(S): Mus musculus

SUBMITTER: Michael Salazar

PROVIDER: E-GEOD-2252 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Increased DNA microarray hybridization specificity using sscDNA targets.

Barker Christopher S CS Griffin Chandi C Dolganov Gregory M GM Hanspers Kristina K Yang Jean Yee Hwa JY Erle David J DJ

BMC genomics 20050422

<h4>Background</h4>The most widely used amplification method for microarray analysis of gene expression uses T7 RNA polymerase-driven in vitro transcription (IVT) to produce complementary RNA (cRNA) that can be hybridized to arrays. However, multiple rounds of amplification are required when assaying very small amounts of starting RNA. Moreover, certain cRNA-DNA mismatches are more stable than the analogous cDNA-DNA mismatches and this might increase non-specific hybridization. We sought to dete ...[more]

PMID: 15847692

Similar Datasets

Use of an Isothermal Linear Amplification Method with Small Samples on DNA Microarrays

Project description:Experiment 1: U133A arrays (2) hybridized to duplicate sscDNA samples prepared from 20 ng Clontech UHR RNA Experiment 2: Mu6500A arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 5 ng mouse liver RNA and 3 x 100 ng mouse liver RNA Experiment 3: U95Av2 arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 10 ng K562 RNA and 3 x 10 ng Stratagene UHR RNA Experiment 4: U95Av2 array (1) hybridized to sscDNA sample prepared from template minus reaction (negative control) Keywords: parallel sample

2005-05-25 | GSE2252 | GEO

Validation of the linear amplification of single bovine embryos

Project description:To generate expression profiles from single embryos, a protocol for linear amplification of RNA was developed on the basis of Baugh et al. (15). Linear amplification enabled production of sufficient amounts of aRNA for the microarray experiments and has been shown to reliably amplify the initial mRNA population (15, 18-20). Approximately 5 ng of total RNA can be isolated from a blastocyst-stage embryo (21); therefore, it was necessary to carry out multiple rounds of amplification. To test the reproducibility and fidelity of the amplification procedure, a validation experiment was conducted using RNA from the kidney tissue of a newborn calf. Two replicates of the bovine kidney RNA were amplified and hybridized to the microarray. Comparisons were made between aRNA (rounds 1, 2, and 3) and unamplified RNA. Keywords: cDNA microarray

2005-11-30 | GSE3569 | GEO

Abrupt scrib- vs. Abrupt and RasV12 (RasACT) scrib-, NotchICD (NACT) scrib- +/- JNK (Bsk) expression profiles

Project description:Drosophila mosaic eye-antennal discs from the listed genotypes generated using the MARCM system were dissected from 3rd instar larvae at day 5 after egg deposition. 20 pairs of discs for the Abrupt and scrib- + Abrupt samples and 50 pairs from FRT control, NACT scrib- +/- BskDN and RasACT scrib- +/- BskDN were used to prepare RNA. Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen). Probes were hybridized to GeneChip Drosophila 2.0 Genome Arrays (Affymetrix).

2013-08-15 | GSE42938 | GEO

Expression data from TGF-beta treated Panc-1 pancreatic adenocarcinoma cell line

Project description:TGF-beta treatment of Panc-1 pancreatic adenocarcinoma cell line on Affymetrix HG_U133_plus_2 arrays; triplicate experiments. The goal of the experiment is to profile temporal gene expression changes during TGF-beta-induced epithelial-mesenchymal transition (EMT). During EMT cancer cells lose their epithelial specifc proteins and gain mesenchymal proteins to acquire migratory and invasive phenotype essential for metastasis. Human Panc-1 pancreatic adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 48 h to induce EMT. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques.

2010-09-03 | GSE23952 | GEO

Microarray expression data from the Mus musculus intestine

Project description:Genome wide expression profiling to determine the overlap of Affymetrix-signals with SOLID sequencing RNA was extracted using the Qiagen RNeasy kit following the manufacturers guidelines, arrays were prepared and hybridized following the Affymetrix protocol.

2011-01-06 | GSE19767 | GEO

Combining gene expression data from different generations of oligonucleotide arrays

Project description:Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively. The dataset of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays for this purpose. Signal values from GCOS 1.2 with Detection call and p-value are provided here, and CEL files are also available for download. Keywords: parallel sample

2004-12-08 | GSE2044 | GEO

Oxidative metabolism and PGC-1 attenuate macrophage-mediated inflammation

Project description:Total RNA was prepared from three independent experimental replicates using Trizol reagent (Invitrogen) and validated by northern blot. Microarray experiments were performed with 20-25 ?g of total RNA, which was labelled with fluorescent nucleotides and hybridized to murine cDNA slides. Hybridized slides were interrogated via an Agilent scanner. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2006-06-07 | GSE5003 | GEO

Hepatic Gene Expression in LIRKO Mice

Project description:Control and Liver Insulin Receptor KO mice (LIRKO) were sacrificed in the non-fasted state. RNA was prepared from liver samples and subjected to expression microarray analysis Each array was hybridized with sample derived from 2-3 mice of the same genotype.

2015-02-05 | GSE65624 | GEO

Effect of ligase on T7 based RNA linear amplification

Project description:Zhao et al. Amplification Table 3 This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3561 | GEO

Suz12, EZH2, EED1, H3me3K27, H3me3K9 and RNA Pol II target promoters in mouse F9 and mES cells

Project description:For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

2006-06-06 | GSE4908 | GEO

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