Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inter-species array between human, rat and mouse

ABSTRACT: We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice.

ORGANISM(S): Mus musculus Rattus norvegicus Homo sapiens

PROVIDER: GSE31201 | GEO | 2011/11/01

SECONDARY ACCESSION(S): PRJNA154071

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Inter-species array between human, rat and mouse

Project description:We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice. Single array with multiple species samples.

2011-11-01 | E-GEOD-31201 | biostudies-arrayexpress

Affymetrix SNP array data for wild Dutch great tits (Parus major)

Project description:The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.

2018-02-19 | GSE105131 | GEO

Genome-wide inter-primate comparison of gene expression profiles in multiple tissues

Project description:Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques. Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle. For each tissue, we hybridized RNA samples from 6 individuals from each of the three species, and preformed two technical replicates for each sample. The total number of arrays analyzed is therefore 108 (= 3 species X 3 tissues X 6 individuals X 2 technical replicates). Following hybridization, washing, and scanning, raw data was extracted from the images using the NimbleScan software (version 2.4). We performed background correction using the normexp function in limma with an offset of 32, and normalization using an adaptation of the quantile normalization approach.

2008-09-17 | E-GEOD-11560 | biostudies-arrayexpress

Inter-species array between human, rat and mouse

Project description:Inter-species array between human, rat and mouse

| PRJNA154071 | ENA

Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v1 array)

Project description:Design a human-mouse dual-species microarray to provide a technology for investigation of cancer-stromal interaction in xenograft model. Reference RNA from human and mouse were labeled using Cy5, while the mixture of human and mouse RNA were labeled using Cy3. Samples were hybridized on customized-commercial array with Agilent probes and user-designed species-specific probes (Human-mouse dual-species array HomoMusArray v1).

2010-07-22 | E-GEOD-23054 | biostudies-arrayexpress

Genome-wide inter-primate comparison of gene expression profiles in multiple tissues

2008-09-17 | GSE11560 | GEO

Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v2 array)

Project description:Design a human-mouse dual-species microarray to provide a technology for investigation of cancer-stromal interaction in xenograft model. The 2 reference RNA were used to evaluate and identify probes with potential the cross-species hybridization, so that we can label these probes and exclude them before analysis of biological samples/data. Reference RNA from human and mouse were labeled using Cy3. Samples were hybridized on customized-commercial array with Agilent probes and user-designed species-specific probes (Human-mouse dual-species array HomoMus_v2). This array is designed and improved from hte first version GPL10714

2010-08-04 | E-GEOD-23364 | biostudies-arrayexpress

Inter-strain Heterogeneity in Responses to TCDD

2011-08-17 | GSE31411 | GEO

Tendon methylation microarray after particulate matter inhalation

Project description:Open tenotomy of the Achilles tendon of 6 rats was performed. The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group). After 6 weeks of PM exposure, the tendon DNA was extracted and anlyzed. Genome-wide DNA methylation profiles were determinen. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Customized Agilent Rat CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of tendon tissue according to partciulate matter exposure.

2022-08-03 | GSE200709 | GEO

Inter-strain Heterogeneity in Responses to TCDD

Project description:We profiled hepatic transcriptional responses of 6 strains of rats with varying sensitivity to a dioxin, TCDD, at 19 hours following exposure. The resistant rats exhibited significantly reduced transcriptional responses in comparison to the sensitive strains. We hypothesize that genes which show differential changes between the resistant and sensitive rats may potentially explain sensitivity. Rats with varying sensitivities (Long-Evans, L-E; Han/Wistar, H/W; Fischer 344, F344; Wistar, Wis; Line-A, Ln-A; and Line-C, Ln-C) were treated with 100 ug/kg TCDD or corn oil vehicle and euthanized 19 hours post-treatment. Each treatment group contains four or six animals (biological replicates), each of which was assayed on an individual microarray.

2011-08-16 | E-GEOD-31411 | 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