Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mouse dermal fibroblasts upon UV irradiation in a time-, dose- and lesion-dependent manner

ABSTRACT: Each labeled cDNA sample constituted a unique combination of UV dose (2J, 4J or 8J), time point (-30min, 0h, 2h, 4h, 8h and 24h) and photoreactivation status (PR or non-PR) that defined a distinctive matrix point. All samples were hybridized to non-irradiated, non-photoreactivated MDFs of the pertinent time point. As a consequence, the net observed differences in gene expression profiles between treated and non-treated cells depicted only the time-dependent expression profiles of significant gene entries upon a 2J, 4J or 8J of UV-C irradiation and subsequent photoreactivation or not.
To allow for the estimation and removal of gene specific dye effects, all samples were reversed labeled during the total RNA reverse transcription step. A pair of self-hybridizations (dye-reversed) preceded each batch of six microarrays.
Any deviation from a ratio of 1 (centered to 0 for log ratio data) in self-hybridizations was therefore assigned to either dye effect or residual error.
Dye-reversed hybridizations were considered as technical replicates that allowed gene-specific dye effects to be averaged out during clustering while enabled us to
exclude dye-dependent variances during the ANOVA analysis. In order to assure a balanced design, the same number of technical dye-reversed replicates was used for all samples and experimental conditions.
To account for inherent experimental variation, all samples were each represented by a pool of five
(occasionally six) MDF culture dishes that were subjected under identical experimental conditions.

ORGANISM(S): Mus musculus

SUBMITTER: George Garinis

PROVIDER: E-MEXP-117 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of human cells expressing FoxM1-ER fusion protein

Project description:Experiment description To identify FoxM1-regulated genes, we carried out gene expression profile analysis after inducible activation of a FoxM1-ER fusion protein using high-density human cDNA microarrays. We constructed a stable line of U2OS cells expressing full-length HA-FoxM1 fused at its C-terminus to the ligand-binding domain of the estrogen receptor (ER), mutated such that it specifically responds to 4-hydroxytamoxifen (4-OHT) but not to estrogen. In the absence of 4-OHT the activity of the ER fusion protein is turned off, but can be rapidly induced when cells are exposed to 4-OHT. We isolated total RNA from untreated cultures and cultures treated with 4-OHT for 6 or 16 hr. As activation of FoxM1 results in accumulation of cells in G2/M, we additionally analyzed the induction of gene expression by FoxM1 in G1/S-synchronized cells by a thymidine block. Total RNA derived from untreated or stimulated FoxM1-ER cells was amplified, reverse transcribed, labeled and hybridized to cDNA microarrays containing 18,000 cDNAs and expressed sequence tags (ESTs). Bound cDNA was detected using Cy3 or Cy5 dyes. In each independent experiment we included reverted color controls (Cy3 (4-OHT treated); Cy5 (untreated) or Cy3 (untreated); Cy5 (treated)) and the expression profile was expressed as a Cy5:Cy3 ratio.

2005-01-01 | E-MEXP-230 | biostudies-arrayexpress

Transcription profiling of mouse aorta (whole or regions) from mice of different embryonic ages

Project description:In order to identify novel regulators of haematopoietic stem cell emergence in the mouse embryonic AGM region, 3 different types of gene expression comparisons were performed. In the first one, whole dorsal aortas from embryonic day (E) 11 embryos and E9 embryos were dissected, tissues from each time point were pooled and their expression profile compared (whole aorta (WA) E9 vs E11). 3 different pools/biological replicas were obtained for each time point, a dye swap was included in each experiment, a technical replicate was performed for each pool (including the dye swap) and 2 self-self hybridisation controls were included. In the second comparison, GFP+ cells were isolated by fluorescence-activated cell sorting from pooled E9 and E11 aortas from transgenic embryos that express GFP under the regulatory elements of the Ly-6A gene. We obtained one pool for each time point and compared their transcription profile (GFP E9 vs E11). This comparison also contained a dye swap and a technical replicate (also of the dye swap). In the third comparison, the E11 aorta was cut into 3 roughly equal parts. Pools were obtained of the middle region ("m") and the two outer regions, rostral and caudal, together ("r+c") and their expression profile compared (11AO m vs r+c). There was one pool of each population, and the experiment included a dye swap and a technical replicate (also of the dye swap) and one self-self hybridisation control. Isolated RNA was amplified by T7-mediated in vitro transcription, with one round for the first and the third comparison and two rounds for the second comparison (sorted GFP+ cells). Probes were labelled during the reverse transcription step. Within array normalisation was achieved with Lowess Smooth and between arrays with Z scores. ANOVA analysis identified differentially expressed genes and K means clustering was used to segregate them into upregulated and downregulated genes.

2009-06-06 | E-TABM-659 | biostudies-arrayexpress

Transcription profiling of prostates from normal and Pten knock-out mice, and comparing the gene expression profile in the proximal and distal part of normal prostates

Project description:1. Comparison of gene expression profiles of normal prostates and prostates isolated from 4-5 months old PSA-Cre;Pten-loxP/loxP mice<br>2.Comparison of the gene expression profile in the proximal and distal part of normal prostates

2009-08-07 | E-MEXP-2029 | biostudies-arrayexpress

Transcription profiling of wild type, sco1 and sco2 knock out mutants of S. cerevisiae BY4741 in early response to different doses of oleic acid

Project description:This experiment describes the transcriptional response to oleic acid as a sole carbon source of yeast strains differing in their respiratory competence: the BY4741 wild type strain is considered as normal, sco1 knock out mutant is respiratory deficient and sco2 knock out mutant has a better respiratory competence then the wild type strain. The three strains underwent metabolic shift from 2% glucose as a carbon source to oleic acid at both standard (0.1%) and high (5%) concentration. The transcriptional profiling comprises two time points after metabolic shift: 2 hours and 5 hours. mRNA levels were compared with reference growth condition: exponential phase in 2% glucose. The purpose of this experiment is to gain deeper insight in the relationship between fatty acid metabolism and respiratory metabolism.

2011-01-31 | E-TABM-614 | biostudies-arrayexpress

Transcription profiling of N. gonorrhoeae wild type strain grown in anaerobic conditions with sodium nitrate supplied in media compared to those grown in capnoaerobic conditions

Project description:Transcriptional profiling of N. gonorrhoeae grown in anaerobic conditions (with sodium nitrite supplied by adding 20% w/v solution to a final concentration of 5mM) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)

2011-05-01 | E-MEXP-1660 | biostudies-arrayexpress

Transcription profiling of N. gonorrhoeae wild type strain grown in microaeropilic and capnoaerobic conditions

Project description:Transcriptional profiling of N. gonorrhoeae grown in microaerophilic conditions compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)

2011-05-01 | E-MEXP-1661 | biostudies-arrayexpress

Transcription profiling of N. gonorrhoeae wild type strain grown in anaerobic conditions with sodium nitrate supplied in sterile disc to those grown in capnoaerobic conditions

Project description:Transcriptional profiling of N. gonorrhoeae grown in anaerobic conditions (with sodium nitrite supplied by adding 40ul 20% w/v solution onto a sterile disc in the centre of the plate) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)

2011-05-01 | E-MEXP-1659 | biostudies-arrayexpress

Transcription profiling of N. meningitidis NMB0067 knockout mutant grown in anaerobic conditions with sodium nitrate supplied in sterile disc compared to those grown in capnoaerobic conditions

Project description:Transcriptional profiling of N. meningitidis grown in anaerobic conditions (with sodium nitrite supplied by adding 40ul 20% w/v solution onto a sterile disc in the centre of the plate) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)

2011-05-01 | E-MEXP-1662 | biostudies-arrayexpress

Transcription profiling of N. meningitidis NMB0067 knockout mutant grown in microaerophilic and capnoaerobic conditions

Project description:Transcriptional profiling of N. meningitidis grown in microaerophilic conditions compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)

2011-05-01 | E-MEXP-1663 | biostudies-arrayexpress

Transcription profiling by array of yeast after treatment with pyrrolidine dithiocarbamate (PDTC) for 1, 3 or 5 hours

Project description:Effects of the compound Pyrrolidine dithiocarbamate (PDTC) on the gene expression of Saccharomyces cerevisiae after incubation times of 1, 3 and 5 hours with 75uM PDTC.

2010-08-12 | E-MEXP-2864 | 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