Transcriptomics

Dataset Information

2

Calibration of a custom designed microarray for European Fire Salamander


ABSTRACT: A custom 8x60 k expression microarray for larvae of European fire salamander (Salamandra salamandra) was designed based on transcriptome sequencing. It is known the fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution) for more information. Labeled cRNA was prepared from Salamander larvae kept at 9°C and 17°C. A cRNA calibration pool was prepared with equimolar amounts of cRNA prepared from (a) a larvae (temperature: 9°C: source: pond KOE), (b) a larvae (temperature: 17°C: source: pond KOE), (c) a larvae (temperature: 9°C: source: stream KoGB (Klufterbach) and (d) a larvae (temperature: 17°C: source: stream KoGB (Klufterbach). See Steinfartz et al. (2007) (doi: 10.1111/j.1365-294X.2007.03490.x) for information of the source populations. Increasing amounts of labeled cRNA (75 ng, 150 ng, 300 ng, 600 ng, 1000 ng, 1400 ng, 1800 ng, 2200 ng), corresponding to (1/8, 1/4, 1/2, 1, 1 2/3, 2 1/3, 3 and 3 3/3 times the recommended amount of 600 ng) were hybridized to 8 microarrays (one microarray per dilution). The change in observed signal intensity in relation to the change in amount of labeled cRNA was used to infer the target-binding behavior of the individual probes. This information was extracted, to be used for a normalization procedure in another experiment with the same microarray (see Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution). The current study provides only raw data for a calibration experiment, to validate the binding behavior of the different probes on a newly designed microarray for a non model organism (European Fire salamander). This calibration is based only on raw data. More information on targeted genes is provided in a different GEO dataset (currently submitted), where biological meaningful analysis are performed with data which are normalized based on this calibration.

ORGANISM(S): Salamandra salamandra  

SUBMITTER: Till Czypionka   Arne W Nolte  Leon Blaustein  Alan R Templeton  Sebastian Steinfartz  Janine Altmueller  Tamar Krugman 

PROVIDER: E-GEOD-70055 | ArrayExpress | 2015-06-20

SECONDARY ACCESSION(S): GSE70055PRJNA287545

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

| GSE70055 | GEO
2012-03-26 | E-GEOD-36800 | ArrayExpress
| PRJNA287545 | ENA
| GSE110893 | GEO
| GSE113525 | GEO
2015-06-20 | E-GEOD-70054 | ArrayExpress
2014-10-26 | E-GEOD-33283 | ArrayExpress
2016-10-24 | E-GEOD-33250 | ArrayExpress
| GSE93063 | GEO
| PRJNA287544 | ENA