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| Status |
Public on Sep 18, 2017 |
| Title |
Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 2 |
| Organism |
Daphnia pulex |
| Experiment type |
Expression profiling by array
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| Summary |
This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). Long-term-acclimated animals were kept at three different temperatures (i.e., 10 ± 0.5°C, 20 ± 0.3°C, and 24 ± 0.3°C) under normoxia (Po2 ≥ 20 kPa) for at least twelve weeks. Time-resolved experiments (acute heat stress) were carried out with long-term 20°C acclimated animals, which were exposed for three different time intervals (2, 4, and 8 h) to either 30 ± 0.2°C (test conditions) or 20 ± 0.3°C (control conditions). For this, 50 animals each were rapidly transferred with a sieve (mesh size: 1.2 mm) from 20°C-medium to a set of beakers containing 30°C-medium. As control, 50 animals each were transferred from 20°C-medium to another set of beakers with 20°C-medium. Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments. Animals were not fed during short-term exposures. During experiments, all animals were in good physical condition. After thermal acclimation or heat exposure, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C. For all experimental conditions, four independent replicates (50 animals each) were analyzed.
This GEO record is for the acute heat stress temperature contrasts between animals conditioned to 20 degrees Celsius (condition 1) versus heat shock to 30 degrees Celsius (condition 2) exposed for 2 hours (treatment 1), 4 hours (treatment 2), and 8 hours (treatment 3).
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| Overall design |
We compared the gene expression patterns for condition 1 versus condition 2 for each treatment 1, treatment 2 and treatment 3 using four biological replicates for each treatment, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.
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| Contributor(s) |
Becker D, Colbourne JK, Lopez J, Choi J |
| Citation(s) |
28854641 |
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| Submission date |
Dec 08, 2016 |
| Last update date |
Sep 18, 2017 |
| Contact name |
John Kenneth Colbourne |
| E-mail(s) |
J.K.Colbourne@bham.ac.uk
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| Phone |
+44 121 414 5423
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| Organization name |
University of Birmingham
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| Department |
School of Biosciences
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| Lab |
Environmental Genomics Group
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| Street address |
Edgbaston
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| City |
Birmingham |
| State/province |
West Midlands |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL11278 |
NimbleGen Daphnia pulex Expression Array 12x135k (All Probes) [080925_Daphnia_UI_JC_expr] |
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| Samples (12)
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| GSM2419956 |
Treatment 1 conditions 1 vs 2 replicate 1 |
| GSM2419957 |
Treatment 1 conditions 1 vs 2 replicate 2 |
| GSM2419958 |
Treatment 1 conditions 1 vs 2 replicate 3 |
| GSM2419959 |
Treatment 1 conditions 1 vs 2 replicate 4 |
| GSM2419960 |
Treatment 2 conditions 1 vs 2 replicate 1 |
| GSM2419961 |
Treatment 2 conditions 1 vs 2 replicate 2 |
| GSM2419962 |
Treatment 2 conditions 1 vs 2 replicate 3 |
| GSM2419963 |
Treatment 2 conditions 1 vs 2 replicate 4 |
| GSM2419964 |
Treatment 3 conditions 1 vs 2 replicate 1 |
| GSM2419965 |
Treatment 3 conditions 1 vs 2 replicate 2 |
| GSM2419966 |
Treatment 3 conditions 1 vs 2 replicate 3 |
| GSM2419967 |
Treatment 3 conditions 1 vs 2 replicate 4 |
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| This SubSeries is part of SuperSeries: |
| GSE91031 |
Phenotypic plasticity of temperature induced Daphnia gene expression |
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| Relations |
| BioProject |
PRJNA357527 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE91030_GEO2_Matrix.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE91030_RAW.tar |
146.8 Mb |
(http)(custom) |
TAR (of PAIR, TXT) |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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