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Sample GSM2419888 Query DataSets for GSM2419888
Status Public on Sep 18, 2017
Title Conditions 2 vs 3 replicate 2
Sample type RNA
 
Channel 1
Source name condition 2
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: adult
tissue: whole body
strain: Gräfenhain
condition: 20C
Treatment protocol 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. During experiments, all animals were in good physical condition. After thermal acclimation, 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.
Growth protocol 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). 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.
Extracted molecule total RNA
Extraction protocol Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
Label Cy3
Label protocol DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.
 
Channel 2
Source name condition 3
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: adult
tissue: whole body
strain: Gräfenhain
condition: 24C
Treatment protocol 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. During experiments, all animals were in good physical condition. After thermal acclimation, 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.
Growth protocol 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). 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.
Extracted molecule total RNA
Extraction protocol Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
Label Cy5
Label protocol DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.
 
 
Hybridization protocol Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate was applied to each of 12 subarrays with the appropriate Sample Tracking Control (STC) following protocols described in Lopez, J.A. and J.K. Colbourne. 2011. Dual-Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations. CGB Technical Report 2011-02. doi:10.2506/cgbtr-201102.
Scan protocol Axon GenePix 4200 Professional, 5 micron resolution
Data processing Raw signal intensity extract with NimbleScan 2.6 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
The Sample*.txt files are the normalized data values for the probes on the array.
GEO1_Matrix.txt is the final, processed data file reporting log2 ratios of the first condition over second condition, quantile normalized, four biological replicates averaged.
 
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
Phone +44 121 414 5423
Organization name University of Birmingham
Department School of Biosciences
Lab Environmental Genomics Group
Street address Edgbaston
City Birmingham
State/province West Midlands
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL11278
Series (2)
GSE91025 Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 1
GSE91031 Phenotypic plasticity of temperature induced Daphnia gene expression

Supplementary file Size Download File type/resource
GSM2419888_503537A10_HX12_U01_daphnia_532.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM2419888_503537A10_HX12_U01_daphnia_635.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM2419888_Sample10_A14.txt.gz 1.4 Mb (ftp)(http) TXT
GSM2419888_Sample10_A15.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data provided as supplementary file
Processed data are available on Series record

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