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Sample GSM1232577 Query DataSets for GSM1232577
Status Public on Oct 01, 2015
Title Dynamic2_Ambient27C_GenotypeZ_MR466
Sample type RNA
 
Source name Acropora palmata adult tissue homogenate
Organism Acropora palmata
Characteristics phenotype: Dynamic
phenotype replicate: 2
temperature: 27°C
temperature class: Ambient
genotype: Z
sample id: MR466
Treatment protocol Fragments (~10 cm2) from each of the target coral genotypes were transported to temperature-controlled aquaria. One piece of each genotype was transferred to one of three separate bins containing filtered seawater maintained at temperatures of 20 (cold), 27 (ambient), or 34°C (hot). The fragments were kept in temperature treatments for three days; temperatures stayed within ±0.4°C of the targets.
Growth protocol In Spring 2011, colonies of Acropora palmata were sampled from a reef in Puerto Morelos, Mexico (N 20°52.461', W 86°51.073') and genotyped at five neutral microsatellite loci according to Baums et al. (2005). The Symbiodinium ‘fitti’ strain in each colony was genotyped at ten microsatellite loci (Pinzon et al. 2011). Six of the host genotypes harbored the same strain of S ‘fitti’. These six colonies were targeted for temperature experiments. Colonies hosting symbionts with a small cold stress response (hosts B and Z) and a large cold stress response (hosts D and Y) were binned as replicates. Their host gene expression was contrasted via microarray. Each holobiont phenotype was subsequently called Dynamic and Static, respectively.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the ~3 polyps of each host genotype at each temperature taken 3.5 h after exposure to treatment. Extractions were performed at the Pennsylvania State University with the RNeasy Mini Kit (Qiagen, CA). Concentration and quality of RNA extracts were quantified on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to ensure that high molecular weight RNA was present.
Label Cy3
Label protocol To prepare samples for microarray hybridization, one cycle of amplification was per-formed on 1ug of each RNA sample using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Life Technologies, AM1753) following the manufacturer’s protocol. Dye coupling of 15 ug of aRNA was performed with Cy3 or Cy5 (GE Health Care, RPN5661), and subsequently purified according to the Ambion Kit instructions. For each pair of samples that were to be hybridized to the same array, 2µg each of the Cy3 and Cy5 labeled sample were combined and fragmented using RNA Fragmentation Reagents (Ambion, AM8740) according the manufacturer’s instructions, then dried down completely in a speed-vac
 
Hybridization protocol Samples were resuspended in the appropriate tracking control and hybridization solution master mix was added following manufacturer’s instructions (Roche NimbleGen). Following two 5-minute incubations at 95°C and 42°C, the mixer was attached to the array and hybridization solutions were added according to the manufacturer’s instructions. Hybridization was performed while mixing overnight at 42°C in a MAUI hybridization instrument (BioMicro Systems, UT). Hybridized slides were washed according to the manufacturer’s instructions (Roche NimbleGen), and spun at 1000 RPM for 3 minutes in a 50 ml conical tube filled with N2 gas. Dried slides were placed in fresh tubes with 2.5 ml of DyeSaver (Genisphere Inc.) and rotated for 45 seconds to coat the slide. A final spin at 700 RPM for 3 seconds removed excess DyeSaver.
Scan protocol Scanning was performed with an Axon GenePix 4000B
Description Both host and symbiont RNA are present in sample.
Data processing Raw probe intensities were read into R for analysis in the Bioconductor package LIMMA (Smyth 2005; R Development Core Team 2008). Probe intensities were normalized within arrays using lowess normalization, and between arrays using the quantile normalization method which ensures that the average intensities have the same empirical distribution across arrays (Yang and Thorne 2003).
 
Submission date Sep 17, 2013
Last update date Oct 01, 2015
Contact name John Everett Parkinson
E-mail(s) jparkinson@psu.edu
Organization name Penn State University
Department Biology
Lab Baums
Street address 208 Mueller Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL15393
Series (1)
GSE50926 Intraspecific diversity among partners drives functional variation in coral symbioses

Data table header descriptions
ID_REF
VALUE LIMMA probe intensities normalized within arrays with lowess normalization and between arrays with quantile normalization for separate channel analysis

Data table
ID_REF VALUE
AOKF1013_g2_cP00480 9.744246009
AOKF1022_b2_cP00261 9.741690938
AOKF1022_g2_cP00510 8.579674031
AOKF1024_g2_cP00156 8.590381527
AOKF1029_g2_cP00533 10.70067112
AOKF1031_g2_cP00692 9.268238266
AOKF1034_g2_cP00454 8.223246077
AOKF1040_g2_cP00558 10.91087823
AOKF1045_g2_cP00610 9.390040297
AOKF1046_g2_cP00633 8.62696434
AOKF1050_b2_cP00005 9.069404816
AOKF1050_b2_cP00022 8.973791032
AOKF1050_b2_cP00042 8.88788121
AOKF1057_b2_cP00397 12.67796938
AOKF1057_g2_cP00418 8.955979621
AOKF1062_g2_cP00320 8.493438059
AOKF1064_b2_cP00086 8.91518916
AOKF1091_g2_cP00594 8.546485304
AOKF1098_g2_cP00402 8.818947776
AOKF1100_g2_cP00607 8.664977525

Total number of rows: 137604

Table truncated, full table size 4205 Kbytes.




Supplementary file Size Download File type/resource
GSM1232577_5102012_521833_A01_MR466_532.pair.gz 2.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

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