NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1299052 Query DataSets for GSM1299052
Status Public on Oct 02, 2014
Title 28K-28C_Rep1
Sample type RNA
 
Channel 1
Source name whole body
Organism Daphnia pulex
Characteristics treatment: 28 C
phenotype: heat sensitive
Extracted molecule total RNA
Extraction protocol ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Label Cy3
Label protocol ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
 
Channel 2
Source name whole body
Organism Daphnia pulex
Characteristics treatment: 28 C
phenotype: heat tolerant
Extracted molecule total RNA
Extraction protocol ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Label Cy5
Label protocol ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
 
 
Hybridization protocol Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
Scan protocol Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.
Description 28K-28C_Rep1
Biological replicate 1
Biological replicate 1
Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations. aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA extracted with Phenol:Chloroform:IAA and purified with Ethanol in the pressence of ammonium acetate and glycogen.
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
Data processing Raw signal intensities extracted with NimbleScan 2.4 Software (Roche NimbleGen) as PAIR files.
 
Submission date Dec 27, 2013
Last update date Oct 02, 2014
Contact name Jacqueline Lopez
E-mail(s) [email protected]
Phone 574-631-1902
Organization name University of Notre Dame
Department Biology
Lab Pfrender Laboratory
Street address 019 Galvin Life Science Center
City Notre Dame
State/province Indiana
ZIP/Postal code 46556
Country USA
 
Platform ID GPL11278
Series (1)
GSE53692 Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

Data table header descriptions
ID_REF
VALUE quantilie normalized, log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1000060_1_sc_30_1000060_1000180P00001 0.0214120097972561
100008_1_sc_67_100008_100137P00004 -0.00940722481680556
100009_3_1399871_1400680_1_SC13_1399882_1400677P00 0.267353047140569
100009_4_1403128_1403367_1_SC13_1403155_1403360P00 0.246947876519741
100009_5_1403624_1403706_1_SC13_1403624_1403706P00 0.074617728150991
100010_1_sc_76_100010_100385P00154 0.734237699118077
1000131_1_sc_15_1000131_1000301P00033 -0.167111352201049
1000210_1_sc_8_1000216_1000403P00001 0.479436760908024
1000228_1_sc_5_1000228_1000303P00005 -0.148713645995477
1000235_1_sc_12_1000235_1000385P00001 -0.62235497323997
1000302_1_sc_1_1000302_1002651P00649 -0.405055645029154
1000302_2_sc_1_1000302_1002651P00020 0.26420279162525
1000335_1_sc_24_1000335_1000630P00035 0.0879344624934761
1000336_1_sc_4_1000336_1001676P00018 -0.138228642641222
1000336_2_sc_4_1000336_1001676P00002 0.810872668009487
1000336_4_sc_4_1000336_1001676P00001 0.471942572008787
100034_1_sc_211_100034_100104P00001 0.0518681111247741
1000361_1_sc_15_1000361_1000506P00001 0.585766184347836
100036_2_1504384_1505256_1_SC13_1504408_1505253P00 -0.746158533292933
100036_3_1505325_1505953_1_SC13_1505355_1505953P00 -0.702351250815738

Total number of rows: 134558

Table truncated, full table size 7776 Kbytes.




Supplementary file Size Download File type/resource
GSM1299052_429156A09_HX12_U01_Daphnia_532.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM1299052_429156A09_HX12_U01_Daphnia_635.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM1299052_processed_sample9.txt.gz 7.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap