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Sample GSM1299055 Query DataSets for GSM1299055
Status Public on Oct 02, 2014
Title 28C-28B_Rep1
Sample type RNA
 
Channel 1
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 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 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 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 28C-28B_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) jacqueline.ann.lopez@gmail.com
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 -0.690205345683482
100008_1_sc_67_100008_100137P00004 -0.103156968912676
100009_3_1399871_1400680_1_SC13_1399882_1400677P00 0.165013061437859
100009_4_1403128_1403367_1_SC13_1403155_1403360P00 0.314257971453616
100009_5_1403624_1403706_1_SC13_1403624_1403706P00 -0.0116802792276998
100010_1_sc_76_100010_100385P00154 -0.14645223188595
1000131_1_sc_15_1000131_1000301P00033 -0.0906021373472612
1000210_1_sc_8_1000216_1000403P00001 -0.441093976448835
1000228_1_sc_5_1000228_1000303P00005 -0.0609225406705391
1000235_1_sc_12_1000235_1000385P00001 -0.551226823130436
1000302_1_sc_1_1000302_1002651P00649 -0.402966899705145
1000302_2_sc_1_1000302_1002651P00020 0.161131152588643
1000335_1_sc_24_1000335_1000630P00035 -0.485925411932773
1000336_1_sc_4_1000336_1001676P00018 -0.214540065470114
1000336_2_sc_4_1000336_1001676P00002 -0.25751343435978
1000336_4_sc_4_1000336_1001676P00001 -0.0311392711953982
100034_1_sc_211_100034_100104P00001 -0.97261529519305
1000361_1_sc_15_1000361_1000506P00001 0.0944682129448999
100036_2_1504384_1505256_1_SC13_1504408_1505253P00 1.29599660609775
100036_3_1505325_1505953_1_SC13_1505355_1505953P00 -0.250350444595684

Total number of rows: 134558

Table truncated, full table size 7773 Kbytes.




Supplementary file Size Download File type/resource
GSM1299055_429156A12_HX12_U01_Daphnia_532.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM1299055_429156A12_HX12_U01_Daphnia_635.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM1299055_processed_sample12.txt.gz 7.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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