NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM634866 Query DataSets for GSM634866
Status Public on Feb 01, 2011
Title Sample3_J1J2_replicate3
Sample type RNA
 
Channel 1
Source name Total RNA from experiment J1
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: juvenile
tissue: whole body
Treatment protocol J1
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 Total RNA from experiment J2
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: juvenile
tissue: whole body
Treatment protocol J2
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 hybridization master for a given source and biological replicate.
Scan protocol Axon GenePix 4200 Professional, 5 micron resolution.
Data processing Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
 
Submission date Dec 03, 2010
Last update date Jun 25, 2012
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 (2)
GSE25823 The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome
GSE25850 Evolutionary Diversification of Duplicated Genes; Experiment J

Data table header descriptions
ID_REF
VALUE Log2 ratio of Cy5/Cy3, quantile normalized

Data table
ID_REF VALUE
1000060_1_sc_30_1000060_1000180P00001 -0.0456062860310977
100008_1_sc_67_100008_100137P00004 0.0634904777274166
100009_3_1399871_1400680_1_SC13_1399882_1400677P00 -0.373329711908008
100009_4_1403128_1403367_1_SC13_1403155_1403360P00 -0.192379490259114
100009_5_1403624_1403706_1_SC13_1403624_1403706P00 -0.271323630656625
100010_1_sc_76_100010_100385P00154 0.266842030492601
1000131_1_sc_15_1000131_1000301P00033 0.092456917346512
1000210_1_sc_8_1000216_1000403P00001 -0.142557037553003
1000228_1_sc_5_1000228_1000303P00005 -0.107679206684749
1000235_1_sc_12_1000235_1000385P00001 0.357860709638727
1000302_1_sc_1_1000302_1002651P00649 -0.270500107259034
1000302_2_sc_1_1000302_1002651P00020 0.542176362410911
1000335_1_sc_24_1000335_1000630P00035 0.0262851095142427
1000336_1_sc_4_1000336_1001676P00018 -0.287867611231169
1000336_2_sc_4_1000336_1001676P00002 0.247326242543673
1000336_4_sc_4_1000336_1001676P00001 -0.490795694118303
100034_1_sc_211_100034_100104P00001 -0.355085730240534
1000361_1_sc_15_1000361_1000506P00001 0.370634023589204
100036_2_1504384_1505256_1_SC13_1504408_1505253P00 -0.262206165278085
100036_3_1505325_1505953_1_SC13_1505355_1505953P00 -0.142987232924648

Total number of rows: 134558

Table truncated, full table size 7803 Kbytes.




Supplementary file Size Download File type/resource
GSM634866_278137A09_HX12_U01_Daphnia_532.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM634866_278137A09_HX12_U01_Daphnia_635.pair.gz 3.9 Mb (ftp)(http) PAIR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap