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Sample GSM634811 Query DataSets for GSM634811
Status Public on Feb 01, 2011
Title Sample45_M1M2_replicate4
Sample type RNA
 
Channel 1
Source name Total RNA from experiment M1
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: adult
age: 21 days
tissue: whole body
strain: BH14
Treatment protocol M1
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 M2
Organism Daphnia pulex
Characteristics Sex: female
developmental stage: adult
age: 21 days
tissue: whole body
strain: K10
Treatment protocol M2
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) 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 (2)
GSE25823 The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome
GSE25843 Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P

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 0.561769461449853
100008_1_sc_67_100008_100137P00004 -0.305684474507343
100009_3_1399871_1400680_1_SC13_1399882_1400677P00 0.413788463114178
100009_4_1403128_1403367_1_SC13_1403155_1403360P00 -0.0728423107229954
100009_5_1403624_1403706_1_SC13_1403624_1403706P00 0.143294895382684
100010_1_sc_76_100010_100385P00154 -0.703734111165227
1000131_1_sc_15_1000131_1000301P00033 -0.247747403426107
1000210_1_sc_8_1000216_1000403P00001 -0.324227608064160
1000228_1_sc_5_1000228_1000303P00005 -0.830714652438479
1000235_1_sc_12_1000235_1000385P00001 0.791863323047384
1000302_1_sc_1_1000302_1002651P00649 0.0467047334989026
1000302_2_sc_1_1000302_1002651P00020 -0.233031566827666
1000335_1_sc_24_1000335_1000630P00035 0.131686103992841
1000336_1_sc_4_1000336_1001676P00018 -0.0622386456599049
1000336_2_sc_4_1000336_1001676P00002 -0.365842689302106
1000336_4_sc_4_1000336_1001676P00001 -0.843732213304021
100034_1_sc_211_100034_100104P00001 0.0737027021965613
1000361_1_sc_15_1000361_1000506P00001 -0.0101578039463082
100036_2_1504384_1505256_1_SC13_1504408_1505253P00 0.0495679494922783
100036_3_1505325_1505953_1_SC13_1505355_1505953P00 0.0177323215310441

Total number of rows: 134558

Table truncated, full table size 7771 Kbytes.




Supplementary file Size Download File type/resource
GSM634811_296240A09_HX12_U01_Daphnia_532.pair.gz 3.9 Mb (ftp)(http) PAIR
GSM634811_296240A09_HX12_U01_Daphnia_635.pair.gz 3.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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