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Sample GSM442126 Query DataSets for GSM442126
Status Public on Dec 31, 2009
Title Whole oocyte rep1
Sample type RNA
 
Source name stage VI oocyte
Organism Xenopus laevis
Characteristics developmental stage: full-grown, stage VI oocyte
isolation: collagenase treatment
cell type: oocyte
Extracted molecule total RNA
Extraction protocol Total RNA was prepared by proteinase K digestion followed by phenol extraction and ethanol precipitation. Purified RNA was treated with DNase prior to cDNA synthesis. RNA quality was verified using the Experion System (BioRad) for automated electrophoresis.
Label Biotin
Label protocol 100 ng of total RNA was used to make complementary RNA (cRNA)d, which was amplified using the GeneChip® Two-Cycle cDNA Synthesis Kit (Invitrogen/Affymetrix). cRNA labeling, hybridization and data acquisition were performed by The University of Iowa, Carver College of Medicine DNA Core Facility, using standard Affymetrix protocols and reagents.
 
Hybridization protocol Labelled cRNA was hybridized to Xenopus laevis Genome Arrays (Affymetrix) at 45˚C using Model 640 hyb ovens, processed using the Model 450 GeneChip fluidics station (Affymetrix).
Scan protocol Image files were captured on a Model 3000 GeneArray scanner and processed using Affymetrix micorarray analysis software.
Description Sample Number: 1
Replicate Number: 1
Experimental condition: Control
Data processing Quality control included standard Affymetrix internal controls. GeneChip Operating software was used to generate data files (CEL), and MAS 5 for calculating expression signals.
 
Submission date Aug 18, 2009
Last update date Aug 19, 2009
Contact name Douglas W. Houston
E-mail(s) douglas-houston@uiowa.edu
Phone (319) 335-1316
Organization name The University of Iowa
Department Department of Biology
Street address 257 BB
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL1318
Series (1)
GSE17713 Microarray analysis of mRNAs enriched in the vegetal cortex of Xenopus oocytes

Data table header descriptions
ID_REF
VALUE MAS 5 signal
ABS_CALL present/absent
DETECTION P-VALUE p-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 565.601 P 0.000753643
AFFX-BioB-M_at 727.053 P 7.00668e-05
AFFX-BioB-3_at 441.12 P 4.42873e-05
AFFX-BioC-5_at 1737.35 P 5.16732e-05
AFFX-BioC-3_at 1641.33 P 5.16732e-05
AFFX-BioDn-5_at 3694.29 P 4.42873e-05
AFFX-BioDn-3_at 4854.97 P 6.02111e-05
AFFX-CreX-5_at 17388.9 P 4.42873e-05
AFFX-CreX-3_at 21407.4 P 5.16732e-05
AFFX-DapX-5_at 171.49 P 0.000340305
AFFX-DapX-M_at 2544.48 P 8.14279e-05
AFFX-DapX-3_at 6092.2 P 4.42873e-05
AFFX-LysX-5_at 70.1539 A 0.0629293
AFFX-LysX-M_at 483.791 P 0.000972149
AFFX-LysX-3_at 1060.94 P 5.16732e-05
AFFX-PheX-5_at 76.2272 P 0.0396608
AFFX-PheX-M_at 372.892 P 0.000339937
AFFX-PheX-3_at 964.25 P 5.16732e-05
AFFX-ThrX-5_at 100.082 A 0.250796
AFFX-ThrX-M_at 621.101 P 0.000509415

Total number of rows: 15611

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM442126_DH_Oocyte_1.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM442126_Houston_oocyte1.CHP.gz 86.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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