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Sample GSM442127 Query DataSets for GSM442127
Status Public on Dec 31, 2009
Title Whole oocyte rep2
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: 2
Replicate Number: 2
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
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
VALUE MAS 5 signal
ABS_CALL present/absent

Data table
AFFX-BioB-5_at 572.912 P 0.000753643
AFFX-BioB-M_at 874.738 P 5.16732e-05
AFFX-BioB-3_at 485.055 P 4.42873e-05
AFFX-BioC-5_at 1595.11 P 5.16732e-05
AFFX-BioC-3_at 1819.83 P 4.42873e-05
AFFX-BioDn-5_at 3587.9 P 4.42873e-05
AFFX-BioDn-3_at 4487.59 P 5.16732e-05
AFFX-CreX-5_at 21002.8 P 4.42873e-05
AFFX-CreX-3_at 29079.9 P 4.42873e-05
AFFX-DapX-5_at 20.7441 A 0.440646
AFFX-DapX-M_at 69.2376 A 0.0629293
AFFX-DapX-3_at 275.083 P 0.00110197
AFFX-LysX-5_at 19.0934 A 0.659339
AFFX-LysX-M_at 56.1548 A 0.313723
AFFX-LysX-3_at 108.927 P 0.00401721
AFFX-PheX-5_at 3.83174 A 0.949771
AFFX-PheX-M_at 6.80211 A 0.876428
AFFX-PheX-3_at 82.5121 A 0.139482
AFFX-ThrX-5_at 12.3769 A 0.876448
AFFX-ThrX-M_at 27.7766 A 0.659352

Total number of rows: 15611

Table truncated, full table size 569 Kbytes.

Supplementary file Size Download File type/resource
GSM442127_DH_Oocyte_2.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM442127_Houston_oocyte2.CHP.gz 86.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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