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Sample GSM442129 Query DataSets for GSM442129
Status Public on Dec 31, 2009
Title Vegetal cortex rep2
Sample type RNA
Source name stage VI oocyte
Organism Xenopus laevis
Characteristics developmental stage: full-grown, stage VI oocyte
isolation: collagenase treatment
treatment: manual dissection of vegetal cortex
cell part: vegetal cortex
Treatment protocol Manual isolation of vegetal cortices was performed using the methods of Elinson et al. (1993), with modifications. Briefly, collagenased stage VI oocytes were transferred to 1x MEM (100 mM MOPS pH 7.4, 2 mM EGTA, 1 mM MgSO4,) in a clean glass dish and bisected into animal and vegetal halves using a new scalpel blade. The vegetal halves were placed cortex side down onto a nitrocellulose filter, and a cover slip was used to compress away the yolky cytoplasm. After the cover slips were removed, gentle agitation was used to free the cortex from the membrane and to dislodge any additional yolk. Isolated cortices were rinsed in fresh MEM and frozen in batches of ten on dry ice. Intact stage VI oocytes from the same female were frozen as controls.
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: 3
Replicate Number: 1
Experimental condition: Experimental sample
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 1358.05 P 0.000224668
AFFX-BioB-M_at 1536.77 P 4.42873e-05
AFFX-BioB-3_at 1037.1 P 4.42873e-05
AFFX-BioC-5_at 2705.53 P 5.16732e-05
AFFX-BioC-3_at 3093.73 P 5.16732e-05
AFFX-BioDn-5_at 6694.3 P 4.42873e-05
AFFX-BioDn-3_at 9508.97 P 4.42873e-05
AFFX-CreX-5_at 38552.3 P 4.42873e-05
AFFX-CreX-3_at 47377 P 4.42873e-05
AFFX-DapX-5_at 77.3 A 0.227636
AFFX-DapX-M_at 396.443 P 0.00227496
AFFX-DapX-3_at 1106.45 P 8.14279e-05
AFFX-LysX-5_at 47.2578 A 0.574038
AFFX-LysX-M_at 30.359 A 0.772383
AFFX-LysX-3_at 196.802 P 0.00227496
AFFX-PheX-5_at 13.3517 A 0.876428
AFFX-PheX-M_at 45.7003 A 0.455413
AFFX-PheX-3_at 188.582 P 0.0113844
AFFX-ThrX-5_at 11.9997 A 0.876428
AFFX-ThrX-M_at 46.2229 A 0.559354

Total number of rows: 15611

Table truncated, full table size 567 Kbytes.

Supplementary file Size Download File type/resource
GSM442129_DH_Cortex_2.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM442129_Houston_cortex2.CHP.gz 87.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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