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Sample GSM349689 Query DataSets for GSM349689
Status Public on Jan 28, 2009
Title wildtype embryos stage 18
Sample type RNA
Source name Posterior poles dissected from stage 18 embryos
Organism Xenopus laevis
Characteristics Genotype: NA
Age: Neurula Stage 18
Treatment protocol For Derriere depletion, embryos were injected with 2 nanograms MO oligonucleotide in the lateral side of both dorsal blastomeres at 4-cell stage. Localization was verified by fluoresence for co-injected GFP. At stage 18, dorsal posterior fragments were di
Growth protocol Embryos were grown to stage 18.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Xenopus laevis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from posterior poles of embryos containing mostly mesoderm
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 50.
Submission date Dec 09, 2008
Last update date Jan 27, 2009
Contact name Ali H Brivanlou
Phone 212 327-8656
Fax 212-327-8685
Organization name Rockefeller University
Lab Molecular Embryology
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL1318
Series (1)
GSE13882 Derriere targets in Xenopus posterior mesoderm

Data table header descriptions
VALUE MAS5.0 signal intensity

Data table
AFFX-BioB-5_at 204.1 P 0.000225
AFFX-BioB-M_at 208.8 P 0.000052
AFFX-BioB-3_at 167 P 0.000052
AFFX-BioC-5_at 688.6 P 0.000052
AFFX-BioC-3_at 649.9 P 0.000044
AFFX-BioDn-5_at 1030 P 0.000044
AFFX-BioDn-3_at 2180.3 P 0.000044
AFFX-CreX-5_at 5311.2 P 0.000044
AFFX-CreX-3_at 6327 P 0.000044
AFFX-DapX-5_at 19.4 P 0.030976
AFFX-DapX-M_at 75.1 P 0.001593
AFFX-DapX-3_at 233.4 P 0.000095
AFFX-LysX-5_at 1.8 A 0.659339
AFFX-LysX-M_at 19.1 A 0.275146
AFFX-LysX-3_at 69.7 P 0.000095
AFFX-PheX-5_at 0.8 A 0.737173
AFFX-PheX-M_at 20.9 M 0.050229
AFFX-PheX-3_at 50.1 P 0.000754
AFFX-ThrX-5_at 14.2 A 0.368438
AFFX-ThrX-M_at 16.1 A 0.131361

Total number of rows: 15611

Table truncated, full table size 499 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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