GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM349690 Query DataSets for GSM349690
Status Public on Jan 28, 2009
Title Derriere depleted 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 145 P 0.00034
AFFX-BioB-M_at 175.1 P 0.000044
AFFX-BioB-3_at 141 P 0.000052
AFFX-BioC-5_at 542.8 P 0.000044
AFFX-BioC-3_at 566 P 0.000044
AFFX-BioDn-5_at 826.9 P 0.000044
AFFX-BioDn-3_at 1722.4 P 0.000044
AFFX-CreX-5_at 4581.1 P 0.000044
AFFX-CreX-3_at 5965.7 P 0.000044
AFFX-DapX-5_at 14 P 0.000662
AFFX-DapX-M_at 33.8 P 0.004998
AFFX-DapX-3_at 130.8 P 0.000169
AFFX-LysX-5_at 1.2 A 0.724854
AFFX-LysX-M_at 23.4 A 0.175328
AFFX-LysX-3_at 32.8 P 0.000195
AFFX-PheX-5_at 0.7 A 0.783476
AFFX-PheX-M_at 11.5 A 0.205732
AFFX-PheX-3_at 28.5 P 0.004484
AFFX-ThrX-5_at 5.4 A 0.699394
AFFX-ThrX-M_at 9.5 A 0.275146

Total number of rows: 15611

Table truncated, full table size 499 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap