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Sample GSM1298778 Query DataSets for GSM1298778
Status Public on Dec 28, 2013
Title animal cap, stage 14, biological replicate 1
Sample type RNA
Source name Xenopus laevis animal cap explant, stage 14
Organism Xenopus laevis
Characteristics tissue: animal cap explant (epidermis)
Stage: 14
Treatment protocol Neural border, neural plate, anterior neural fold, and animal cap explants were microdissected and incubated with trizol on ice for 5 minutes.
Growth protocol Xenopus laevis embryos were grown at 15°C in 1/3 MMR until the desired stage
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the standard trizol protocol and eppendorf phase-lock gel tubes, followed by proteinase K digestion, and Qiagen Rneasy columns
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA
Hybridization protocol Hybridization was completed using the standard affymetrix protocol
Scan protocol Scanning was completed using an Affymetrix Genechip scanner 3000 7G
Description AC14.1
Data processing The data was analysed with R (v.2.14.2) and the Bioconductor Biobase (v.2.14.0) affy library (v.1.32.1 package) with default settings.
Submission date Dec 27, 2013
Last update date Dec 28, 2013
Contact name Anne-Helene Monsoro-Burq
Organization name Institut Curie
Department Université Paris Sud
Lab U1021 - UMR3347
Street address Bat 110
City Orsay
ZIP/Postal code 91405
Country France
Platform ID GPL1318
Series (2)
GSE53678 Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers [Xenopus_laevis]
GSE53679 Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers

Data table header descriptions
VALUE log2 RMA signal intensity

Data table
AFFX-BioB-3_at 7.786430445
AFFX-BioB-5_at 8.322169872
AFFX-BioB-M_at 8.428110445
AFFX-BioC-3_at 9.169836145
AFFX-BioC-5_at 9.081265208
AFFX-BioDn-3_at 10.85344986
AFFX-BioDn-5_at 10.23061119
AFFX-CreX-3_at 12.97497233
AFFX-CreX-5_at 12.39464335
AFFX-DapX-3_at 11.59203104
AFFX-DapX-5_at 10.05103284
AFFX-DapX-M_at 11.09538191
AFFX-LysX-3_at 8.808313712
AFFX-LysX-5_at 7.531937538
AFFX-LysX-M_at 8.708391835
AFFX-PheX-3_at 9.274716122
AFFX-PheX-5_at 8.356475239
AFFX-PheX-M_at 8.953539959
AFFX-r2-Bs-dap-3_at 10.71412559
AFFX-r2-Bs-dap-5_at 10.22505979

Total number of rows: 15611

Table truncated, full table size 435 Kbytes.

Supplementary file Size Download File type/resource
GSM1298778_signature-1.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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