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Sample GSM1298783 Query DataSets for GSM1298783
Status Public on Dec 28, 2013
Title neural border, stage 14, biological replicate 3
Sample type RNA
Source name Xenopus laevis neural border, stage 14
Organism Xenopus laevis
Characteristics tissue: neural border
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 NB14.6
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 7.715612744
AFFX-BioB-5_at 7.960673759
AFFX-BioB-M_at 8.203580045
AFFX-BioC-3_at 9.268558391
AFFX-BioC-5_at 9.061200993
AFFX-BioDn-3_at 10.82983785
AFFX-BioDn-5_at 10.33809755
AFFX-CreX-3_at 13.34599144
AFFX-CreX-5_at 12.57123402
AFFX-DapX-3_at 11.47685046
AFFX-DapX-5_at 9.76539424
AFFX-DapX-M_at 10.86088621
AFFX-LysX-3_at 8.72269077
AFFX-LysX-5_at 7.554516778
AFFX-LysX-M_at 8.390295929
AFFX-PheX-3_at 8.949994035
AFFX-PheX-5_at 8.238404521
AFFX-PheX-M_at 8.93773109
AFFX-r2-Bs-dap-3_at 10.50247567
AFFX-r2-Bs-dap-5_at 10.11813005

Total number of rows: 15611

Table truncated, full table size 435 Kbytes.

Supplementary file Size Download File type/resource
GSM1298783_signature-6.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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