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Sample GSM1298788 Query DataSets for GSM1298788
Status Public on Dec 28, 2013
Title anterior neural fold, stage 18, biological replicate 3
Sample type RNA
Source name Xenopus laevis anterior neural fold, stage 18
Organism Xenopus laevis
Characteristics tissue: anterior neural fold
Stage: 18
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 ANF18.16
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 7.105014567
AFFX-BioB-5_at 7.41113693
AFFX-BioB-M_at 7.586643393
AFFX-BioC-3_at 8.636765364
AFFX-BioC-5_at 8.489866227
AFFX-BioDn-3_at 10.36273243
AFFX-BioDn-5_at 9.758169892
AFFX-CreX-3_at 12.93124139
AFFX-CreX-5_at 12.14242208
AFFX-DapX-3_at 11.94892824
AFFX-DapX-5_at 10.33654995
AFFX-DapX-M_at 11.41295574
AFFX-LysX-3_at 9.219757963
AFFX-LysX-5_at 7.960866914
AFFX-LysX-M_at 9.045940891
AFFX-PheX-3_at 9.501313171
AFFX-PheX-5_at 8.806131944
AFFX-PheX-M_at 9.498225341
AFFX-r2-Bs-dap-3_at 10.99903171
AFFX-r2-Bs-dap-5_at 10.6063394

Total number of rows: 15611

Table truncated, full table size 435 Kbytes.

Supplementary file Size Download File type/resource
GSM1298788_signature-16.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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