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Sample GSM1298781 Query DataSets for GSM1298781
Status Public on Dec 28, 2013
Title neural border, stage 14, biological replicate 1
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 NB14.10
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 7.53738198
AFFX-BioB-5_at 7.706136534
AFFX-BioB-M_at 8.010871331
AFFX-BioC-3_at 8.99899678
AFFX-BioC-5_at 8.897876705
AFFX-BioDn-3_at 10.54655147
AFFX-BioDn-5_at 10.15298214
AFFX-CreX-3_at 13.19125412
AFFX-CreX-5_at 12.44291757
AFFX-DapX-3_at 11.9049019
AFFX-DapX-5_at 10.17584489
AFFX-DapX-M_at 11.17441393
AFFX-LysX-3_at 9.119594567
AFFX-LysX-5_at 7.875196327
AFFX-LysX-M_at 8.762713309
AFFX-PheX-3_at 9.355992631
AFFX-PheX-5_at 8.498407917
AFFX-PheX-M_at 9.306295902
AFFX-r2-Bs-dap-3_at 10.9553832
AFFX-r2-Bs-dap-5_at 10.35309004

Total number of rows: 15611

Table truncated, full table size 435 Kbytes.

Supplementary file Size Download File type/resource
GSM1298781_signature-10.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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