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Sample GSM1298779 Query DataSets for GSM1298779
Status Public on Dec 28, 2013
Title neural plate, stage 12, biological replicate 1
Sample type RNA
Source name Xenopus laevis neural plate, stage 12
Organism Xenopus laevis
Characteristics tissue: neural plate
Stage: 12
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 NP12.7
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 7.419761153
AFFX-BioB-5_at 7.737422532
AFFX-BioB-M_at 7.739563626
AFFX-BioC-3_at 9.141716311
AFFX-BioC-5_at 8.941852971
AFFX-BioDn-3_at 10.86249394
AFFX-BioDn-5_at 10.27392695
AFFX-CreX-3_at 13.08045636
AFFX-CreX-5_at 12.42238428
AFFX-DapX-3_at 12.54868077
AFFX-DapX-5_at 10.80860861
AFFX-DapX-M_at 12.05259491
AFFX-LysX-3_at 10.02200112
AFFX-LysX-5_at 8.354159077
AFFX-LysX-M_at 9.453193128
AFFX-PheX-3_at 9.958520921
AFFX-PheX-5_at 9.233589334
AFFX-PheX-M_at 10.09723768
AFFX-r2-Bs-dap-3_at 11.51094389
AFFX-r2-Bs-dap-5_at 11.44294049

Total number of rows: 15611

Table truncated, full table size 435 Kbytes.

Supplementary file Size Download File type/resource
GSM1298779_signature-7.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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