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Sample GSM537527 Query DataSets for GSM537527
Status Public on Feb 22, 2011
Title CNC-MO13+C13-3
Sample type RNA
Source name Xenopus laevis CNC from stage 17 embryos injected with a morpholino to ADAM13 and a GFP-fusion protein containing the ADAM13 cytoplasmic domain.
Organism Xenopus laevis
Characteristics developmental stage: Stage 15-17 embryos
tissue: cranial neural crest explant
agent: a morpholino to ADAM13 and a GFP-fusion protein containing the ADAM13 cytoplasmic domain
Treatment protocol Cranial neural crest cells were dissected and imediately extracted.
Growth protocol Embryos were injected at the one cell stage and grown at 15C until stage 15 to 17.
Extracted molecule total RNA
Extraction protocol RNA extraction was performed as previously described using guanidium thioisocyanate, phenol chlorophorm and lithium chloride precipitation. P. Chomczynski, N. Sacchi, Anal. Biochem. 162, 156 (1987).
Label Biotin
Label protocol Total RNA quality control was performed with the Bioanalyzer 2100 (Agilent). Double stranded cDNA was generated and labeled with the Ovation RNA Amplification System and Encore Biotin Module (NuGen), respectively. Purification was performed using the Qiagen PCR Purification Kit
Hybridization protocol Labeled cDNA were incorporated into a hybridization solution from the Affymetrix GeneChip Hybridization Kit. Each sample was hybridized in separate arrays for 20 hours at 450C.
Scan protocol All arrays were treated by the MIT core facility.
Description 10 ng of MO at the one cell stage plus 300pg of mRNA.
MO13+C13-2 (expt DA2).
Data processing Initial data analysis was generated with the Affymetrix Expression Console and an R package was used to assess data quality. Sample normalization was done using the gcrma method.
Submission date Apr 26, 2010
Last update date Feb 22, 2011
Contact name Dominique Alfandari
Phone 4135774269
Fax 4135456326
Organization name University of Massachusetts
Department Vet & Animal Sciences
Street address 661 North pleasant street
City Amherst
State/province MA
ZIP/Postal code 01003
Country USA
Platform ID GPL1318
Series (1)
GSE21517 ADAM13 knockdown in Xenopus laevis cranial neural crest

Data table header descriptions
VALUE Log2-gcrma method, unfiltered signal intensity

Data table
XlAffx.3.1.S1_at 1.15
XlAffx.2.1.S1_at 1.43
XlAffx.1.9.S1_at 1.04
XlAffx.1.8.S1_at 2.25
XlAffx.1.7.S1_x_at 0.69
XlAffx.1.7.S1_at 0.61
XlAffx.1.6.S1_at 3.73
XlAffx.1.5.S1_at 5.89
XlAffx.1.4.S1_at 1.84
XlAffx.1.3.S1_at 1
XlAffx.1.2.S1_at 1.05
XlAffx.1.12.S1_at 1.23
XlAffx.1.11.S1_at 6.63
XlAffx.1.10.S1_at 1.62
XlAffx.1.1.S1_at 1.06
Xl.9998.2.S1_at 2.48
Xl.9998.2.S1_a_at 9.41
Xl.9998.1.A1_at 8.9
Xl.9997.1.A1_at 5.36
Xl.9996.1.A1_at 1.41

Total number of rows: 15491

Table truncated, full table size 327 Kbytes.

Supplementary file Size Download File type/resource
GSM537527.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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