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Sample GSM99978 Query DataSets for GSM99978
Status Public on Mar 11, 2006
Title Zorn_C3_Xenopus_laevis.txt
Sample type RNA
 
Source name Zorn_C3_Xenopus_laevis.txt
Organism Xenopus laevis
Characteristics condition name: Sox17-MO
Developmental Stage: embryonic stage 11
Treatment protocol Embryo manipulations and microinjections were preformed using standard procedures and embryos were staged according to the normal table of development for Xenopus laevis (Nieuwkoop and Faber, 1994). Two-cell stage embryos were vegetally injected with the following doses of antisense morpholino oligos or synthetic RNA: a combination of antisense morpholino oligos to Sox17a1 + Sox17a2 + Sox17b (20ng each) (Clements et al., 2003), Mixer antisense morpholino oligo (40ng) (Kofron et al., 2004), Cerberus-short RNA (1ng). For each biological sample for profiling, ~20 sibling embryos from a single mating or ~50 micro-dissected explants from sibling embryos were combined for individual RNA sample preparation.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) and purified on RNAeasy columns (Qiagen). Ten micrograms of total RNA was used for cDNA syntheses and labeled RNA probe which was hybridized to Affymetrix Xenopus Genechips by the Cincinnati Children's Research Foundation microarray core facility, using the standard Affymetrix protocol.
Label biotin
Label protocol Quality of total RNA is verified by the Agilent Bioanalyzer 2100 (Hewelett Packard) using the RNA 6000 Nano Assay according to manufactures recommendations. Then 10 micrograms of total RNA is used to make cDNA, from which botinylated cRNA probe was prepared using the standard Genechip Expression 3’ Amplification One-Cycle Target Labeling Kit (Affymetrix).
 
Hybridization protocol 20 micrograms of labeled cRNA in a volume of 200 microliters was hybridized to the Affymetrix Xenopus Genecip in a standard Affymetrix Probe Array Cartridge at 45 degrees Celsius, using the fluidics protocol EukGE-WS2v4_450 of a Fluidics Station 450 (Affymetrix).
Scan protocol The image file was captured on an Affymetrix GeneChip Scanner 3000 and initially processed with Genechip Operating Software 1v4 (Affymetrix).
Description Sample Number: 31
BioReplicate: 1
Experimental condition: Sox17 depleted by antisense morpholino oligos
Data processing Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between 1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Each array was normalized the same. Global scaling is used adjusting the average intensity or signal value of each probe array to the same Target Intensity value (TGT) of 1500. Genechip Operating Software 1v4 (Affymetrix) was then used to generate CEL files from each experiment, which were then imported into GeneSpring for all further data analysis.
GeneSpring 7.1 software (Silicon Genetics) was used for data normalization, clustering and filtering. Raw CEL file data from all the samples was pre-normalized using RMA (Robust Multichip Average). The average log intensity of the biological replicates was then normalized to the average log intensity of stage 11 whole embryo.
 
Submission date Mar 10, 2006
Last update date Mar 10, 2006
Contact name Aaron M Zorn
E-mail(s) aaron.zorn@cchmc.org
Phone 636 3770
Organization name Cincinnati Children's Hospital Medical Center
Department Develpomental Biology
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45236
Country USA
 
Platform ID GPL1318
Series (1)
GSE4448 Global analysis of the transcriptional network controlling Xenopus endoderm formation

Data table header descriptions
ID_REF
VALUE
Control Value
Normalized Value

Data table
ID_REF VALUE Control Value Normalized Value
XlAffx.3.1.S1_at 44.79 38.39 1.167
XlAffx.2.1.S1_at 20.18 16.94 1.191
XlAffx.1.9.S1_at 36.13 23.31 1.55
XlAffx.1.8.S1_at 10.36 8.635 1.2
XlAffx.1.7.S1_x_at 83.96 43.55 1.928
XlAffx.1.7.S1_at 22.59 15.44 1.463
XlAffx.1.6.S1_at 12.02 12.69 0.947
XlAffx.1.5.S1_at 344.1 55.17 6.237
XlAffx.1.4.S1_at 11.86 13.59 0.873
XlAffx.1.3.S1_at 23 13.7 1.679
XlAffx.1.2.S1_at 14.79 14.15 1.045
XlAffx.1.12.S1_at 20.7 15.96 1.297
XlAffx.1.11.S1_at 57.91 141 0.411
XlAffx.1.10.S1_at 29.29 21.6 1.356
XlAffx.1.1.S1_at 50.45 30.86 1.635
Xl.9998.2.S1_at 29.7 32.33 0.919
Xl.9998.2.S1_a_at 463.4 442.1 1.048
Xl.9998.1.A1_at 184 320.5 0.574
Xl.9997.1.A1_at 21.73 16.97 1.281
Xl.9996.1.A1_at 13.52 10.87 1.243

Total number of rows: 15611

Table truncated, full table size 522 Kbytes.




Supplementary file Size Download File type/resource
GSM99978.CEL.gz 3.3 Mb (ftp)(http) CEL

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