7 protocols
AccessionType
normalization data transformation protocol
Data Processing/Normalization:RMA normalization ( in Partek Genomics Suite)
array scanning and feature extraction protocol
Image Analysis Software: GCOS ; Image Analysis Algorithm: GCOS
array scanning and feature extraction protocol
Scanner Hardware: Affymetrix GeneChip Scanner 3000 ; Scanning Software: GCOS
hybridization protocol
Washing/Staining Procedure: FS450_0007 ; Washing/Staining Instrumentation: Fluidics Station 450
labelling protocol
cDNA Synthesis: MessageAmp Premier RNA Amplification Kit ; cDNA Cleanup: MessageAmp Premier RNA Amplification Kit ; cRNA Synthesis: MessageAmp Premier RNA Amplification Kit ; cRNA Cleanup: MessageAmp Premier RNA Amplification Kit; Spike Target Element: mRNA+Target ; Spiking Control: Affymetrix standard ; Dye: biotin
sample collection protocol
We designed the Atoh7 and Hes5.3 siRNAs. siRNA synthesis was performed under contract with Thermo Scientific Dharmacon. siSTABLE nontargeting siRNAs are from Thermo Scientific Dharmacon. Chick embryos from a White Leghorn strain were staged according to Hamburger and Hamilton (1951). Embryonic eyes were positioned in an electroporation chamber (BT 640, BTX, Genetronics) filled with 0.1 ml PBS (pH 7.4) containing reporter plasmids (0.1–0.5 μg/μl each) with or without siRNAs (0.1 μg/μl each). Electroporation consisted in five 12.5 V/cm pulses of 50 ms duration spaced 1 second apart.
nucleic acid extraction protocol
Nucleic Acid Extraction Method: Trizol (Invitrogen) ; Nucleic Acid Type: total_RNA ; Amplification Method: MessageAmp