biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMayuko Hamadatranscription profiling by arrayCiona intestinalisCiona intestinalishttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-59280Microarray analysis indicated many changes in gene expression, including genes related the the Notch signaling system, during oral siphon regeneration in adult Ciona. Subsequent qPCR gene expression and inhibitor of experiments confirm a role of the Notch system, probably in the formation of a regeneration blastema. To identify the genes defferentially expressed in degenerating siphone, gene expressions in intact siphones and excised siphones (after 3 days, 6 days and 9 days) were examined.biostudies-arrayexpressLabeling - Cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.Hybridization - A set of fluorescently labeled cRNA targets (1.5ug for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.Growth Protocol - Animals were obtained by collection from marine environments nearly Woods Hole, MA., USASample Treatment - Regenerating oral siphons were compared to control siphons. For regenerating oral siphons, the entire siphon was removed from animals, and allowed to regenerate for 3, 6, or 9 days. After regeneration was complete, the regenerated siphons were removed from the animals and used for RNA extraction. For control animals, the entire oral siphon was removed and used for RNA.Nucleic Acid Extraction - Total RNA was extracted from five or six siphones and purified using RNAeasy micro kit (QIAGEN) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).Scaning - Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsSpela GorickiMayuko HamadaWilliam JefferyNori SatohMardi ByerlyData Transformation - The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the following analysis. ID_REF = VALUE = Normalized signal intensityfalseMicroarray Analysis Reveals a Role of the Notch System in Ciona Siphon RegenerationMicroarray analysis indicated many changes in gene expression, including genes related the the Notch signaling system, during oral siphon regeneration in adult Ciona. Subsequent qPCR gene expression and inhibitor of experiments confirm a role of the Notch system, probably in the formation of a regeneration blastema. To identify the genes defferentially expressed in degenerating siphone, gene expressions in intact siphones and excised siphones (after 3 days, 6 days and 9 days) were examined.2015-08-01T00:00:00Z2023-09-09T23:05:18.021Z2022-02-03T07:39:59.67ZE-GEOD-59280GSE59280EFO_0002768