biostudies-arrayexpressMansi SrivastavaSchmidtea mediterraneahttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-31618The goal of this study was to identify genes that were expressed in the protonephridial system. Because Six1/2(RNAi) and POU2/3(RNAi) animals lose the tubules, flame cells and accessory cells, these animals were expected to show decreased levels of the genes expressed in the nephridial system relative to control RNAi animals. RNA from Six1/2(RNAi) and POU2/3(RNAi) animals was harvested with Trizol at days 8 and 15 after RNAi initiation for the former and days 15 and 21 for the latter. Three biological replicates were used. RNA from the four samples were competetively hybridized on a microarray with RNA from control RNAi animals of the corresponding days.biostudies-arrayexpressSample Processing - RNA from Six1/2(RNAi) and POU2/3(RNAi) animals was harvested at days 8 and 15 after RNAi initiation for the former and days 15 and 21 for the latter. RNA from control RNAi animals was harvested at days 8, 15, and 21.Nucleic Acid Extraction - RNA was extracted using the standard Trizol method.Growth Protocol - Animals were maintained at 20 degrees celsius.Labeling - Cy3 and Cy5-labeled cRNA was prepared using a QuickAmp labeling kit (Agilent) starting with 1μg total RNAHybridization - Agilent custom planarian 4x44,000 expression arrays were hybridized according manufacturer instructions and scanned using an Agilent DNA microarray scanner.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsFeature Extraction - Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile).Assay Data Transformation - ID_REF = <br>VALUE = log2 (RNAi / control) after loess and Aquantile normalizationImage Adquisition - Array images were quantified and statistical significance of differential expression was calculated using Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocol.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsPlanarians can regenerate any missing body part, requiring mechanisms for the production of organ systems in the adult, including their prominent tubule-based filtration excretory system called protonephridia. Here, we identify a set of genes, Six1/2-2, POU2/3, hunchback, Eya and Sall, that encode transcription regulatory proteins that are required for planarian protonephridia regeneration. During regeneration, planarian stem cells are induced to form a cell population in regeneration blastemas expressing Six1/2-2, POU2/3, Eya, Sall and Osr that is required for excretory system formation. POU2/3 and Six1/2-2 are essential for these precursor cells to form. Eya, Six1/2-2, Sall, Osr and POU2/3-related genes are required for vertebrate kidney development. We determined that planarian and vertebrate excretory cells express homologous proteins involved in reabsorption and waste modification. Furthermore, we identified novel nephridia genes. Our results identify a transcriptional program and cellular mechanisms for the regeneration of an excretory organ and suggest that metazoan excretory systems are regulated by genetic programs that share a common evolutionary origin.transcription profiling by arraySchmidtea mediterraneaA regulatory program for excretory system regeneration in planarians.Scimone ML, Srivastava M, Bell GW, Reddien PWPeter ReddienGeorge BellMansi SrivastavaM ScimonefalseGene expression profiles of Six1/2-1(RNAi) animals and POU2/3(RNAi) animalsThe goal of this study was to identify genes that were expressed in the protonephridial system. Because Six1/2(RNAi) and POU2/3(RNAi) animals lose the tubules, flame cells and accessory cells, these animals were expected to show decreased levels of the genes expressed in the nephridial system relative to control RNAi animals. RNA from Six1/2(RNAi) and POU2/3(RNAi) animals was harvested with Trizol at days 8 and 15 after RNAi initiation for the former and days 15 and 21 for the latter. Three biological replicates were used. RNA from the four samples were competetively hybridized on a microarray with RNA from control RNAi animals of the corresponding days.2011-11-28T00:00:00Z2023-08-19T00:35:58.219Z2022-02-04T01:05:46.258ZE-GEOD-31618GSE3161821937596EFO_000276810.1242/dev.068098