biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsDanielle Wenemosertranscription profiling by arraySchmidtea mediterraneaSchmidtea mediterraneahttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-36945Transcriptional profiling of Schmidtea mediterranea planarians that have been amputated transversely and left to regenerate for different time points (UNIRR); the same experiment was performed on irradiated - neoblast depleted animals (IRR). The purpose of this experiment was to identify transcriptional changes that are induced within the first 12h following amputation. In order to distinguish between gene expression changes in the differentiated tissue and the neoblasts, a second set of time course data was created from irradiated animals Two-color experiment, 3 replicates per condition (including 10 animals/replica)biostudies-arrayexpressLabeling - RNA was labeled using Perkin Elmer's ASAP labeling kitGrowth Protocol - Clone W4 Schmidtea mediterranea were kept at 20degree Celsius in Monbijou SaltsSample Processing - Animals were amputated 7 days following feeding and left to regenerate for indicated time points. Irradiated animals were amputated 5 days following irradiation (Cesium source - 6000rad)Nucleic Acid Extraction - Total RNA was extracted using TRIZOL according to manufacterer's instructionsHybridization - Agilent DNA microarray scannerMIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsDanielle WenemoserAssay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) IRR 30MIN =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) UNIRR 6H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) IRR 1H =Feature Extraction - Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile). Differential expression analysis was performed using a moderated t-test, as implemented in the limma package of Bioconductor, with P-value correction by false discovery rate.Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) IRR 3H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) IRR 6H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) IRR 12H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) UNIRR 1H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) UNIRR 3H =Image Adquisition - Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocolAssay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) UNIRR 12H =Assay Data Transformation - ID_REF = <br>VALUE = normalized average (3 replicates) log2 ratio (Cy5/Cy3) representing test/reference<br>p-value (fdr) UNIRR 30MIN =falseUnirradiated vs. irradiated wounded planariansTranscriptional profiling of Schmidtea mediterranea planarians that have been amputated transversely and left to regenerate for different time points (UNIRR); the same experiment was performed on irradiated - neoblast depleted animals (IRR). The purpose of this experiment was to identify transcriptional changes that are induced within the first 12h following amputation. In order to distinguish between gene expression changes in the differentiated tissue and the neoblasts, a second set of time course data was created from irradiated animals Two-color experiment, 3 replicates per condition (including 10 animals/replica)2012-04-29T00:00:00Z2023-08-21T07:29:36.617Z2022-03-14T20:30:38.346ZE-GEOD-36945GSE36945EFO_0002768