{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alejandro Sánchez Alvarado"],"organism":["Schmidtea mediterranea"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-11503"],"description":["Throughout adulthood, the replacement of cells lost to physiological turnover or injury in planarians is sustained by the proliferation and differentiation of adult stem cells known as neoblasts.  Because neoblasts are the only known mitotic cells in asexual planarians, they can be efficiently eliminated by irradiation without significantly affecting post-mitotic differentiated cells.  We uncovered a cohort of transcripts specific to the stem cells and their division progeny by defining the expression profiles of wild type and irradiated animals at different time points after irradiation.   RNA from wild type animals, or from animals 24 hours or seven days after exposure to radiation, were compared to a common reference."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - The hybridization was carried out overnight at 42 degrees Celcius in a humid chamber","Labeling - 1ug of aRNA was used as a template and random nonamers were used to prime first strand cDNA synthesis using Superscript II in the presence of Cy5-dCTP.  The resulting cDNA/RNA hybrid was treated with 0.25 M NaOH to hydrolyze RNA.  The first strand cDNA molecule was then purified using a Qiagen QIAquick PCR purification kit to remove unincorporated fluorescent nucleotides and primers.  The purified labeled sample was subsequently concentrated through speedvac centrifugation and resuspended in Ambion SlideHyb Glass Array Hyb Buffer#1.","Nucleic Acid Extraction - Total RNA was extracted using Trizol reagent (Invitrogen),  DNAse I treated (Qiagen) at room temperature for 15min, and cleaned up to remove any remaining organics or contaminants using Qiagen RNAeasy spin columns. RNA quality was assessed using an Agilent Bioanalyzer and amplified using the Ambion MessageAmp RNA amplication kit. The quality of the resulting amplified RNA (aRNA) was examined using the Agilent Bioanalyzer and quantified using a Nanodrop spectrophotometer.","Labeling - 1ug of aRNA was used as a template and random nonamers were used to prime first strand cDNA synthesis using Superscript II in the presence of Cy3-dCTP.  The resulting cDNA/RNA hybrid was treated with 0.25 M NaOH to hydrolyze RNA.  The first strand cDNA molecule was then purified using a Qiagen QIAquick PCR purification kit to remove unincorporated fluorescent nucleotides and primers.  The purified labeled sample was subsequently concentrated through speedvac centrifugation and resuspended in Ambion SlideHyb Glass Array Hyb Buffer#1."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Image Adquisition - The hybridized microarray slides were scanned using an Axon GenePix 4000B Scanner at a 10um/pixel resolution.","Assay Data Transformation - ID_REF = <br>VALUE = Normalized Log Ratio.","Feature Extraction - The Cy3(exp)/Cy5(ref) ratio was calculated using Microsoft Excel, the data was mean scale normalized and log 2 transformed using Spotfire Decision Site Software for Functional Genomics (v7.0)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["In adult planarians, the replacement of cells lost to physiological turnover or injury is sustained by the proliferation and differentiation of stem cells known as neoblasts. Neoblast lineage relationships and the molecular changes that take place during differentiation into the appropriate cell types are poorly understood. Here we report the identification and characterization of a cohort of genes specifically expressed in neoblasts and their descendants. We find that genes with severely downregulated expression after irradiation molecularly define at least three discrete subpopulations of cells. Simultaneous BrdU labeling and in situ hybridization experiments in intact and regenerating animals indicate that these cell subpopulations are related by lineage. Our data demonstrate not only the ability to measure and study the in vivo population dynamics of adult stem cells during tissue homeostasis and regeneration, but also the utility of studies in planarians to broadly inform stem cell biology in adult organisms."],"study_type":["transcription profiling by array"],"species":["Schmidtea mediterranea"],"pubmed_title":["Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea."],"pubmed_authors":["Alejandro Sánchez Alvarado","George Eisenhoffer","Hara Kang","Eisenhoffer GT, Kang H, Sánchez Alvarado A"],"additional_accession":[]},"is_claimable":false,"name":"Expression Profiles of Planarain Stem Cells and their Immediate Division Progeny","description":"Throughout adulthood, the replacement of cells lost to physiological turnover or injury in planarians is sustained by the proliferation and differentiation of adult stem cells known as neoblasts.  Because neoblasts are the only known mitotic cells in asexual planarians, they can be efficiently eliminated by irradiation without significantly affecting post-mitotic differentiated cells.  We uncovered a cohort of transcripts specific to the stem cells and their division progeny by defining the expression profiles of wild type and irradiated animals at different time points after irradiation.   RNA from wild type animals, or from animals 24 hours or seven days after exposure to radiation, were compared to a common reference.","dates":{"release":"2008-09-12T00:00:00Z","modification":"2023-08-01T09:43:26.273Z","creation":"2021-10-13T12:30:19Z"},"accession":"E-GEOD-11503","cross_references":{"GEO":["GSE11503"],"pubmed":["18786419"],"EFO":["EFO_0002768"]}}