Renal Regeneration Group

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This document id a DRAFT attempt to describe an wholemount in situ experiment of the developing Urogenital Ridge (UGR) according to the MISFISHIE checklist using EMAGE1.1.2. We have attempted to highlight how the majority of the necessary information is captured in EMAGE. We have also identified some deficiencies and in most case we have been able to address them within the system . Experiment Design: Experiment type: Temporal and spatial profiling of SERPINE2 expression in the developing urogenital tract. Experimental factors: Time, sex, sample The total number of hybridizations performed in the experiment: Six UGRs (3 male, 3 female). URL: http://genex.hgu.mrc.ac.uk/Emage/database/intro.html Contact information: Name: Sean Grimmond, Institution: Institute of Molecular Bioscience, City: St Lucia, Zip: 4072, Country, Australia, Mailing address: IMB, Uni of QLD, St Lucia, QLD Australia, 4072. Telephone: 61 7 33463057, Email: s.grimmond@imb.uq.edu.au Observations: Experiment type and Experiment Factors are not currently recorded in a formal field. We have used the "additional info1 and additional info2" fields of Experimental Notes of EMAGE to store this data.. The contact info for both the Author of the submission and the Principal Investigator responsible for generating the data recorded in this manner. Specimens (BioMaterials) Samples origin: Mouse Urogenital Ridge: Includes metanephros, mesonephros and gonad Provider of sample: Sex: Male Developmental stage: Theiler stage 22, 13.5dpc post coitum Age: Strain: CD1 Genotype: wild type Disease state: normal Treatments: Nil Manipulation of specimens: Specimen Preparation (whole mount or sectioned whole mount). Fixation method (4% paraformaldehyde). Embedding process for sectioned entry (cryo-section) EMAGE captures all of the above apart from Sample origin. We have added this description to the "critical notes for interpreting results " field under specimen. Provider of sample is not listed. Disease state is not captured by EMAGE however "Genotype" is. Genotype is particularly important for model systems where transgenesis is often used. Sample manipulations are summarised in sample preparation, fixation, and if required embedding fields). Probe or antibody information: Probe name: uh86h05 Clone name: PN1 Accession number: AI115537 Level of characterisation of probe: Partially characterised Gene symbol: SERPINE2 Gene Name: Serine (or cysteine) proteinase inhibitor, clade E, member 2 Species from which probe was made: Mouse Strain: C3H/Hej Tissue: Mixture of male and female gonads and UGRs Developmental stage/age: 11.5-12.5dpc. EMAGE has expanded the options on the level characterisation of the probe used in the study. cDNA probes used in WMISH are often taken form existing EST collection and therefore are only characterised by terminal sequences of the insert. EMAGE captures accession number for any partially defined clone that fits this category. While the sequence is not attached for completely characterised genes, the co-ordinates of where it starts and stops on a reference sequence is defined. Staining protocols and parameters: 1 Number of detectable probes used:1 Probe type: RNA RNA type: Antisense Labelling method: Digoxigenin Visualisation method: Alkaline phosphatase + NBT/BCIP. Protocol: PMID:10888606 There is no formal field for pointing towards a source for detailed protocol in EMAGEs other than general definitions of the labelling and visualising method. There is a links page that allows one to append publication info and other database links to an entry. The type of link can be defined and we intend to use this to point toward protocols in the near future. Imaging data and parameters: Image acquisition parameters: Detection method: 35mm film Image magnification: Image acquisition protocol: Imaging hardware: Nikon Imaging software: Photoshop Image(s) : This is an area where we are capturing very little of the checklist data. We have used the "additional info3" in experimental notes to collect the information described above. Image acquisition protocols will be made available via the links page as described above. Image Characterizations: Structural unit ontology: http://genex.hgu.mrc.ac.uk/Databases/Anatomy/new/theiler21.shtml Hybridisation intensity scale: Strong, moderate, weak, possible, not detected, not tested Hybridisation characteristic scale: Homogenous, graded, regional, spotted, single cell, not applicable, no pattern Staining intensity: Strong Staining characteristics: Homogeneous Staining description: Staining notes: Expression strongest in the sex cords of the male gonad.