User Guide

Not sure what resource you need and what it does?

This table briefly summarizes all resource pages in Planosphere. More information on how to use each resource can be found on the linked resource page.

In addition you can find video tutorials on our tutorials page.

Tool Name What is it? Why? Who is it for? Where else is this resource used (Planosphere and Beyond)? Publication
Worm Request Information about and requesting Smed animals Want to start working with Smed? Start here. Qualified Researchers and postsecondary educators    
Cutting Class A Planarian Educational Resource Want to do some experiments with planarians in your classroom or lab? We've got you covered here. Elementary through Undergraduate   Accorsi et al., 2018
Crash Course in Smed Embryogenesis Details main information about Smed embryogensis from Davies et al., 2017 Want to know the basics of Smed embryogensis? Start here. Anyone.   Davies et al., 2017
Embryogenesis Protocols Details protocols used for Smed embryos Want to start working with Smed embryos? Great- here's some how to get started. Researchers   Davies et al., 2017
Molecular Staging Resource Definitions of embryogenesis stages with bulk RNASeq data and individual stage pages including related data and PLANA ontology information Want to know about Smed's embryo stages? Use this. Researchers   Davies et al., 2017
Molecular Fate Mapping Atlas Webpages detailing embryonic tissue types and development of the definitive organ systems. Each page contains an overview,associated supplemental figures, in situ hybridization images and sequences for transcripts validated by WISH. Want to know about tissues and cell types in embryogensis? Start here. Researchers   Davies et al., 2017
Heat Map Generates heat maps from single embryo RNASeq data. Want to know expression levels of your favorite transcript during embryogeneis? This does that. Researchers   Davies et al., 2017
Neoblast Clusters view expression of a transcript of interest in the Neoblast Clusters from Zeng et al.,2018 Wondering where your favorite transcripts map to in sorted, single cell neoblast data? Use this. Researchers   Zeng et al.,2018
Rosetta Stone Transcript Mapper Maps transcripts from many (not all) transcriptomes to and from each other. Got a dd_v6 transcript but need it in SMED3##### format, or want SMED3#### in SMEST? Great this tool does that! Researchers   Nowotarski et al., 2020 preprint
Gene Search Search for transcripts by ID, experimentally determined tissue/pattern, homologs (best BLAST hits), GO terms, and PFAM protein domain terms. Have a transcript and want to know homologs, GO Terms, tissue expression and protein domains? This tool does a lot! Take note the search is cumulative. Researchers    
PLANA Anatomy Ontology Formal vocabulary and relational network of Smed anatomical terms for organizing data and tool building Want to know about anatomy terms used in Smed? Start learning here!
Want to organize anatomical data for Smed by building your own tool? Great use PLANA!
Researchers PAGE Search by Location, PAGE Search by Transcript, PAGE Search by Publication,Molecular Fate Atlas, Gene Search, PlanGexQ Nowotarski et al., 2021
PLANA Query Search relationships and content of PLANA Want to know all anatomical terms that are part of the head? This will do that. Researchers   Nowotarski et al., 2021
PAGE Search by Term Search curated expression data from publications 2005-2019 by PLANA anatomy ontology location. Visit Tutorial. Want to know all the transcripts noted as being expressed in the head by WISH? How about all the transcripts in the eye by FISH? Or transcripts in the neoblast category by single cell? This tool does that. Researchers Direct anatomical terms (no synonyms or relationships) are used in Gene Search location search. Nowotarski et al., 2021
PAGE Search by Transcript Search curated expression data relating transcripts to anatomical locations from publications between 2005 and 2019 by transcript Want to know where your list of candidate transcripts have been marked as being expressed? Start here. Researchers Used in individual transcript pages Nowotarski et al., 2021
PAGE Search by Publication Search curated expression data from publications 2005-2019 by PLANA anatomy ontology location Want to know all the transcripts that were noted as being expressed somewhere by some method in a paper? Plug in a pmid here and get rolling. Researchers   Nowotarski et al., 2021
BLAST BLAST interface Want to find homologs with nucleotide sequence, translated nucleotide sequence or amino acids? This does that. Secondary Educators Researchers    
SMEDGD Genome Browser for the sexual planarian, Schmidtea mediterranea Version=SemdSxl_v31 Want to see the gene structure of a gene in the first assembly, this is where you can do that! Researchers Robb et al., 2015
Analysis A listing and search for all analyses performed on the SMED3##### transcripts that also appears on the transcript pages.