Doing nice science will depend on teamwork, whether or not that is inside the lab or in collaboration with different labs. Nonetheless, generally the sources that assist our work may be missed. Our ‘Featured useful resource’ collection goals to shine a light-weight on these unsung heroes of the science world. On this put up, the workforce behind Xenbase introduces the important thing options on the database and suggests how the neighborhood can contribute to the mission of Xenbase.

When was the Xenbase established and what are its goals?

Xenbase was the brainchild of Peter Vize. Initially conceived of as a web based catalog of gene expression photos within the late 1990’s, the golden age of gene expression screens, the place basically each lab was producing 100s of photos of gene expression all through embryonic improvement, but these photos have been sitting on a lab pc not being shared or annotated in any significant method. Peter noticed {that a} useful resource to share this data would have a huge effect to chop down on wasted time, effort and sources (i.e. save funding {dollars}).

The primary iteration of Xenbase was launched in 2000, and by 2002, Xenopus tropicalis was earmarked for complete genome sequencing by the Joint Genome Institute (JGI), so the imaginative and prescient for Xenbase rapidly morphed into a much bigger undertaking: built-in genomics and gene expression on a completely searchable database.  

The preliminary problem confronted when constructing Xenbase was to mix the analysis from two  Xenopus species utilized in complementary however (virtually) non-overlapping fields of cell biology and embryology. Xenopus laevis had a protracted historical past as a lab frog, with a long time of literature overlaying organogenesis, cell destiny maps and cell biology, gene perform and gene expression, however as a polyploid of hybrid origin, the genome hadn’t been sequenced (and was a good distance off). As compared, the diploid Xenopus tropicalis genome was being sequenced and this smaller frog was being adopted for illness modeling, and had plenty of EST information, however there wasn’t numerous different organic information for ‘trops’. It was clear each Xenopus species have been in want of database assist, and the Xenbase founders met that problem head on, largely by studying from the already established MODs like MGI (mouse) and Zfin (zebrafish). Xenbase was the primary MOD to assist two species and basically three genomes (i.e.,  X. tropicalis and the two subgenomes of X. laevis). 

The overarching purpose of Xenbase is to concurrently assist labs utilizing Xenopus as a analysis mannequin, share the genomes and bioinformatic details about genes/proteins, codify the outcomes of the analysis through deep and professional curation and thus assist fundamental and utilized science to speed up discovery. Having all the info about Xenopus in a single place has big benefits. Inside just a few years sufficient folks discovered that ‘what works for X. laevis, works for X. tropicalis’, e.g., gene expression in X. laevis and X. tropicalis are practically at all times the identical (or very related), so the identical reagents (reminiscent of MOs, gRNAs, and antibodies) can be utilized in each species.

Who’re the folks behind the useful resource/ who runs the useful resource?

Xenbase has two groups and two efficiency websites. The curation workforce is predicated on the Division of Developmental Biology, at Cincinnati Kids’s in Ohio, USA, led by Prof. Aaron Zorn. We at the moment have 4 curators and bioinformatician/genome analyst within the Cincinnati-based curation workforce: VG Ponferrada, Malcolm Fisher, Andrew Bell, Christina James-Zorn, and Ngoc Ly. We even have a scholar assistant,  Nguyen Thuy Vy Ngo, who helps triage the brand new literature. The event workforce, headed by Prof. Peter Vize, is predicated within the Division of Organic Sciences on the College of Calgary, in Alberta, Canada. The Calgary improvement workforce is  led by Kamran Karimi, with assist of the database architect Troy Pells, and the Bioinformatian/genome specialist, Vaneet Lotay, who’re additional supported by software program builders, Joe Wang and Stan Chu. We additionally share code and improvement with our sister-website, Echinobase, so the Calgary based mostly workforce is ably supported by Brad Arshinoff and Sergei Agalakov.

What instruments/sources can be found for researchers?  

Xenbase is a gene-centric database, with a single ‘umbrella’ gene web page exhibiting the X. tropicalis gene and the 2 X. laevis paralogs, typical gene expression photos at totally different embryonic levels (when obtainable) and different information reminiscent of reagents, orthologs and  OMIM/DO related illnesses (and lots of extra hyperlinks to related information). Every gene web page then has a collection of tabs, like a folder, beginning with the Expression (all photos in database with expression), Phenotypes (all experiments that both manipulate or assay the gene(s)) and Literature (all literature that cite the gene(s)). The following set of tabs cowl GO phrases, Nucleotides, Proteins and Interactants, which collate annotations and/or accession in regards to the genes/protein merchandise with information pulled in from, and linked to, quite a few trusted databases (NCBI, ENSEMBL, UniProt, InterPro/TrEMBL, GO and IntAct). 

Xenbase has numerous instruments which might be extensively used. The genome viewer JBrowse has the newest v10 Xenopus genomes, and an enormous number of different helpful tracks reminiscent of CRISPR-Scan predicted information RNAs to assist design your mutant traces, a morpholino monitor, and an infinite variety of RNA-seq and ChIP-seq tracks, tracks for histone marks and transcriptions issue binding websites, and lots of extra.

The opposite information module which is de facto cool is our GEO information ( accessed through Expression Menu/GEO information @ Xenbase). We took the publicly submitted excessive throughput sequence information from the NCBI’s GEO database, manually curated the supporting metadata after which we processed it via a pipeline that ‘harmonizes’ the totally different research (see Fortriede et al 2020 for all the main points). Though the info  are from totally different research, researchers can view all of this information in a standardized format, aligned to the newest v10 genomes and through warmth maps that visualize DEGs (differentially expressed genes). As well as, now we have 1000’s of ‘computational’ gene expression phenotype statements from these experiments, the place we generate statements within the readable format, e.g., “manipulation X will increase/decreases the expression of gene Y in tissue Z at NF stage #”, all linked to genes, literature and the unique GEO information.  These ‘gene expression phenotypes’ are most simply returned through our Phenotypes search (e.g., seek for six1 . We hope this mass of curated RANSeq and ChIPSeq information will assist inform GRNs, and let researchers see all the outcomes from different peoples experiments that pertain to their gene of curiosity.  

Any hidden gems, options which might be new, or that researchers is perhaps much less conscious of?

Two new options we’re tremendous pleased with are the open entry drawings of Xenopus embryonic levels (the Regular desk) by Natalya Zahn and the accompanying Landmarks Desk. The Zahn drawings, that are in the identical fashion because the traditional 1950’s Nieuwkoop and Faber drawings, are open entry and canopy extra views- particularly anterior and ventral views. Additionally, the accompanying Staging Landmarks Desk that we constructed to assist researchers within the moist lab stage embryos additionally contains inner developmental milestones and gene markers. We hope each of those sources develop into indispensable for college programs, in moist labs and embryology programs. 

I feel the Xenopus Neighborhood pages, which embrace private profiles and lab pages, are each nice methods to advertise one’s analysis and entice college students and collaborators.  I like to recommend PIs appoint a trainee within the lab to ensure their Xenbase profiles & Lab web page is up-to-date, and that each one members of the Lab have a profile to report their analysis pursuits and an inventory of their publications. The Xenbase Jobs Board can be obtainable to put up any open positions, from graduate college students to postdocs and group leaders and  division chairs.

We’re continuously working to maintain the knowledge on Xenbase updated and synchronized with the opposite main databases and repositories, and we just lately joined the Alliance of Genome Assets. By collating information from various mannequin organisms (worm, yeast, fly, mice, frogs, rats and fish) the Alliance goals to enhance the understanding of the genetic and genomic foundation of human biology, well being and illness. Frogs have performed, and proceed to play, an necessary a part of that discovery course of.

How can the neighborhood contribute?

The only best method for researchers to contribute to the mission of Xenbase, is to decide on open entry (OA) choices to publish their analysis, every time potential. When information is locked up behind a paywall, we actually can’t see it, so we are able to’t curate it. If we don’t curate the info, the outcomes develop into basically invisible over time, and its quick and long run  impression is tremendously lowered. Accessible information turns into curated information, which is discoverable and will likely be cited extra too. Uncurated information is definitely missed. 

One other method folks can contribute is to ship us their photos of novel gene expression, particularly photos of levels past what’s included of their papers. As a substitute of being saved in an inaccessible folder on a lab pc, ship them to Xenbase and share them with the world!. All neighborhood submitted photos are absolutely attributed to the folks and that lab that makes them!

We additionally run a assist desk: xenbase@cchmc.org. Contact us anytime with neighborhood submissions, questions, suggestions, considerations, troubleshooting assist and your concepts to make Xenbase an excellent  higher, extra helpful useful resource.

The place does funding come from?

Xenbase is at the moment supported by the Eunice Kennedy Shriver Nationwide Institute of Youngster Well being and Human Improvement (NICHD). Earlier monetary assist additionally got here from the Nationwide Science Basis (NSF), the Wellcome Belief (UK), the BBSRC (UK), the Alberta Community for Proteomics Innovation (ANPI).

If cash was no object, what would you want so as to add to Xenbase?

We’re trying into some new nice instruments together with updating to JBrowse2 (to permit viewing a number of genomes without delay), and new information graphics to indicate/assess synteny throughout Xenopus genomes, and supporting single-cell information. We’d additionally wish to develop extra academic sources to assist college students and instructing labs, together with a excessive tech histology or a 3D atlas of Xenopus from embryos to adults, extra anatomy atlas modules, maybe together with digital dissection of grownup Xenopus frogs. We wish to fund extra illustrations of Xenopus improvement, to essentially fill within the Regular Desk we printed in Zahn et al  2022 in Improvement! We’d additionally like to get films (that are increasingly frequent in publications) embedded on the articles pages.  All of those concepts have been floated, so we’ll see what we are able to get executed.

References

Fortriede JD, Pells TJ, Chu S, Chaturvedi P, Wang D, Fisher ME, James-Zorn C, Wang Y, Nenni MJ, Burns KA, Lotay VS, Ponferrada VG, Karimi Okay, Zorn AM, Vize PD, Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq information in a mannequin organism database, Nucleic Acids Res., Quantity 48, Problem D1, Pages D776-D782, doi:10.1093/nar/gkz933

Zahn N, James-Zorn C, Ponferrada VG, Adams DS, Grzymkowski J, Buchholz DR, Nascone-Yoder NM, Horb M, Moody SA, Vize PD, Zorn AM, Regular Desk of Xenopus improvement: a brand new graphical useful resource, Improvement, 2022 Jul 15;149(14):dev200356, doi:10.1242/dev.200356

Fisher M, James-Zorn C, Ponferrada V, Bell AJ, Sundararaj N, Segerdell E, Chaturvedi P, Bayyari N, Chu S, Pells T, Lotay V, Agalakov S, Wang DZ, Arshinoff BI, Foley S, Karimi Okay, Vize PD, Zorn AM. Xenbase: key options and sources of the Xenopus mannequin organism knowledgebase. Genetics. 2023 Might 4;224(1):iyad018. doi: 10.1093/genetics/iyad018. PMID: 36755307; PMCID: PMC10158840.

(No Scores But)
Loading…