Naming Xenopus transgenic lines and mutant lines: new rules

Naming Xenopus transgenic lines and mutant lines: new rules

Postby xenbase » 22 Oct 2015 11:02

Working guidelines for naming Xenopus transgenic lines and mutant lines

These working nomenclature guidelines were developed in consultation with the Xenopus stock centers, following best practices used by all other model organisms. Using standard nomenclature is critical to make your research accessible to the broad scientific community and to ensure consistency and provenance.

Note - I can not make text superscript here in Forums posts, but serial number and lab code at end of text is in superscript!!- so everything in RED is to be in superscript in your Tg names).

1. Transgenic Constructs: Overview

STANDARD Tg CONSTRUCT NAME

Tg(enhancer or promoter:ORF or gene symbol)#Lab code

Example: Tg(cryga:GFP)2Grngr
A gamma crystallin GFP construct from the Grainger Lab

Example: Tg(Rno.elas:DNthra-GFP)1Ryff
Construct with Rat elastase promoter driving dominant negative thyroid hormone receptor, from the Ryfell Lab.

• Brevity and clarity in the transgenic construct name are encouraged.
• Tg indicates transgene, and the entire construct name is italicized.
• The most salient features of the transgene should be described within parentheses/brackets, no spaces.
• List regulatory sequences to the left of colon ( : ) and coding sequences to right.
• Use the official gene symbol for Xenopus genes (e.g., tubb2b not NBT).
• Fluorescent proteins are capitalized or start with a capital letter (e.g., GFP, Katushka, Tomato)
• Fluorescent protein prefixes are in lower case (e.g., eGFP, mCherry) (do not underline).
• Hyphens ( – ) indicate fusion proteins (do not use equals sign = or double colons ::)
• Modified functionality (e.g., CA = constitutively active, DN = dominant negative) is indicated as prefix to gene symbol, (e.g., DNthra).
• If gene sequence(s) are from another species, precede gene symbol with 3-letter species code, and a period (eg., Dre.ins ; Hsa=human, Rno=rat, Dre=zebrafish, Mmu=mouse, Ssa=salmon, etc).
• Multiple cassettes are separated by a comma ( , ) (e.g, Tg(tubb2b:GFP,NBTtau:GFP)1Amaya
• Where one regulatory sequence drives more than one coding sequence, state regulatory sequence once and separate coding sequences with a comma (e.g, Tg(CMV:GFP,RFP)2Senk).
• Origin/source is identified with a serial number and ILAR lab code, in superscript, at end of name.
• Do not indicate the method used for transgenesis (e.g., sperm-mediated, pTrangenesis, REMI).
• Engineered sequences (e.g., GFP, Cre, rtTA, tetO) do not need foreign/bacterial species prefixes.
• Do not include the size of the promoter/enhancer cis-regulatory sequence in the Tg name, rather report this in the full description of the transgene in the publication and in Stock Center records.
• The full transgenic construct or line name should be included in the methods section. Once fully defined, it is acceptable to use an abbreviated name in the body of a manuscript. Example Tg(Rno.elas.DNthra-GFP)1Ryff could be simplified to Tg(elas:DNthra-GFP).

2. Transgenic Xenopus Lines: Overview

STANDARD Tg XENOPUS LINE NAME

Species.Tg(enhancer or promoter:ORF or gene symbol)[color=#FF4040]#Lab code[/color]

Example: Xtr.Tg(cryga:GFP)3NXR

A X. tropicalis Tg line carrying a gamma crystallin GFP construct, the 3rd line made by the NXR

Each maintained Tg Xenopus line is given an official, stable name that is based on the Tg construct(s) used, with the following additions:

• Species is indicated using a 3-letter code, followed by a period ( . ).
Xla is the abbreviation for X. laevis
Xtr is the abbreviation for X. tropicalis

• Each line should be fully described, including background strain, and generation number if known.
• When a sequence of the alternate Xenopus species is used i.e., a X. laevis line that carries a construct made with X. tropicalis sequence, indicate this within the cassette/construct name using the
3-letter abbreviation, as is done for other foreign genes.

Example: Xla.Tg(Xtr.shh:eGFP)2NXR
This Tg X. laevis line carries a X. tropicalis sequence for the sonic hedgehog gene cis-regulatory elements, driving enhanced GFP. The second line with this transgene established by the NXR.

3. Mutant Xenopus Lines: Overview

STANDARD MUTANT XENOPUS LINE NAME

Species.gene symbol or phenotype/mutation#Lab code

Example: Xla.apctm5Vlemx
The 5th mutant X. laevis line generated by TALEN targeted mutation of the adenomateous polyposis coli (apc) gene, from the Vleminckx lab.

• Each maintained mutant Xenopus line is given an official, stable name.
• Species is indicated using a 3-letter code, Xla or Xtr, followed by a period.
• The line is named after the location of the mutation, whether it is known (use a gene symbol) or unknown (use a described phenotype), in italics, with no spaces.
• The mutation type is indicated in superscript (e.g., tm=targeted mutation, ins=insertion m=mutation, del=deletion), followed by a serial number and ILAR lab code, also in superscript.

The Working Xenopus Transgenic & Mutant Nomenclature Guidelines will be available on Xenbase.
These working guidelines are under constant review.

Please address all comments or questions to Xenbase: xenbase@ucalgary.ca
Last Updated: 10/22/2015
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What are ILAR lab codes?

Postby xenbase » 22 Oct 2015 11:44

The source or lab of origin of Xenopus transgenic and mutant lines needs to be made obvious to the research community. The Institute for Laboratory Animal research maintains an online registry for unique lab codes. http://www.dels.nas.edu.ilar

These lab codes tell everyone who made the Tg or mutant line you are working with.

As there are a manageable number of Xenopus labs worldwide that are generating transgenics, we used longer ILAR Codes, which can be the entire surname ( eg., Amaya) or an abbreviated version of a longer surname, (eg., Kellr, Buchz, Mazab).

This will make it (almost) immediately obvious as to the lab source of each Tg line. The serial number is also important, and sometime lines are transient, others die off or are 'regenerated' from fresh crosses every few generations, and each would then be given a new higher serial number.

Importantly ILAR lab codes have to be unique, and not conflict with gene symbols ( check Xenbase!) or mutation abbreviations (such as tm, del, cre, etc), even if those are the PIs initials.

A current list of Xenopus labs generating and/or providing transgenic lines to the stock centers, and their lLAR lab codes are listed below. If you register your lab- let Xenbase know and we will add your code to this list.

● Amaya: Enrique Amaya, Manchester, UK (registered 10/8/14)
● Brown: Don Brown, Carnegie Institute, USA (registered 10/8/14)
● Buchz: Dan Buchholz, Univ. Cincinnati (registered 10/8/14)
● Exrc: European Xenopus Resource Center, Portsmouth, UK (registered 10/9/14)
● Gurdn: John Gurdon (registered 10/9/14)
● Green: Jeremy Green, London, (registered 10/9/14)
● Grngr: Robert Grainger (registered 10/9/14)
● Hank: James Hanken, Harvard (registered 9/3/14)
● Horb: Marko Horb, NXR (registered 10/9/14)
● Jmws: Jonathan M. W. Slack (registered 10/20/14)
● Jpsj: Jean-Pierre Saint-Jeannet, New York University. (registered 10/17/14)
● Kellr: Ray Keller, Univ. Virginia (registered 10/9/14)
● Khok:Mustafa Khokha, Yale School of Medicine (registered 10/9/14)
● Knox: Barry Knox, SUNY (registered 10/9/14)
● Krieg: Paul A Krieg, UA (registered 10/9/14)
● Mayor: Roberto Mayor, University College London (registered 10/9/14)
● Mazab: Andre Mazabraud, Orsey, France (registered 10/9/14)
● Mead: Paul Mead, St Jude Research Hospital. (registered 10/17/14)
● Mohun: Tim Mohun, NIMR, UK (registered 10/9/14)
● Nasco: NASCO Inc., Fort Atkinson, WI , USA (registered 10/17/14)
● Nxr: National Xenopus Resource, MBL, USA (registered 10/17/14)
● Papal: Nancy Papalopulu, Manchester UK ((registered 10/17/14)
● Patnt: Roger Patient, Oxford (registered 10/20/14)
● Pec: Peter Carmeliet (already registered at ILAR- tho institution has changed)
● Rmh: Richard Harland, UC Berkeley (registered at ILAR 2002-07-15)
● Ryffl: Gerhart Ryffel (registered 10/17/14)
● Senk: Sabine Senkel (ex Ryffel lab) (registered 10/17/14)
● Tamur: Koji Tamura, Sendai, Japan (registered 10/17/14)
● Ueno: Naoto Ueno, Okazaki, Japan (registered 10/17/14)
● Walfd: John Wallingford, Univ. Texas at Austin. (registered 10/17/14)
● Vlemx: Kris Vleminckx (Vlem in use at ILAR) (registered 10/17/14)
● Zorn: Aaron Zorn, CCHMC (registered at ILAR)
● Zimml: Lyle Zimmerman, UK (registered 10/17/14)
● Zuber: Michael Zuber, Upstate Med. University, NY. ( registered 9/2/14)
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Re: Naming Xenopus transgenic lines and mutant lines: new ru

Postby MandySwift » 22 Oct 2015 21:47

Naming professionally is the first step to access to the professional community. I bookmarked it for recommendation.
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