Submitting Expression data for a micropublication

 

What is a micropublication

Not all funded research ends up being published. Frequently, smaller pieces of information that for a number of reasons are not incorporated in research articles are left forever in a lab book. These smaller pieces of information are often high quality novel findings and could be shared with the scientific community upon quick stamp approval from an expert in the field.

If you have unpublished reporter gene fusion localization data you can submit it through the micropublication form.

 

Filling out the form

Mandatory fields are marked with a red M. If you fail to provide mandatory information the form will not be sent.

 

Start out by providing your Name and e-mail address.

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Your Name: This field auto completes on persons registered in WormBase –as WBPerson IDs. If you do not have a WBPerson ID please contact WormBase to have one assigned. After the first submission, the form will recognize your computer via the IP address so you do not have to re-enter the information for subsequent submissions.

 

Co-authors- Since the form is designed to support a micropublication model, you could add the name of other contributors. It works similarly as listing co-authors of a publication. The co-author field also auto completes on persons registered in WormBase –as WBPerson IDs. You can add more than one co-author. As soon as you will input the first name, a new box will appear.

 

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Species- Start typing the name of the species and select your choice from the dropdown. You can enter only one species per submission.

A full list of supported Species list will appear by clicking the Question mark next to the Species tag.

 

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If you want to submit data for a species that is not in the list, please contact WormBase.

 

Choose an image- Each submission should have an image depicting the localization of a reporter gene fusion. The image should be high resolution as it will be used as evidence of expression and should be unequivocally interpreted by a reviewer.  When necessary, arrows and labels to facilitate interpretation should be added. You can submit more than one image for one specific expression pattern by creating a panel as if you were generating a figure for a research article. Remember that the reporter should be the same for all images.

 

Example:

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From Rhiner et al., 2005

Figure 5. SDN-1 expression in neural and hypodermal tissue. (A-F) Expression pattern of the translational Psdn-1::sdn-1::gfp reporter. (A') SDN-1::GFP is broadly expressed in the three-fold embryo, and is particularly strong in the pharynx (pha) and the motoneurons (mn) of the VNC. (B) In L1 larvae, expression is seen in the VNC (arrow) and around the seam cells (arrowhead). SDN-1::GFP expression is also visible in embryonic DD commissures (out of focal plane in B). (C) During later larval stages, SDN-1::GFP is predominantly found in the nervous system. The nerve ring (nr), and the VNC motoneurons and commissures (com) show the highest expression levels (arrowheads; B,F), but the reporter is also present in touch neurons (arrow; E) and other sensory neurons in the head (arrow; F). SDN-1::GFP can also be detected at a lower level in the body wall hypodermis (arrowhead; D); expression is stronger in hypodermal tissue in the tail (arrow; C).  

 

Expression pattern for Gene- In this field you should select the gene you are describing the expression of. Once you start typing the name of the gene of interest, the list will auto complete on all existing genes in WormBase. If a locus has no gene name assigned yet, you can select a sequence identifier, e.g. C10F3.12. You can select one gene per submission.

 

Existing OR New Transgene-   You should select either Existing transgene OR New Transgene.

 

Existing Transgene- If you click on Existing transgene you will be able to select from a pre-compiled list of transgenes that have already been described in the literature. What you need to do is to select the transgene of interest and then move to the Ò Where and when did you observe expression?Ó section.

 

For colocalization experiments: you can add any additional transgene that you used for verifying cell or cellular component identity. See example below:

 

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New Transgene- If you have generated a new construct then you will need to provide specific information about it. Not all fields are mandatory but try to be as comprehensive as you can. Below is a list of the different fields:

 

Genotype- enter a genotype summary that will include the gene and reporter, for example lin-3::GFP.

Construction Details- In this box you should enter a descriptive text that will provide information on how the construct was generated, including restriction sites, plasmid information and everything that pertains cloning details. Example: [pkd-2::GFP] translational fusion. The pkd-2-GFP plasmid was made using plasmid pPD95.75 as parent vector, and a fusion of a long range PCR fragment of genomic pkd-2 (promoter and 5Õ-end) with a 3Õ-end fragment derived from yk219e1 to produce a 7,153-kb fusion containing the full-length pkd-2 gene.

DNA sequence- paste here the sequence used to drive the reporter, excluding the reporter sequence itself or the backbone vector sequence. For example, if you used 2.2-kb putative promoter fragment of lin-3 you should paste the 2.2kb sequence. In this way the expression object can be directly mapped to the genome browser and be discoverable also from there.

3ÕUTR- If you included in your construct the 3ÕUTR of another gene, please specify here which gene.

Reporter- specify which reporter you used- e.g. GFP, YFP, mCherry. A full list of reporters will appear by clicking the Question mark next to the Reporter tag. If you want to submit data for a reporter that is not in the list, please contact WormBase.

Backbone Vector- select here the backbone vector into which you cloned your insert. Fusion Type- Select a value from the pre-canned ones. A full list of Fusion types will appear by clicking the Question mark next to the Fusion Type tag.

Laboratory- Start typing the PI name and select an entry from the list.

Public Name- Please assign a name to your construct e.g. otEx103, utIs18. More information can be found in the userguide by clicking here.

Construct Comments- Write here any information you think is important to add and does not seem to fit in any other field.

Strain- We aim to capture gene expression in wild type background so most of the times the strain should be N2 but if you conducted a rescue experiment, please select the strain you used for your study.

Conijected with- you can provide here the information on any additional transgene that was used in the study. For example, a transgene used to resolve cell identity in a colocalization study.

Injection Concentration- type here the concentration you used to inject the worms. E.g.: 50 ng/ul.

Integrated by- select an integration method. A full list of integration methods will appear by clicking the Question mark next to the Integrated by tag.

 

 

Where and when did you observe expression?

In this section of the form you should provide information about the spatio-temporal localization of the gene product.

The fields are marked with a green A as a successful submission requires you to fill in information in at least one of those fields.

 

You have the possibility to describe a complex pattern within this section by correctly using the different fields. We will provide below few examples that will guide you through the process.

 

Examples for the Certainly expressed box:

 

1) Gene A (e.g. lin-3) is certainly expressed in cell X (e.g. Anchor Cell): select cell X (Anchor Cell) from the ÔCertainly expressed inÕ field.

 

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2) Gene A (e.g. lin-3) is certainly expressed in cell X (e.g. Anchor Cell) during developmental stage 1 (e.g. L3 larva): select cell X (e.g. Anchor Cell) from the ÔCertainly expressed inÕ field and developmental stage 1 (e.g. L3 larva) in the ÔDuringÕ field right next to it.

 

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3) Gene A is certainly expressed in cell X during developmental stage 1 and 2: select cell X from the the ÔCertainly expressed inÕ field and developmental stage 1 in the ÔDuringÕ field right next to it.

A new Certainly Expressed in box will appear -> select again cell X from the ÔCertainly expressed inÕ field and developmental stage 2 in the ÔDuringÕ field right next to it.

 

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4) Gene A is certainly expressed in cell X (Anchor Cell) and tissue Y (pharynx) during developmental stage 1: select cell X from the Certainly expressed field and developmental stage 1 in the ÔDuringÕ field right next to it.

A new Certainly Expressed in box will appear -> select tissue Y from the ÔCertainly expressed inÕ field and developmental stage 1 in the ÔDuringÕ field right next to it.

                                                                                                    

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5) Gene A is certainly expressed in Developmental stage 1: select Developmental stage 1 in the ÔDuringÕ field next to the ÔCertainly Expressed inÕ field.

 

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The same rules apply to the ÔPartially Expressed inÕ, ÔPossibly Expressed inÕ and ÔNot Expressed inÕ boxes.

 

Remember that :

 

Partially expressed in means: Gene A was observed to be expressed in some cells of a group of cells that include Y. Example 1: "Expressed in 4-5 pairs of amphid neurons." You should select amphid neuron in the ÕPartially Expressed inÕ box.
Example 2: "Expressed in the anterior intestine." Select Intestine in the ÕPartially Expressed inÕ box.

 

Possibly Expressed in means: Gene A was sometimes observed to be expressed in cell Y OR Gene A was observed to be expressed in a cell that could be Y. Example 1: "Occasional expression of DDL-2 in one adult intestinal cell." You should select intestinal cell in the ÕPossibly expressed inÕ box. Example 2: "Expression was observed less frequently in the PVPL/R interneurons." You should select PVPL and PVPR in the ÕPossibly expressed inÕ box.

 

The ÔNot expressed inÕ field should contain information about where the gene product is Certainly NOT expressed in.

 

Subcellular localization information should be captured in the ÔSubcellular localizationÕ field. For example, if the protein was observed in the cytoplasm, you should select cytoplasm in this field. If you have also spatial information –i.e. the cell or tissue where it was observed to be in the cytoplasm, please enter it in the ÔIn tissue/cellÕ field next to it. In this way cellular component and anatomical dependencies will be maintained.

 

Lastly in the Pattern Description field you should provide a most comprehensive description of what you observed as if you were writing a paragraph for gene expression for a research article. In case you used arrows and labels in the image you provided, please explain what they are pointing to.

 

An example is the figure caption of the panel displayed above:

ÒSDN-1 expression in neural and hypodermal tissue. (A-F) Expression pattern of the translational Psdn-1::sdn-1::gfp reporter. (A') SDN-1::GFP is broadly expressed in the three-fold embryo, and is particularly strong in the pharynx (pha) and the motoneurons (mn) of the VNC. (B) In L1 larvae, expression is seen in the VNC (arrow) and around the seam cells (arrowhead). SDN-1::GFP expression is also visible in embryonic DD commissures (out of focal plane in B). (C) During later larval stages, SDN-1::GFP is predominantly found in the nervous system. The nerve ring (nr), and the VNC motoneurons and commissures (com) show the highest expression levels (arrowheads; B,F), but the reporter is also present in touch neurons (arrow; E) and other sensory neurons in the head (arrow; F). SDN-1::GFP can also be detected at a lower level in the body wall hypodermis (arrowhead; D); expression is stronger in hypodermal tissue in the tail (arrow; C).Ó