RNA interference experiments (RNAi) allow for targeted gene knock down in many species in order to identify potential drug targets and to determine functional annotation of genes. RNAi is a very powerful tool in the functional genomics toolbox and RNAi annotation is one of the core features of LiceBase. Only well annotated experiments enable good data analysis and interpretation. Recording all relevant experimental parameters and protocols enables reproducible science and good analysis of experiments. Also, completely annotated experiments could enable computational biologists to help design better experiments or to pick promising target automatically.
Requirements and preparation
Before an experiment can be successfully annotated a few bits of mandatory information need to be collected. Make sure to have these written down. There are several mandatory fields in the annotation form and the system will prevent you from saving the information. This can be annoying if the information you need is hard to find and you have already
- Note down the target Transcript ID or Gene ID, this has to be an Ensembl stable ID (start with EMLSAT, e.g. ). If the target sequence has not been designed against an Ensembl transcript or if you for other reasons do not know the stable ID, please refer to the gene finding guide (under construction).
- Get the primer sequences (4 sequences) with forward and reverse primers
- The Fragment Label ID an unique ID that allows you to locate the fragment, label written on the fragment container. If the container is not labeled yet, and you have fragment left to use in it, label it now.
- Experiment contacts, get the names of those people involved in the experiment
How to schedule data entry
The data entry form supports multiple sessions of data entry and data should be entered in at least two session: all data about genes and sequences and the experimental setup should be entered at the start of the experiment; all phenotype related data should be entered at the termination of the experiment. As a general rule all data should be entered as soon as possible to reduce mistakes, and all previously filled fields should be re-visited for correctness at the end of the experiment.
To add additional information to an experiment, open the experiment and click the edit button at the top:
The data entry form is divided into 8 subsections (tabs) to structure it:
The data entry form is composed of form elements (widgets) which are mostly working like any other form: text fields, select boxes, upload widgets, etc., some of them are specifically designed to assist the user to select values. Here are some specialties:
- Mandatory fields are marked with a yellow asterisk: Primary target ID: *
Auto-complete fields are text fields that provide a proposal for a valid value out of very many based on what is typed. They are marked with a small grey circle on the right side. Type a partial text and proposals for a completion will be shown. In most cases one of the proposed options has to be selected, or the submission will result in an error.
To chose a value from an auto-complete field, type something, then once the correct option appears, click the option with the mouse.