Welcome to the sample submission form

Introduction

This is NASC's sample submission form for our Affymetrix service. We collect full MIAME-compliant data for all of the experiments we perform, so that we can put the data in our microarray database, and further disseminate the data outside of NASC.

All of our customers must fill in this form unless alternative arrangements have been made. No samples will be processed unless completed forms are received!

Fill in this form one sample at a time. To make it easier once you have filled in one form, you can fill in the form for the next sample based on the answers you gave in the first form. That way, you only have to change what was different about each sample. One form per sample, please

Information you will need

In order to successfully fill in the following forms, you will need the following information. Make sure you've collected all of this information together before you start! You will need...

  1. Full sample details about sample preparation including:
    1. Information about the plants used, including full details on any mutants involved. Please supply NASC stock codes where available.
    2. Information about growth protocols, including growth room specifications etc.
    3. Details about any treatments you will be applying to the material
  2. Extraction protocol used for RNA extraction

If you do not have all of these details available now, you will not be able to fill in these forms. NASC does not run experiments if a full experimental description is not received. There is no facility for coming back to a half filled application form later. If you are unsure, come in and have a look around first!

Sightseers welcome!

If you want to come in just to look around- feel free! The application is not submitted until the very end. This should give you more details about what information we require.

We appreciate that filling in these forms can be boring. Thanks for your patience.

Pitfalls

These forms are new and although they have been tested, some problems may remain. If you have any problems, please help us by writing to affy@arabidopsis.info.

Start by giving us your name, and the sample name

Fill in some of the boxes on each page, then press "Next Page" to move to the next page. Some boxes are compulsory: these are marked *. Some boxes have help attached- click on the ? next to them to read a more detailed description of what should go in the box. If you press Next and nothing happens, you've probably missed out a compulsory field. A message will appear next to the box you have missed out.

Your name: *  ?You must supply your name (please omit slashes and unusual characters):
The name of the sample:*  ?You must supply a name for your sample

Sample submission form: Step 2 of 5: the germplasm

Tell us all about sample "" part 1: the germplasm

Next, please tell us about this sample you have prepared to send us. The next few pages include details about the original germplasm (the type of plant you are growing) you used, how they were grown and their subsequent treatment. This page is about the germplasm.

Fill in this form for sample ""

About the germplasm

Don't remember your Stock code?
Look it up using the NASC Stock Catalogue

This section is about the original plant material you used to make the samples. These can be thought of as "properties of the seed". If you have done a cell culture, or a tissue culture, it is the line the plants came from originally. We refer to this throughout this page as "your line" for brevity.

Is your line:Arabidopsis thaliana, has a NASC/ABRC stock codeArabidopsis thaliana, has not got a NASC/ABRC stock code  ?The specified value is invalid

Arabidopsis thaliana: has stock code

Line name:  ?Should not see me
Stock Code: *  ?This field must be a NASC or ABRC stock code
This stock code is a population, and we used a line from this population*The specified value is invalid

Arabidopsis thaliana: not in stock centre

Is this line:An ecotype (a naturally occurring wild-type)A genetically altered mutantA line from a Recombinant-Inbred (RI) population  ?The specified value is invalid

Ecotype

What is the name of this ecotype?*This field is compulsory
Geographical location where this ecotype was collected or publication/address of where seed was obtainedThe specified value is invalid

Recombinant Inbred (RI) line

Name of this line:  ?This field is compulsory
Line 1:  ?This field is compulsory
Line 2:  ?This field is compulsory
Describe which line in the collection used::  ?The specified value is invalid

Mutant

What is the name of this mutant?*This field is compulsory
Is this line:A gene knock out (e.g. T-DNA, transposon)A gene knock in (e.g. overexpressor, GUS fusion)An induced mutation (e.g. EMS)The specified value is invalid
Describe the gene knock out/knock in/mutation technique (T-DNA,transposon, EMS etc.)The specified value is invalid
What is the background line for this mutant:  ?The specified value is invalid

List the genes knocked out/in/modified here. AGI codes if possible.

The specified value is invalid
The specified value is invalid
The specified value is invalid

Sample submission form: Step 3 of 5: germplasm treatment

Tell us all about sample "" part 2: the treatments

Now you've described the germplasm sample "" was derived from, you need to tell us how this was turned into the RNA sample you are going to send us.

First you describe whether the RNA sample came from a plant (or a bit of a plant), or whether you extracted RNA from seed. Then we ask you questions about the various ways you prepared the plants before you sent them to us.

This page asks you for many protocols. You may find it easier to edit your protocols in another program (e.g. a word processor), and copy and paste the protocols in, rather than type directly into this page.

Fill in this form for sample ""

Sample origin:*  ?The specified value is invalid

Seed treatments before growth

In this section there are some optional boxes to describe how the seeds were sterilised and stratified before they were grown. If you did not do any of these steps either leave these boxes as "none", or make the boxes blank. If you did, please fill in the protocol here.

Stratification protocol:  ?The specified value is invalid
Sterilisation protocol:  ?The specified value is invalid
Other seed preparation comments:  ?The specified value is invalid

Growth Conditions

In this section, please describe how you grew these seeds into plants. This section is for the growth protocol before any treatments have been applied.

This section is split into two parts. Firstly please write the growth conditions as a protocol into the box below. Secondly fill in some specific details below into the individual boxes.

Text description

This section is for describing the growth protocol as a text document, as you would in a publication in a journal.

Growth protocol:*  ?This field must be filled in
Reference for this protocol, if published:  ?The specified value is invalid
URL for this protocol  ?The specified value is invalid

Specific details

This section is for describing the growth protocol as a series of keyword-like boxes. It serves two purposes:

  • it allows us to allow users to search more powerfully
  • it makes sure you include all relevant details.
Where was this plant grown?*We need to know where you grew your plants
Average annual rainfall (mm)  ?The specified value is invalid
Irrigation method  ?The specified value is invalid

Growth Substrate

The growth substrate is soil, agar, etc.- whatever the plant was grown on.

Which growth substrate was used?*  ?The specified value is invalid
% agroseThe specified value is invalid
Hydroponics constituentsThe specified value is invalid
Soil details (Manufacturer, composition etc.)The specified value is invalid
Substrate sterilisation protocol:  ?The specified value is invalid
Average daily humidity (%):Day humidity (%):Night humidity (%):
*compulsory*compulsory*compulsory
Average daily temperature (°C):Day temperature (°C):Night temperature (°C):
*compulsory*compulsory*compulsory
Spacing/density of plants:  ?The specified value is invalid
Watering conditions:  ?The specified value is invalid

Growth medium

Growth medium is the "mix" with nutrients etc. to mix with the substrate, above. You have the opportunity to write about any modifications to the you made below.

Which growth medium was used?The specified value is invalid
Describe the makeup of your "own medium":  ?The specified value is invalid
Concentration of medium added:  ?The specified value is invalid
If you made any modifications to the medium, please list them here:The specified value is invalid
Growth medium application frequency:The specified value is invalid

Now please describe any additives you added on top of the medium described above.

AdditiveApplication frequencyConcentration
Fertiliser:
Herbicides:
Pesticides:
Biological control agents:
Sugars:
Hormones:
Vitamins:
Other additives:

Lighting conditions

Light duration (photoperiod)The specified value is invalid
Day length (mins)The specified value is invalid
Night length (mins)The specified value is invalid
Light type:The specified value is invalid
manufacturerThe specified value is invalid
Light intensity (µEinsteins)The specified value is invalid
WavelengthThe specified value is invalid

Sample submission form: Step 4 of 5: germplasm treatment

Tell us about sample "" part 3: the treatments

Treatments

You will need to fill in this section if you used a treatment on your grown plants, or on your seed. Treatments include things like "heat shock", "chemical treatment", "wounding" and so on.

Did you apply a treatment to your plants/seeds:*The specified value is invalid
Which of these treatments were applied?Temperature stress (e.g. heat shock, cold treatment)
Light stress (e.g. UV treatment)
Mechanical stress (e.g. wounding)
Plant nutrient (e.g. excess sucrose)
Chemicals (including salt stress)
Infection with pathogen or microbe (e.g. fungal, bacterial, nematodes)
Stress due to animals
Stress due to plants
Other
 ?The specified value is invalid
Please describe the treatment protocol:The specified value is invalid

Timecourse

Is this sample part of a timecourse?  ?The specified value is invalid
Which time point is this sample?  ?The specified value is invalid
How did you determine the start time of the timecourse?  ?The specified value is invalid

Sample description: The Plant

You have now described how you grew your plants, and applied any treatments. Now you need to describe the plant after the experiment was finished, and which bit of the plant you extracted RNA from.

Please type in a general description of the plant from which your sample was derived:The specified value is invalid
Which part of the plant's anatomy was the RNA extracted from?  ?The specified value is invalid
Separation technique:  ?The specified value is invalid
Chronological Age:  ?The specified value is invalid

At NASC we use Paradigm Genetics system of measuring developmental stages for Arabidopsis- e.g. 1.08, 6.0 etc. See Boyes et. al., "Growth Stage-Based Phenotypic Analysis of Arabidopsis: A Model for High Throughput Functional Genomics in Plants" The Plant Cell, Vol. 13, 1499-1510, July 2001.

Please describe what developmental stage you grew these plants to before you did any further steps:  ?The specified value is invalid

Sample submission form: Step 5 of 5: extraction protocol

Tell us about the extraction protocol used for ""

The extraction protocol describes how you extracted RNA from the biological material. Now please describe the extraction protocol you used for this sample.

Extraction protocol

Name:*  ?The specified value is invalid
Protocol:*  ?The specified value is invalid
What type of nucleic acid did you extract?*  ?The specified value is invalid
Was the sample:The specified value is invalid
How much RNA did you extract for this sample (µg)?*  ?The specified value is invalid
How much RNA are you sending to us (µg)?  ?The specified value is invalid

The end!

Thank you for taking the time to fill in these forms. Once you press submit, your form will be sent and you will be taken back to the first page. If you have any more samples to fill in, please fill in the forms again. (One form per sample, please!). The forms will be pre-filled-in with all of the data for this sample. You do not need to fill in the forms from scratch again. Only alter what is different about your subsequent samples.

Please email any problems with these forms to affy@arabidopsis.info
* - required |  ? - help