No

Question

Your response

1.

What is your organisation=s name and are your public or private (optional)?

Of the 32 responses, two came from industry, 25 from public institutes and five did not state their allegiance.

2.

Do you currently use cereal microarrays?

Fifty eight percent of those that responded to this question are currently not using microarrays whereas 42% of you are. We suspect that some of the respondents who said they were using microarrays are in fact using filter-based macroarrays. There were 24 responses to this question.

3.

If so, which cereal species?

Forty one percent of those that responded to this question are currently using wheat microarrays, 33% are currently using barley microarrays, 13% are currently using both barley and wheat microarrays, 4% are currently using oat microarrays and 9% are currently using maize microarrays. There were 22 responses to this question.

4.

If so, are the arrays made in your lab, your organisation, your country, or elsewhere?

Forty six percent of those that responded to this question currently make their own microarrays, 7% obtain their microarrays from people within their own organisation, 40% currently obtain their microarrays from other organisations within their country and 7% currently obtain their microarrays from “elsewhere. There were 15 responses to this question.

5.

If you do not use microarrays, why not? For instance, you may have no need for them, or they may not be available to your lab.

Eighty seven percent of those that responded to this question said that they did not use microarrays because they were just not available. Thirteen percent said that they were just too expensive. There were 15 responses to this question.

6.

If you do not use microarrays now, do you feel that you will use them in the future? If so, how far into the future?

If arrays were available then 94% of you that responded to this question said that they expected to use microarrays within the next 12 months and a further 6% said that they expected to use them within the next 24 months. There were 17 responses to this question.

7.

Would you be interested in a commercially available Triticeae microarray?

Eighty six percent of those that responded to this question said that they would be interested in commercial microarrays. Seven percent said that they were not interested in commercial arrays and seven percent did not know. There were 28 responses to this question.

8.

Do you feel that there are now sufficient Triticeae ESTs in the public database for such a Apublic@ array to be produced?

Seventy nine percent of those that responded to this question said that they thought that there were enough ESTs in the public database to start making a public array. Fourteen percent said that we should wait until there were more public ESTs and seven percent did not know. There were 28 responses to this question.

9.

If so, do you believe that we should continue with the various public EST programmes?

One hundred percent of those that responded to this question said that they thought that the titriceae community should continue to sequence ESTs for inclusion in the public database. However, many of you suggested that we should co-ordinate our effort better. From your comments it would seem that at the moment there is too much attention being placed on the developing grain and not enough effort on other development stages or the response to biotic and abiotic stress. There were 29 responses to this question.

10.

If not, how many ESTs do you think would be required before such an array would be worthwhile?

This was a rotten question! Only three people responded. Of those that did respond one said we should continue until we had 95% of the transcriptome, one said that we should stop when we had ~400,000 ESTs and one said that we should stop when we had ~30,000 contigs.

11.

Do you feel that a commercially available rice array (EST or oligo, consisting of the entire rice transcriptome) would be a suitable surrogate for a Triticeae array?

Fifteen percent of those that responded to this question said that they thought that rice microarrays were a suitable alternative to wheat/barley arrays. Sixty three percent said that rice microarrays were a poor (or no) substitute for wheat/barley microarrays. Twenty two percent did not know. There were 27 responses to this question.

12.

How much would you be prepared to pay ($ per slide) for a 10,000 feature array?

Forty eight percent of those that responded to this question said that they would be prepared to pay “a few hundred dollars” per microarrays. Thirty two percent said that you would be prepared to pay anything from $300 to $1,000 per microarray. Three percent would be prepared to pay more than $1,000 per microarray, whilst seven percent said that you would not be prepared to pay anything for your microarrays. Finally, ten percent were not sure how much you would be prepared to pay. There were 25 responses to this question.

13.

If the arrays cost $600 per 10,000-feature slide, how many slides do you feel you might use in the next 12 months?

Nine percent of those that responded to this question said that if the commercial arrays cost $600, they would not buy any microarrays over the next 12 months. Thirty six percent said that you would possibly buy 1-10 microarrays. Thirty six percent said that they would possibly buy 11-20 microarrays, whilst fourteen percent said that they might possibly buy more than 20 microarrays. Finally, four percent were not sure how many they might buy. There were 22 responses to this question.

14a.

Would you prefer an EST or an oligo array?

Forty three percent of those that responded to this question said that they would prefer to use microarrays based on oligonucleotides. Twenty five percent said that they would prefer microarrays based on ESTs. Twenty one percent said that they would prefer to have access to both oligo and EST microarrays. Finally, seven percent were not sure. There were 28 responses to this question.

14b.

If you chose oligo, do you prefer short (24-mer) arrays (eg. Affymetrix) or long (60-70 mer) arrays (eg. Agilent, Operon)?

Twenty one percent of those that responded to this question said that they would prefer microarrays based on short oligos. Seventy one percent said that they would prefer microarrays based on long oligos. Finally, seven percent were unsure. There were 14 responses to this question.

15.

Do you think that your organisation or government might be prepared to contribute funds to help design and have manufactured a standard public A Triticeae@ array

Sixty nine percent of those that responded to this question said that they thought that their organisation or government might be prepared to make a contribution to fund the fabrication of a standard public array. Twelve percent were unsure and nineteen percent thought that their organisation/government would not be prepared to contribute. There were 26 responses to this question.

16.

Would you prefer it if a service provider also carried out the hybridisation steps for you, as per the Affymetrix based arrays?

Forty six percent of those that responded to this question said that they would prefer it if a service provider carried out all the steps on your behalf, while forty two percent were not interested in using a service provider. Eleven percent were unsure. However, many of the responses made it quite clear that cost was a major consideration on whether or not a service provider would be used. There were 26 responses to this question.

17.

Do you have a dedicated bioinformatic support post for analysing your array-based data?

Fifty five percent of those that responded to this question said that they did have dedicated bioinformatics support whilst forty one percent did not. Four percent of you did not know (?). There were 27 responses to this question.

18.

If such a repository existed, would you be prepared to place your array-based data in a public database similar to the public EST databases? What sorts of quality controls should be put on public postings of array-based data?

Seventy two percent of those that responded to this question said that they would be interesting in depositing their array-based data in a public repository (but many of you asked if there would be minimum standards). Sixteen percent said that they would not be interested in such a repository and twelve percent did not know. There were 25 responses to this question.

19.

Do you have any other comments to make about the possibility of the academic community developing a Triticeae -based array?

The following comments covered the general feelings stated in your reply:

1. As a community, we need to move fast. The provision of a widely available microarray facility should be a high priority.

2. The cost of microarrays will be a major factor on their widespread use. Costs must be kept down.

3. Unencumbered public funding should be found to establish a public trit-chip.

4. The deposition of microarray-based data in a pubic repository should be compulsory for all published work.