Carnegie Institute/Stanford Ge\ nome Technology Center Chlamydomonas MicroArray Project

Who do I email for more information?

Orders and general information: Arthur Grossman (arthur@andrew2.stanford.edu)<\ /a>
Specific biological information: Olivier Vallon (vallon@andrew2.stanford.edu)
Technical details and computational information: Arthur Grossman

How can I make formal citation to the microarray project?

Please cite at least this web site, and:

CS Im, Z-D Zhang, J Shrager, C-W Chang, A Grossman (2003). Analysis of light and CO2 regulation in Chlamydomonas reinhardtii using genome-wide approaches. Photosynthesis Res. 75: 111-125.

and possibly:

J Shrager, C Hauser, C-W Chang, EH Harris, J Davies, J McDermott, R Tamse, Z-D Zhang, AR Grossman (2003) Chlamydomonas reinhardtii Genome Project. A guide to the generation and use of the cDNA information. Plant Physiology 131:401-8.

You may also wish to cite the Chlamy resource center web site.

How many probes are on the chip?

(Photo: Jeff Shrager)

There are 12,316 total spots, which is 4x of 3,079 different probes. (See the Array\ Info Spreadsheet (AIS), described below)

Are control spots included?

Yes.  There are several spots dedicated to Salmon DNA, which can be used as a "spike" control. (See the Array Info Spreadsheet (AIS), desc\ ribed below) There are some empty spots that will also be useful as controls. Your experiment\ should use "design" controls.

What is the average length of the cDNAs fixed on the chip?

Approx. 400nt.

What area is covered by the probes?

The probes appear in two groups of 16 blocks, each block consisting of 20x20 spots. (That comes to 12,800; There are some empty \ spots.) This covers about 2/3 of the array surface.

What kind of reference RNA should be used to allow a comparison between different probes?

This depends upon your experiment.

What type of glass is used for the carrier?

We use Corning product #40006 GAPS II coated slides. They are described in detail here [pdf].

When will the chips be ready for distribution?

These are the current array version, and are in production, ready for immediate distribution.

How much do they cost?

$100 each slide. (Subject to change!)

How do I order them?

Email orders to Arthur Grossman (arthur@andrew2.stanford.edu)

What specifically is on the chip?

A: The Array Info Spreadsheet (AIS) gives you the details. Download it for Excel by clicking here, or as a tab-separated values (tsv) file by clicking here. (Please note that this spreadsheet\ is undergoing update; the specific version that you download may change in some details, such as format, and some columns may not yet be filled in. However, the specific sequences spotted will not change in this version.)

Warning: If you download the file "layout.tsv" and try to import it into Excel you MUST PREFORMAT all the columns as type TEXT otherwise weird things will happen, like some of the block numbers will be negative, and some of the clone names will come out as weird numbers, like 1234E12! This is caused by bugs in Excel that cause it to interpret, for example, the clone name: "1234056E12", as a number in scientific (E) notation! (Even though it appeared in quotes!), and another bug that causes it to interpret separate fields, like: "-" "13" as a negative number. If you're on a Windows platform, you probabaly want to just load the Excel formatted file, or else carefully set all the columns to type TEXT before importing the .TSV file.

Columns of the AIS:

Chip row/col: The spot row/col on the chip (with the chip held narrow-edge up, inscribed numbers forward and at the bottom). The top left spot is (1,1). There is approx. one row/col left out where each block ends, either horizontally or vertically. (IMPORTANT: The actual size of the break at this point may be larger than one spot; Don't get confused by this! The chip row/col geometry is NOT METRICAL. If you want metrical positions, for example for doing your own image processing, you will have to make your own measurements; Each chip is very slightly different

Block: There are 32 blocks on the chip, numbered from left-to-right, top-to-bottom (with the chip help narrow-edge up, inscribed numbers on the front surface, at the bottom). So, the top left most block is #1, and there are four across (columns) and 8 down (rows); the top right most block is #4, and the lower right most block is #32.

Block row/col: Each block contains 20x20 spots. The top left spot is (1,1).

Description: This is supposed to be the latest annotation indicating what DNA is represented in the spot. For spots that come from clones in the ChlamyDB assembly, you will have to follow the live link to figure out the text functional annotation.

Source: The plate and well (or other info) identifying where we got the clone. (This is usually only internally useful.)

EST: The clone number from which the spot DNA was amplified.

Chlamy DB link: This is a live link to the entry for the ESTs printed on the chip in ChlamyDB.

I can't get the "live links" to ChlamyDB in the AIS to work when I click them.

There seems to an incompatibility for some versions of Excel that does not make links clickable when the spreadsheet is loaded. Either you can simply paste the URL into an open web browser, or if you select and "edit" the URL (although don't actually make any changes in it!) then it is live. You can tell that it's live because it is highlighted (usually in blue) by Excel.

When I open the file layout.tsv in Excel, weird things happen, like some of the block numbers are negative, and some of the clone names come out as weird numbers, like 1234E12!

You have almost certainly loaded the TSV file into Excel without first telling Excel that the columns are formatted as TEXT. If you don't do this on import (!!) Excel has several bugs that cause it to interpret, for example, the clone name: "1234056E12", as a number in scientific (E) notation! (Even though it appeared in quotes!), and another bug that causes it to interpret separate fields, like: "-" "13" as a negative number. If you're on a Windows platform, you probabaly want to just load the Excel formatted file, or else carefully set all the columns to type TEXT before importing the .TSV file.

What are the sequences of the probes?

The sequences are described in the following files:

SternSeqs.txt: Sequences of Chloroplast-related genes (called "Stern..." in the AIS).

cv11.fasta: Sequences of the "x" clones produced by the Stanford Genome Tech Center (as: 1024023A11.x1 in\ the AIS).

Do you have a detailed but uninterpretable set of powerpoint slides that proport to explain the chip layout and how it was derived from the original clone libraries?

I don't know why you could possibly want this, but here you go!

How can I tell which side of the array is the "top" (that is, the one with the spots on it)?

As these slides have no edge cut, it can be quite difficult to tell which surface it the top. One way is to look at the indirect reflection of a light off of the inscribed chip number, which is always on the front surface (although it may be in any orientation).