# Lymphochip spot to gene mapping scheme

Feb 28, 2000

Since we cannot easily serve a database capturing these relationships the moment, we have prepared 2 text tab-delimited flat files. They are as follows:

A. RELATIONSHIPS: Chip data (ScanAlyze .DAT file) -> ScanAlyze assigned unique spot number -> Inhouse DNA ID number

FILE: "chip_spot_well.tab.txt", which contains 3 columns:

* column 1 is the chip batch: the first 4 characters of the DAT file name (eg, lc8n125rex2.DAT corresponds to chip batch lc8n)

* column 2 is spot number as assigned by ScanAlyze and as listed in the SPOT column in any DAT file

* column 3 is the inhouse DNA ID number we call the LCWELLINDEX

B. RELATIONSHIPS: Inhouse DNA ID number -> Clone ID number -> Sequence accession(s) -> Curated gene name

FILE: "well_cloneid_name.tab.txt", also contains 3 columns:

* column 1 is the LCWELLINDEX

* column 2 is CLONEID (numbers below 10,000 were handmade by us, >10,000 are IMAGE Clones)

* column 3 is a curated name (curated as of Nov 11, 1999)

Unfortunately, at the moment these relationships are a messy puzzle which users will have to piece together, until we erect a public database which is capable of handling several thousand requests per day (the current load on the web page). We must apologize for this and hope you don't mind waiting for a better solution. We are working on this database at the moment (as part of the Oracle based Stanford Microarray Database) and will post a link to it as soon as it becomes available.