Array Core Analysis

Analysis Software

UCSF SPOT

UCSF Spot is a program for microarray image quantification. It is fully automatic, from the gridding process through ratio derivation.

Spot is available for research purposes to academic and non-profit organizations. No warranties are expressed or implied. We request that publications in which UCSF Spot has been used reference the following paper:

A. N. Jain, T. A. Tokuyasu, A. M. Snijders, R. Segraves, D. G. Albertson, and D. Pinkel. Fully automatic quantification of microarray image data. Genome Research 12: 325-332, 2002.

To obtain the most recent version of SPOT and SPROC, please visit the UCSF Bioinformatics Lab of Dr. Ajay Jain: http://www.jainlab.org/downloads.html.

SPROC mapping files for Hum32k can be downloaded here:

• HA32K_A.clonepos.20050919.txt (Left array)
• HA32K_A.spotclone.20060222.txt (Left array)
• HA32K_B.clonepos.20050919.txt (Right array)
• HA32K_B.spotclone.20060222.txt (Right array)

SPROC mapping files for HumArray3.2 can be downloaded here:

• HA3.2_clonepos_May04.20060811.txt
• HA3.2_spotclone.20060802.txt
• HA3.2_spotclone.axon.20060802.txt (rotated 90 degrees)

SPROC mapping files for HumArray3.1 can be downloaded here:

• HA3.1_clonepos_May04.20060811.txt
• HA3.1_spotclone.20060807.txt
• HA3.1_spotclone.axon.20060807.txt (rotated 90 degrees)

SPROC mapping files for HumArray2.0 can be downloaded here:

• HA2.0_clonepos_May04.20060811.txt
• HA2.0_spotclone.20060807.txt
• HA2.0_spotclone.axon.20060807.txt (rotated 90 degrees)

SPROC mapping files for HumArray1.14 can be downloaded here:

• HA1.14_clonepos_May04.20060811.txt
• HA1.14_spotclone.20060809.txt
• HA1.14_spotclone.axon.20060809.txt (rotated 90 degrees)

SPROC mapping files for MouseArray1.5 can be downloaded here:

• MA1.5_clonepos_beta20060207.txt
• MA1.5_spotclone_beta20050428.txt

Additional Resources
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.