Optimization of a microarray for fission yeast

Cited 0 time in scopus
Metadata Downloads
Title
Optimization of a microarray for fission yeast
Author(s)
Dong Uk Kim; M Lee; S Han; M Nam; S Lee; J Lee; J Woo; D Kim; K L Hoe
Bibliographic Citation
Genomics & Informatics, vol. 17, no. 3, pp. e28-e28
Publication Year
2019
Abstract
Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up- and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 μm, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 μm, 48K) could represent ~10,000 up-/down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58°C for both tags. Intriguingly, up-tags required 3? higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25°C) was optimal for cultivation instead of a normal temperature (30°C) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.
Keyword
fission yeastgene-deletionmicroarraytagbar-code
ISSN
I000-0158
Publisher
Korea Soc-Assoc-Inst
DOI
http://dx.doi.org/10.5808/GI.2019.17.3.e28
Type
Article
Appears in Collections:
Division of Biomedical Research > Rare Disease Research Center > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.