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| Status |
Public on Sep 23, 2021 |
| Title |
ChIP-seq analysis of transcription factor Upc2A binding across the Candida glabrata genome [Upc2A ChIP-seq] |
| Organism |
Nakaseomyces glabratus CBS 138 |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To determine the genomic binding sites for the Candida glabrata transcription factor Upc2A, we utilized three different strains. One was the wild-type KKY2001 which contains a wild-type copy of UPC2A but lacks any HA tag. The other two are both derived from KKY2001 but contain a 3X HA tag immediately after the start codon of UPC2A. These strains are BVGC82 and BVGC84, respectively. Both contain a single copy of a loxP element located 252 bp downstream from the UPC2A stop codon. BVGC82 contains a wild-type copy of the UPC2A gene while BVGC84 contains a mutant form of UPC2A (G898D) that confers elevated resistance to fluconazole. ChIP was performed with anti-HA antibodies in all cases. Strains containing the wild-type UPC2A gene (no HA tag) are referred to as C1 and C2. Strains containing the 3X HA epitope tag at the N-terminus of the wild-type UPC2A gene are referred to as wt1 and wt2. These same strains challenged with fluconazole prior to ChIP are referred to as wtf1 and wtf2. The strain containing the G898D UPC2A allele are referred to as M1 and M2 (no fluconazole challenge) and MF1 and MF2 (with fluconazole challenge.
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| Overall design |
ChIP-seq using anti-HA antibody against strains expressing HA-tagged Upc2A as a wild-type protein or a gain-of-function form (G899D Upc2A). Prior to chromatin preparation and shearing, parallel cultures were either left untreated or challenged with 20 microgram/ml of fluconazole for two hours at 30 degrees C.
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| Contributor(s) |
Vu BG, Stamnes M, Moye-Rowley S |
| Citation(s) |
34591857 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 AI152494 |
Genetic analysis of pleiotropic drug resistance |
THE UNIVERSITY OF IOWA |
W Scott Moye-Rowley |
|
| Submission date |
Aug 19, 2021 |
| Last update date |
Dec 27, 2021 |
| Contact name |
Scott Moye-Rowley |
| E-mail(s) |
scott-moye-rowley@uiowa.edu
|
| Phone |
3193357874
|
| Organization name |
University of Iowa
|
| Department |
Molecular Physiology & Biophysics
|
| Street address |
6-530 Bowen Science Bldg./Dept. of Mol Physio
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL30531 |
Illumina HiSeq 2500 ([Candida] glabrata CBS 138) |
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| Samples (10)
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| GSM5530073 |
ChIP-seq with no HA tag present [C-1] |
| GSM5530074 |
ChiP-seq with HA-Upc2A tag present [WT-1] |
| GSM5530075 |
ChiP-seq with HA-Upc2A tag present + Fluconazole Challenge [WTF-1] |
| GSM5530076 |
ChiP-seq with HA-Upc2A G898D tag present [M-1] |
| GSM5530077 |
ChiP-seq with HA-Upc2A G898D tag present + Fluconazole Challenge [MF-1] |
| GSM5530078 |
ChIP-seq with no HA tag present [C-2] |
| GSM5530079 |
ChiP-seq with HA-Upc2A tag present [WT-2] |
| GSM5530080 |
ChiP-seq with HA-Upc2A tag present + Fluconazole Challenge [WTF-2] |
| GSM5530081 |
ChiP-seq with HA-Upc2A G898D tag present [M-2] |
| GSM5530082 |
ChiP-seq with HA-Upc2A G898D tag present + Fluconazole Challenge [MF-2] |
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| This SubSeries is part of SuperSeries: |
| GSE182516 |
Genomic level analysis of Upc2A-regulated transcription in Candida glabrata |
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| Relations |
| BioProject |
PRJNA756362 |
| SRA |
SRP333406 |
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