GEO DataSets

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34174

48 Samples

Download data: BW

(Submitter supplied) Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.

Organism:

Schizosaccharomyces pombe; Nakaseomyces glabratus; Kluyveromyces lactis; Candida albicans; Lachancea waltii; Saccharomyces cerevisiae; Schizosaccharomyces japonicus; Schizosaccharomyces octosporus; Saccharomyces bayanus; Yarrowia lipolytica; Naumovozyma castellii

Type:

Expression profiling by high throughput sequencing

11 related Platforms

11 Samples

Download data: TXT

(Submitter supplied) The goal of the study was to compare the response to Protien Kinase A (PKA) inhibition between Saccharomyces cerevisiae and Kluyveromyces lactis. The ancestor of K. lactis did not undergo the Whole Genome Duplication (or Whole Genome Hybridization) event that S. cerevisiae experienced. We found that many paralog pairs in S. cerevisiae were differentially induced in response to PKA inhibition, and that the shared ortholog for these paralog paris in K. more...

Organism:

Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21656 GPL22716

95 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nakaseomyces glabratus; Naumovozyma castellii; Saccharomyces paradoxus; Saccharomyces cerevisiae; Kluyveromyces lactis; Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

10 related Platforms

128 Samples

Download data: BW

(Submitter supplied) We measured global expression profiles in SFP1 deletion mutants and isogenic wild type strains during lag and log phase growth. To match the physiology of each species as well as minimize the effect on gene expression from differences in early growth rates, we profiled expression during log growth and lag after glucose repletion as previously described (Thompson et al., 2013).

Organism:

Nakaseomyces glabratus; Naumovozyma castellii; Saccharomyces paradoxus; Schizosaccharomyces pombe; Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Expression profiling by high throughput sequencing

6 related Platforms

58 Samples

Download data: TXT

(Submitter supplied) We set out to determine how Sfp1 binding targets evolved over time. We sampled our species of interest to include one pre-whole genome duplicaton (WGD) species containing SFP1A (K. lactis), one post-WGD species containing both SFP1 and SFP1PL (N. castellii), two post-WGD species containing only SFP1 (S. cerevisiae and S. paradoxus) and performed ChIP for each Sfp1 homolog in each species using an antibody that recognizes a conserved subdomain of Sfp1 common to both Sfp1, Sfp1a, and Sfp1pl. more...

Organism:

Saccharomyces paradoxus; Saccharomyces cerevisiae; Naumovozyma castellii; Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

70 Samples

Download data: BW

(Submitter supplied) This data set contains microarray data for wild type and Sfp1 mutant strains in each of several yeast species in the LOG growth phase. This was done at several time points (mainly the T=30, 60 or 90 min post glucose repletion) for S. cerevisiae, C. glabrata, N. castellii, K. lactis and S. pombe. For S. cerevisiae samples were taken for both WT and Sfp1 mutant conditions for both the BY and RM strains of this species. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe; Nakaseomyces glabratus; Naumovozyma castellii; Kluyveromyces lactis

Type:

Expression profiling by array

6 related Platforms

184 Samples

Download data: XLSX

(Submitter supplied) Chromatin Immunoprecipitation followed by microarray analysis to identify the location of Sir2 and Orc1 genomic enrichment.

Organism:

Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL22318

4 Samples

Download data: TXT

(Submitter supplied) Evaluation of the differential expression of mRNA between WT and sir2∆in K. lactis yeast strains.

Organism:

Kluyveromyces lactis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22158

6 Samples

Download data: TXT

(Submitter supplied) Evaluation of the differential expression of mRNA between WT and sir2∆, WT and sir4∆, WT and sum1∆ in K. lactis yeast strains.

Organism:

Kluyveromyces lactis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22158

8 Samples

Download data: TXT

(Submitter supplied) Alternative polyadenylation generates numerous 3' mRNA isoforms per gene; regulation of this process is critical in development and impaired in cancer. Individual isoforms from the same gene can vary greatly in biological properties such as translational efficiency, localization, and half-life. Even closely related isoforms - including those differing by a single nt - can have different biological properties, but the underlying mechanisms are unknown. more...

Organism:

Saccharomyces cerevisiae; Kluyveromyces lactis; Debaryomyces hansenii

Type:

Expression profiling by high throughput sequencing

4 related Platforms

42 Samples

Download data: TXT

(Submitter supplied) This experiment was performed to measure differences in pathway-level evolution of cis-regulation between closely related Kluyveromyces species. Sequencing of mRNA as well as DNA was performed in hybrids of Kl. lactis with two other species, Kl. wickerhamii and Kl. marxianus. Cells were grown overnight for DNA sequencing and for 4-8h to an OD600=0.7-1.0 for mRNA sequencing. DNA and mRNA reads were mapped to hybrid genomes, multimapping reads discarded, and allele-specific expression ratio for each gene was calculated after first normalizing mRNA reads to the number of DNA reads for each gene in each species. more...

Organism:

Kluyveromyces lactis x Kluyveromyces marxianus; Kluyveromyces lactis; Kluyveromyces lactis x Kluyveromyces wickerhamii; Kluyveromyces marxianus; Kluyveromyces wickerhamii

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

24 Samples

Download data: TXT

(Submitter supplied) Although the RNA polymerase (Pol) II machinery inherently initiates transcription in one direction, promoter regions are often “bidirectional” in vivo, giving rise to divergent RNA transcripts, many of which are non-coding and highly unstable. Here, we use a functional evolutionary approach to address whether bidirectional promoter regions are a mechanistic consequence of Pol II transcription or serve an evolved biological function. more...

Organism:

Debaryomyces hansenii; Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Other

Platforms:

GPL22535 GPL19756 GPL22534

14 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe; Candida albicans; Naumovozyma castellii; Nakaseomyces glabratus; Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

9 related Platforms

135 Samples

Download data: TXT

(Submitter supplied) A phylogenetic framework to study the evolution of transcriptional regulatory networks

Organism:

Naumovozyma castellii; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Nakaseomyces glabratus; Kluyveromyces lactis; Candida albicans

Type:

Expression profiling by array

6 related Platforms

103 Samples

Download data: TXT

(Submitter supplied) Eukaryotic genomes are replicated in a reproducible temporal order, however, the physiological significance is poorly understood. We compared replication dynamics in divergent yeast species and identified genomic features with conserved replication times. Histone genes were amongst the earliest replicating loci in all species. We delayed the replication of HTA1-HTB1 and discovered that this halved the histone gene expression. more...

Organism:

Henningerozyma blattae; Zygosaccharomyces rouxii; Nakaseomyces glabratus; Lachancea kluyveri; Saccharomyces cerevisiae; Naumovozyma castellii; Kluyveromyces lactis

Type:

Other

7 related Platforms

14 Samples

Download data: FASTA, WIG

(Submitter supplied) The purpose of this experiment was to identify the genes bound by Ndt80 in K. lactis when constitutively expressed. Ndt80 was tagged with c-myc, the native Ndt80 promoter was replaced with the K. lactis Gal1 promoter and the protein was immunoprecipitated with a c-myc antibody. Cells were grown overnight in SRaffinose until log-phase, then in SRaffinose + 1.7% Galactose for 5 hours. Each experiment was repeated twice and sequenced on an Illumina HiSeq 4000.

Organism:

Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22716

4 Samples

Download data: WIG, XLS

(Submitter supplied) The transcription factor KlPdr1p, belonging to the Zn2Cys6 family, is a central regulator of efflux pump expression in Kluyveromyces lactis. To better understand how KlPDR1-mediated drug resistance is achieved in K. lactis, we used DNA microarrays to identify genes whose expression was affected by deletion or overexpression of the KlPDR1 gene. All microarray experiments were performed using the 30K Kluyveromyces lactis NRRL Y-1140 microarray (MYcroarray, 5692 Plymouth Road, Ann Arbor, MI 48105, USA). more...

Organism:

Kluyveromyces lactis NRRL Y-1140; Kluyveromyces lactis

Type:

Expression profiling by array

Platform:

GPL21259

2 Samples

Download data: GPR

(Submitter supplied) The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. more...

Organism:

Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19759

4 Samples

Download data: BEDGRAPH

(Submitter supplied) The transcriptional response of K. lactis yeast was investigated following exposure to sodium arsenite (As(III)) and tert-butyl hydroperoxide (t-BOOH). We compared the genome-wide expression profile of Klyap8∆ mutant cells to that of the wild type.

Organism:

Kluyveromyces lactis

Type:

Expression profiling by array

Platform:

GPL11307

12 Samples

Download data: TXT