GEO DataSets

(Submitter supplied) The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects is still controversial. To determine how changes in chromosome positioning affect transcription we characterized nuclear organization and global gene expression after large-scale chromosomal rearrangements in budding yeast. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

42 Samples

Download data: TSV

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

Organism:

Saccharomyces cerevisiae; Mus musculus

Type:

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

Platforms:

GPL13112 GPL13821

37 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. more...

Organism:

Saccharomyces cerevisiae

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13821

19 Samples

Download data: WIG

(Submitter supplied) Transcriptome comparison of cells from 4 and 7 day-old microcolonies of wild Saccharomyces cerevisiae BR-F strain, 4 and 7 day-old microcolonies of feral BR-RF strain and 4- and 7 day-old microcolonies of domesticated BR-S strain. All colonies grown on solid complex media with glycerol as carbon source. The aim of the study was to identify genes required for fluffy (structured) colony formation as well as the genes specific for certain phenotypic variant. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3458

18 Samples

Download data: MEV

(Submitter supplied) We report here the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene, encoding the catalytic subunit. Deleting RHN201 alters mRNA expression for hundreds of genes. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch) and are seen for many genes involved in stress responses and genome maintenance, consistent with a role of RNase H2 in removing ribonucleotides incorporated into DNA during replication. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7542

14 Samples

Download data: TXT

(Submitter supplied) S. cerevisiae hog1 mutant strain was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 µg/ml. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1433

4 Samples

Download data

(Submitter supplied) S. cerevisiae was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 µg/ml. Cells were collected at 4hours of growth, frozen at -80 °C and processed for RNA extraction. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL1433 GPL1428

12 Samples

Download data

(Submitter supplied) Data processing included: 1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization) 2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL1433 GPL1428

20 Samples

Download data

(Submitter supplied) S. cerevisiae rlm1Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL927 GPL920

4 Samples

Download data

(Submitter supplied) S. cerevisiae slt2Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL920

4 Samples

Download data

(Submitter supplied) S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL920 GPL927

4 Samples

Download data

(Submitter supplied) Data processing included: 1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization) 2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL920 GPL927 GPL764

26 Samples

Download data