GEO DataSets

(Submitter supplied) We compare patterns of H2Bub and H2B across genes in WT, ubp8 KO and Dot1 OE cells

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

12 Samples

Download data: BW

(Submitter supplied) Strain background is Saccharomyces cerevisiae wzy42 histone mutant strain with pWZ403 Myc-HHT2-HHF2 plasmid and pGAL1/10 FLAG-HHT1-HHF1 integrated gene. Cells were grown in YP+2% raffinose until mid-log (OD600=0.5) and arrested with alpha factor. When most of Cells were in G1 phase, added galactose (final conc. 2%) and harvested cells after 1 hour. Fixed cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

40 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Dot1 is a methyl transferase that has been shown through a reporter gene to be involved in position effect variegation of gene expression in heterochrmatic regions such as telomeres and the mating type loci in yeast. This study examines the effect of mutation of DOT1 and two other proteins involved in H3K79 methylation, SWI4 and ARD1, on gene expression relative to wt cells.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

8 Samples

Download data: CEL

(Submitter supplied) We compare patterns of H3K79me and H2Bub across genes in budding yeast

Organism:

Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18330

20 Samples

Download data: BW

(Submitter supplied) Monoubiquitination of histone H2B on lysine 123  (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively.  Many of the factors such as Rad6/Bre1, the Paf1 complex, and the Bur1/Bur2 complex were identified to be required for proper histone H3K4 and H3K79 trimethylation, and were shown to function by regulating H2BK123ub levels. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL13821

10 Samples

Download data: BED

(Submitter supplied) Purpose: We want to know whether Ino80C contribute to chromatin silencing at both euchromatin and heterochromatin Methods: All yeast cells were collected in exponential phase. Total RNA was extracted with phenol, digested with DNase and further purified by Trizol. Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or stranded RNA Sample Prep Kits. Libraries were sequenced on Illumina HiSeq 2000. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL13821

27 Samples

Download data: BED, TXT

(Submitter supplied) The goal of the project was to study the effects on transctiptome of some mutations related with SAGA complex

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24365

4 Samples

Download data: TXT

(Submitter supplied) DOT1L, the only H3K79 methyltransferase in human cells and a homolog of the yeast Dot1, normally forms a complex with AF10, AF17 and ENL/AF9, is dysregulated in most of the cases of mixed lineage leukemia (MLL) and is believed to regulate transcriptional elongation without much evidence. Here we show that the depletion of DOT1L reduced the global occupancy without affecting the traveling ratio or the elongation rate of Pol II, suggesting it not a major player in elongation. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20795 GPL16791 GPL24676

74 Samples

Download data: BW, TXT

(Submitter supplied) Methylation of histone H3 lysine 4 (H3K4) by the Set1/COMPASS complex is coupled with active transcription, and this modification is important for regulating gene expression. Set1/COMPASS associates with the RNA polymerase II (RNApII) C-terminal domain (CTD) to establish proper levels and distribution of H3K4 methylations.To ask how the Set1-RNApII CTD binding affects the occupancy and overall level of H3K4 methylations, ChIP-Seq was pefromed in cells transformed with full length or N-terminal truncated Set1. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

27 Samples

Download data: BW

(Submitter supplied) H2B mono-ubiquitylation is required for multiple methylations of both H3K4 and H3K79 and has been implicated in gene expression from yeast to human. However, molecular crosstalk between H2BUb1 and other modifications, especially H3K4 and H3K79 methylations, remains unclear in vertebrates. To understand the functional role of H2BUb1, genome-wide histone modification patterns were measured in human cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL9052

14 Samples

Download data: BED, SAM, TXT

(Submitter supplied) The PAT-seq approach was utilised to determine the gene expression changes over the cell-cycle of wildtype and delta-set1 yeast strains. The cell were synchronised by alpha-factor arrest and cell-cycle release

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18085

20 Samples

Download data: CSV

(Submitter supplied) In Saccharomyces cerevisiae histone H2B is ubiquitylated at lysine 123. The SAGA complex component, Ubp8, is one of two proteases that remove this ubiquitin moiety. We analyzed gene expression in a strain containing a variant of histone H2B with lysine 123 converted to arginine to address the mechanisms by which ubiquitylation and deubiquitylation of histone H2B affects gene expression. We show that changes in gene expression observed upon deletion of ubp8 are suppressed by htb1K123R. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL884 GPL2883

9 Samples

Download data: TXT

(Submitter supplied) Comparison of DOT4-6Myc/dot4-1-6Myc cells, DOT4-6Myc/dot4-5-6Myc cells, DOT4-6Myc/dot4 null cells, DOT4-6Myc/DOT4 cells in YEPD Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1879

24 Samples

Download data

(Submitter supplied) Comparison of DOT4/dot4 null cells, UBP8/ubp8 null cells, and DOT4UBP8/dot4ubp8 null cells in YEPD. Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1879

18 Samples

Download data

(Submitter supplied) We generated high-throughput sequencing (ChIP-seq) data for genome wide occupancy of hDot1L and RNAPII-5p in human embryonic carcinoma cell.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: BED

(Submitter supplied) Purpose: Understand the synergistic relationship between the methyltransferases Set1 and Set5 in the regulation of gene expression. Methods: Total mRNA was obtained from two independent biological replicates each of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ S. cerevisiae strains. Libraries were generated and sequenced using an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were mapped using TopHat and expression levels were quantified using Cufflinks. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

10 Samples

Download data: TXT

(Submitter supplied) Inhibition of transcriptional elongation plays an important role in gene regulation in metazoans, including C. elegans, which lacks Negative Elongation Factor homologs. Here we combine genomic and biochemical approaches to dissect a novel role of C. elegans AF10 homolog, ZFP-1, in transcriptional control. We show that ZFP-1 and its interacting partner DOT-1.1 have a global role in negatively modulating the level of Pol II transcription on essential widely expressed genes. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL13657

4 Samples

Download data: WIG

(Submitter supplied) The mutation in the budding yeast gene PCNA, pol30-8, as well as deletion of DOT1 (dot1Δ), encoding the only histone H3 K79 methyltransferase in budding yeast, have been implicated in telomeric silencing. To further analyze these mutants, we used microarrays to study whether either pol30-8, dot1Δ or the double mutant leads to changes in gene expression levels when compared to isogenic wild-type strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13150

12 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

27 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) The deubiquitinating module (DUBm) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and ATXN7, ATXN7L3 and ENY2 adaptor proteins, which are all needed for the full activity of USP22 enzyme. In addition, ATXN7L3 is critical for directing the DUB module substrate specificity towards H2Bub1. We reported that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK