GEO DataSets

(Submitter supplied) The initial step of RNA polymerase II (Pol II) transcription involves a large number of transcription factors and arises at multiple sites within most promoters. TFIIH is an essential, multi-subunit transcription factor that assembles on promoter DNA with Pol II and five other general transcription factors (GTFs) to form a pre-initiation complex (PIC) for basal transcription. During transcription initiation, TFIIH melts promoter DNA through the ATPase activity of its Ssl2 subunit. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

58 Samples

Download data: BEDGRAPH, CSV, TXT

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

264 Samples

Download data: CSV, WIG

(Submitter supplied) Human BET family members are promising targets in the therapy of cancer and immunoinflammatory diseases, but their mechanism of action and functional redundancies are poorly understood. Yeast BET factors Bdf1/2 were previously proposed to act as anchors for coactivator TFIID. We investigated their genome wide roles in transcription and found that, while they cooperate with TFIID at many genes, their contributions to transcription are often significantly different. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

42 Samples

Download data: CSV

(Submitter supplied) Human BET family members are promising targets in the therapy of cancer and immunoinflammatory diseases, but their mechanism of action and functional redundancies are poorly understood. Yeast BET factors Bdf1/2 were previously proposed to act as anchors for coactivator TFIID. We investigated their genome wide roles in transcription and found that, while they cooperate with TFIID at many genes, their contributions to transcription are often significantly different. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

100 Samples

Download data: WIG

(Submitter supplied) Human BET family members are promising targets in the therapy of cancer and immunoinflammatory diseases, but their mechanism of action and functional redundancies are poorly understood. Yeast BET factors Bdf1/2 were previously proposed to act as anchors for coactivator TFIID. We investigated their genome wide roles in transcription and found that, while they cooperate with TFIID at many genes, their contributions to transcription are often significantly different. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

122 Samples

Download data: WIG

(Submitter supplied) Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC). We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements. However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17143

16 Samples

Download data: BIGWIG, SGR

(Submitter supplied) Transcription coupled-nucleotide excision repair (TC-NER) repairs DNA lesions that stall RNA polymerase II (Pol II) transcription. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD is required for efficient Rad26-dependent and Rad26-independent TC-NER across the yeast genome. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL27831 GPL18249

16 Samples

Download data: TXT, WIG

(Submitter supplied) Nucleosomes are a significant barrier to the repair of UV damage because they impede damage recognition by nucleotide excision repair (NER). The RSC and SWI/SNF chromatin remodelers function in cells to promote DNA access by moving or evicting nucleosomes and both have been linked to NER in yeast. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking RSC or SWI/SNF activity. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL18249

23 Samples

Download data: TXT, WIG

(Submitter supplied) Elf1 is an important transcription elongation factor that has been implicated in transcription coupled-nucleotide excision repair (TC-NER). Here, we have used a high-throughput sequencing method known as CPD-seq to map the repair of UV-induced cyclobutane pyrimidine dimers (CPDs) at single nucleotide resolution across the yeast genome in elf1 mutant cells. Analysis of CPD repair indicates that Elf1 is important for CPD repair in the transcribed strand (TS) of yeast genes, indicating it plays an important role in TC-NER.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL18249

6 Samples

Download data: WIG

(Submitter supplied) Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that responds to RNA polymerase (RNAP) stalling and removes DNA lesions from transcribed genes. Activation of TC-NER requires specific factors, such as human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. Mutations in CSB are associated with the severe neurological disorder Cockayne syndrome. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL18249

18 Samples

Download data: BED, WIG

(Submitter supplied) Rad16 is required for global genomic nucleotide excision repair (GG-NER) of UV-induced CPD lesions. Here we have used a novel high-throughput sequencing method known as CPD-seq to map the repair of UV-induced cyclobutane pyrimidine dimers (CPDs) at single nucleotide resolution across the yeast genome in rad16 mutant cells. Analysis of CPD repair indicates that rad16 is generally required for CPD repair in the non-transcribed strand (NTS) of yeast genes and non-transcribed genomic regions.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL18249

5 Samples

Download data: BED, WIG

(Submitter supplied) Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here, we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, NTP substrate levels, and RNA polymerase II (Pol II) activity to TSS selection by "promoter scanning" in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, "Pol II MASTER"). more...

Organism:

Saccharomyces cerevisiae; Escherichia coli

Type:

Other

Platforms:

GPL19756 GPL27812 GPL25368

90 Samples

Download data: CSV, TXT

(Submitter supplied) Using a modification of the yeast anchor away and PAR-CLIP protocols, we have mapped the position of Pol II genome-wide in living yeast cells after depletion of components of either the polyadenylation (pA) or non-pA termination complexes. Depletion of Ysh1 from the nucleus does not lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

5 Samples

Download data: WIG

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

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

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

Platforms:

GPL31112 GPL19756 GPL29170

119 Samples

Download data

(Submitter supplied) A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs) which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29170

24 Samples

Download data: CSV

(Submitter supplied) A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs) which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL31112 GPL19756

95 Samples

Download data: TXT

(Submitter supplied) We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

6 Samples

Download data: BW, TSV

(Submitter supplied) We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

13 Samples

Download data: BB, BW

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18330

40 Samples

Download data: BED, WIG

(Submitter supplied) Gene expression is controlled by a variety of proteins (the epigenome) whose precise organization and mechanism of action at every promoter remains to be worked out. Here we examine a functionally diverse subset of these proteins: RSC (Rsc9), SAGA (Spt3), Hsf1, general transcription factors (GTFs), FACT (Spt16), and RNA polymerase (Pol) II, under normal and acute heat shock conditions, using the ultra-high resolution genome-wide ChIP-exo assay. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL13821

178 Samples

Download data: CSV, GFF, TAB, TXT