GEO DataSets

(Submitter supplied) IL-23 and IL-17 are well-validated therapeutic targets in autoinflammatory diseases. Antibodies targeting IL-23 and IL-17 have shown clinical efficacy but are limited by high costs, safety risks, lack of sustained efficacy, and poor patient convenience as they require parenteral administration. Here we present designed miniproteins inhibiting IL-23R and IL-17 with antibody-like low picomolar affinities at a fraction of the molecular size. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL17143

34 Samples

Download data: XLSX

(Submitter supplied) Alternative polyadenylation gives rise to a wide variety of mRNA isoforms with distinct 3' ends; an individual gene can yield many 3' mRNA isoforms and has a typical pattern of poly(A) site use. To identify possible determinants of polyadenylation site distribution, we have used CRISPR to create Saccharomyces cerevisiae strains harboring precise ORF deletions in candidate genes encoding various factors involved in gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

2 Samples

Download data: TXT

(Submitter supplied) How parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications, are transferred to leading and lagging strands of DNA replication forks following DNA replication is an important question that remains not well understood. Here we show that DNA polymerase clamp PCNA and its partner involved in lagging strand DNA synthesis, Pol d, regulate parental histone transfer to lagging strands. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

274 Samples

Download data

(Submitter supplied) We report the ChIP-seq profiling of a transcriptional factor Sef1 in Sccharomyces cerevisiae, and show that ScSef1 targets many TCA cycle and many others genes but has very limited regulatory effects to these target genes.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

14 Samples

Download data: BIGWIG, NARROWPEAK, TXT, WIG

(Submitter supplied) Arabidopsis gene expression is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for most Arabidopsis TFs, we lack knowledge about the presence, location, and transcriptional strength of their ADs. To address this gap, we experimentally identified Arabidopsis ADs on a proteome-wide scale, finding that over half of Arabidopsis TFs carry an AD. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL27812

164 Samples

Download data: CSV

(Submitter supplied) Protein folding is driven by the burial of hydrophobic amino acids in a tightly-packed core that excludes water. The genetics, biophysics and evolution of hydrophobic cores are not well understood, in part because of a lack of systematic experimental data on sequence combinations that do - and do not - constitute stable and functional cores. Here we randomize protein hydrophobic cores and evaluate their stability and function at scale. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL31112

16 Samples

Download data: CSV

(Submitter supplied) Missense variants that change the amino acid sequences of proteins cause one third of human genetic diseases. Tens of millions of missense variants exist in the current human population, with the vast majority having unknown functional consequences. Here we present the first large-scale experimental analysis of human missense variants. Using DNA synthesis and cellular selection experiments we quantify the impact of >500,000 variants on the abundance of >500 human protein domains. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL27812 GPL19756 GPL31112

78 Samples

Download data: TXT

(Submitter supplied) Thousands of protein domains encoded in the human genome function by binding up to a million short linear motifs embedded in intrinsically disordered regions of other proteins. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of ‘fuzzy’ dynamic residues to affinity and specificity in protein-protein interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

32 Samples

Download data: CSV

(Submitter supplied) Epigenetic mechanisms contribute to gene regulation by altering the accessibility of the chromatin, resulting in transcription factor (TF) and nucleosome occupancy changes throughout the genome. A major challenge is defining and dissecting this complex chromatin-mediated code to model transcriptional regulation and predict gene expression. We address this by employing a factor-agnostic, reverse-genetics approach to capture TF and nucleosome occupancies genome-wide in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae using MNase-seq, totalling nearly 1,000,000 possible mutant-gene interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

201 Samples

Download data: RDS

(Submitter supplied) Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

122 Samples

Download data: WIG

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

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL25739

134 Samples

Download data: WIG

(Submitter supplied) Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ~20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL19756

24 Samples

Download data: TXT

(Submitter supplied) The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase, and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates an enrichment of axis proteins at nucleosome-rich genomic islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19756

46 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, repair pathway choice – the cellular decision making underlying DSB repair – occurs at the level of DSB resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate DSB resection and repair by homologous recombination (HR). more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27812 GPL19756

96 Samples

Download data: BEDGRAPH

(Submitter supplied) Differentially expression analysis to evaluate transcriptome comparing among 25, 30 and 37°C grown yeast cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

6 Samples

Download data: XLSX

(Submitter supplied) Gene expression results from mRNA - RNA-binding protein (RBP) interactions within messenger ribonucleoprotein (mRNP) particles. We identified heterogeniety of nuclear mRNP composition involved in mRNA biogenesis and export with different occupancy and stoichiometry of RNA-binding proteins. Especially, mRNA export adopter protein Yra1 showed large variation of its stoichiometry on single mRNPs. We identified stoichiometry of Yra1 in the nuclear cap binding complex (Cbp80) bound mRNPs and it can be dissected into two categories (one and multiple Yra1 bound mRNPs). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

44 Samples

Download data: XLSX

(Submitter supplied) Genomes from yeast to human are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

5 Samples

Download data: BEDGRAPH

(Submitter supplied) As training dataset for Random Promoter DREAM Challenge 2022, we generated ~6.7 million synthetic promoters (in yeast) comprised of random DNA (N80) and measured their expression by FACS (sorting into 18 bins). As test dataset for Random Promoter DREAM Challenge 2022, we generated ~71k synthetic promoters (in yeast) comprised of designed DNA (NBT) and measured their expression by FACS (sorting into 18 bins).

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

36 Samples

Download data: TXT

(Submitter supplied) Study to identify genes for which a decrease or an increase in gene expression resulted in increased secretion of α-amylase.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

28 Samples

Download data: TXT

(Submitter supplied) Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1,2,3,4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. more...

Organism:

Mus musculus; Saccharomyces cerevisiae

Type:

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

Platforms:

GPL19057 GPL19756

160 Samples

Download data: BW, NARROWPEAK