Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling of chromatin deposition bias in RPE-1 cells using Double-click-seq and SCAR-seq

ABSTRACT: We used double-click-seq and SCAR-seq methods to profile chromatin deposition bias in RPE-1 cells. Untreated cells and treatments promoting G4 formation (hydroxyurea, NMM) and their combination were profiled for characterizing chromatin protein redistribution asymmetry during DNA replication. This is an extension of our previous submission E-MTAB-8624

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Victor Guryev

PROVIDER: E-MTAB-13346 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Profiling of chromatin deposition bias in RPE-1 cells using Double-click-seq

Project description:We used double-click-seq method to profile chromatin deposition bias in RPE-1 cells. Untreated wild-type, p53 knock-out and several treatments (hydroxyurea, ATR inhibitor, curaxin) and their combinations were profiled for characterizing assymetry during DNA replication.

2021-10-04 | E-MTAB-8624 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (III)

Project description:RIP-chip experiments to identify RNAs associated with the Mmi1 protein in fission yeast

2015-09-25 | E-MTAB-3058 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (VI)

Project description:RIP-chip experiments to identify RNAs associated with components of the Ccr4-Not complex in fission yeast

2015-09-25 | E-MTAB-3065 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (II)

Project description:RIP-chip experiments to identify RNAs associated with components of the Ccr4-Not complex in fission yeast

2015-09-25 | E-MTAB-3057 | biostudies-arrayexpress

RIp-chip experiments with the Scw1 RNA-binding protein on ageing samples

Project description:We have used RIp-chip to identify mRNAs that coprecipitate with specific Scw1 RNA-binding protein on ageing samples

2019-06-01 | E-MTAB-7618 | biostudies-arrayexpress

Proteomics reveals coordinated stress adaptation by a MazF toxin to conserve carbon, sustain central metabolism, and preserve PDIM biosynthesis in Mycobacterium tuberculosis

Project description:In response to host-generated stresses, Mycobacterium tuberculosis (Mtb) reprograms its physiology in myriad ways to establish and maintain an infection, yet the signals that underlie this transformation are not well defined. The abundant toxin-antitoxin (TA) systems harbored in the Mtb genome, including eleven in the mazEF family, are thought to act as stress sensors, yet their roles are largely unknown. Although TA systems from other bacteria are generally thought to impart reversible growth arrest in response to stress, the exquisite specificity of Mtb tRNase toxins instead portends a more nuanced role. Here, we used a proteomics approach to track de novo protein synthesis to uncover molecular events initiated by the Mtb MazF-mt9 toxin (MazF7, Rv2063A). First, we documented striking enrichment of enzymes and transporters derived from the contiguous 36 gene region for phthiocerol dimycocerosate (PDIM) synthesis without an accompanying increase in PDIM lipid production. This paradox was reconciled by concomitant downregulation of proteins comprising the Mce1 transporter (imports host fatty acids), cholesterol breakdown, and β oxidation enzymes (limiting the PDIM precursor methylmalonyl-CoA). Thus, increased catalytic efficiency of the PDIM pathway appears to offset substrate starvation to ensure adequate production of PDIMs essential for Mtb early immune escape and virulence. Finally, isocitrate lyase 1 levels also increased, which in this context are expected to primarily catalyze the glyoxylate shunt to sustain central carbon metabolism while minimizing carbon loss. These exacting proteomic signatures are paralleled within the bedaquiline-treated Mtb transcriptome, highlighting a critical role for MazF-mt9 in orchestrating Mtb stress survival.

2026-03-06 | PXD052177 | Pride

Critical role of histone turnover in neuronal transcription and plasticity

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-22 | E-GEOD-69808 | biostudies-arrayexpress

Critical role of histone turnover in neuronal transcription and plasticity [ChIP-seq]

Project description:Turnover and exchange of nucleosomal histones and their variants, a process long believed to be static in post-replicative cells, remains largely unexplored in brain. Here, we describe a novel mechanistic role for HIRA (histone cell cycle regulator) and proteasomal degradation associated histone dynamics in the regulation of activity-dependent transcription, synaptic connectivity and behavior. We uncover a dramatic developmental profile of nucleosome occupancy across the lifespan of both rodents and humans, with the histone variant H3.3 accumulating to near saturating levels throughout the neuronal genome by mid-adolescence. Despite such accumulation, H3.3 containing nucleosomes remain highly dynamic–in a modification independent manner–to control neuronal- and glial- specific gene expression patterns throughout life. Manipulating H3.3 dynamics in both embryonic and adult neurons confirmed its essential role in neuronal plasticity and cognition. Our findings establish histone turnover as a critical, and previously undocumented, regulator of cell-type specific transcription and plasticity in mammalian brain. All ChIP-seq samples were generated to test the impact of neuronal activity/adult physiological plasticity on histone turnover in the central nervous system. This was tested in cultured neurons and astrocytes, FACS purified neurons or FACS purified Glia.

2015-06-23 | E-GEOD-69806 | biostudies-arrayexpress

A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrids accumulation

Project description:Transcriptionally active loci are particularly prone to breakage and mounting evidence suggest that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncovered a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we found that BLM promotes cell death. We report that upon excessive R-loop accumulation, DNA synthesis is enhanced at DSBs, in a anner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs.

2022-04-13 | E-MTAB-11592 | biostudies-arrayexpress

PEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress

Project description:Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.

2023-10-24 | PXD042395 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data