Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

ABSTRACT: Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE157415 | GEO | 2020/10/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

Project description:Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

2020-10-28 | GSE157416 | GEO

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

Project description:Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

| PRJNA661263 | ENA

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-10-28 | GSE157418 | GEO

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

Project description:Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

| PRJNA661264 | ENA

Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in <i>Caenorhabditis elegans</i>.

Project description:Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (RNA-seq) studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 3901 candidate genes with putatively active transcription in XXX cells, including the few previously known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.

| S-EPMC7768263 | biostudies-literature

Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

Project description:Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

| PRJNA661258 | ENA

DNA-Protein Crosslink sequencing (DPC-seq) in RPE-1 cells treated with formaldehyde

Project description:Covalent DNA-protein crosslinks (DPC) are toxic DNA lesions that require repair by global-genome and replication-coupled pathways. How cells respond when RNA polymerases stall at DPCs during transcription is unknown. DPC-seq is new method for the genome-wide mapping of covalent DNA-protein adducts.

2024-02-24 | E-MTAB-12912 | biostudies-arrayexpress

Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.

2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

Project description:Here we describe CapTrap-Seq, an experimental workflow designed to address the problem of reduced transcript end detection by long-read RNA sequencing methods, especially at the 5' ends. We apply CapTrap-Seq to profile transcriptomes of the human heart and brain and we compared the obtained results with other library preparation approaches. CapTrap-Seq is a platform-agnostic method and here tested the method by using 3 different long-read sequencing platforms: MinION (ONT), Sequel (PacBaio) and Sequel II (PacBio).

2023-12-20 | E-MTAB-13063 | biostudies-arrayexpress

Lysine-targeting, covalent inhibitors of bromodomain BD1 of BET proteins in live cells and animals

Project description:Bromodomain (BRD) is an epigenetic reader of acetylated lysine. It has emerged as a therapeutic target for cancer and other diseases. Current nonselective BRD inhibitors (BRDis) face several adverse events (i.e. gastrointestinal toxicity and thrombocytopenia), making the development of target covalent inhibitor (TCI) for BD1/2 as a fresh avenue to overcome safety challenges. We report herein a set of activity-based probes (ABPs; P3-P7) based on various lysine-reactive covalent warheads capable of global profiling of ligandable lysine within BRDs in live cells and animals. Chemoproteomic experiments with P7 by utilizing 2-ethynylbenzaldehyde (EBA) identified 16 endogenous BRDs, thus giving a global landscape of ligandable lysines in BRDs. By further introducing EBA and salicylaldehyde into PLX51107 (a non-covalent BRDi), we generated novel irreversible (BDS1-4) and reversible (BDS5-6) lysine-reactive TCIs. Mass spectrometry and X-ray crystallography confirmed the successful covalent engagement between the covalent warhead and lysine near Kac binding site. BDS4 showed 104-fold selectivity for BD1 over BD2 with prolonged anti-cancer effect than non-covalent BRDi. Importantly, BDS4 retained robust activity against fibrosis in cells and animals in comparison to the marginal effect of BD2 inhibitor RVX-208. Our work serves as a useful tool to delineate the distinct function of BD1 and BD2.

2024-12-11 | GSE283487 | GEO

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