ID-JPL934
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA640964 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:marine metagenome [Taxonomy ID: 408172] Targeted loci environmental
| PRJNA1106516 | ENA
Project description:mouse gut metagenome [Taxonomy ID: 410661] Targeted loci
| PRJNA641570 | ENA
Project description:We developed CUT&ID, that simultaneously profiles genome-wide DNA and protein associations of any endogenous target in its native state, from one sample in a single streamlined workflow, and with no need of cloning or transgenesis. CUT&ID is enabled by a single fusion protein combining TurboID, protein A/G, and micrococcal nuclease, which drives sequential target recognition, proximal proteinity biotinylation and targeted DNA cleavage in living cells. We applied CUT&ID to CTCF, SMARCA4, H3K27ac, TCF7L2, b-catenin, JUN, RAD21, and HDAC1 in HCT116 cells.
2025-12-28 | E-MTAB-16382 | biostudies-arrayexpress
Project description:Serratia sp. ID 25-353 Genome sequencing
| PRJNA1404968 | ENA
Project description:Geobacillus thermoleovorans strain:ID-1 Genome sequencing
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Project description:Bacteria strain:Strain ID: SM10 Genome sequencing
| PRJNA1467613 | ENA
Project description:Stem cell functions require activation of stem cell-intrinsic transcriptional programs as well as intimate extracellular interactions with a niche microenvironment. How the core pluripotency transcriptional machinery controls residency of stem cells in the niche microenvironment is unknown. Here we show that the helix loop helix transcriptional regulators Id (Inhibitors of DNA binding) are the master regulators that coordinate stem cell activities with anchorage of neural stem cells (NSCs) to the embryonic and postnatal niche. Conditional inactivation of Id genes (Id1, Id2 and Id3) in the mouse NSC compartment triggered detachment of embryonic and post-natal NSCs from the ventricular and vascular niche respectively, followed by premature differentiation. Through an unbiased interrogation of the gene modules directly targeted by deletion of Id genes in NSCs, we discovered that Id proteins repress the bHLH-mediated activation of Rap1GAP, thus serving to maintain the GTPase activity of RAP1, a key mediator of cell adhesion. Preventing the elevation of Rap1GAP efficiently countered the consequences of Id loss on NSC-niche interaction and stem cell identity. Thus, by preserving anchorage to the extracellular environment of NSCs, Id activity synchronizes NSC functions to residency in the specialized niche.
2012-03-15 | GSE36488 | GEO
Project description:Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is however poorly characterized. The reason for this is that current methods to quantify RNA metabolism use short-read sequencing that cannot detect RNA isoforms. Here we present nanopore sequencing-based Isoform Dynamics (nano-ID), a method that detects newly synthesized RNA isoforms and monitors isoform metabolism. nano-ID combines metabolic RNA labeling, long-read nanopore sequencing of native RNA molecules and machine learning. nano-ID derived RNA stability estimates enable a distinctive evaluation of stability determining factors such as sequence, poly(A)-tail length, RNA secondary structure, translation efficiency and RNA binding proteins. Application of nano-ID to the heat shock response in human cells reveals that many RNA isoforms change their stability. nano-ID also shows that the metabolism of individual RNA isoforms differs strongly from that estimated for the combined RNA signal at a specific gene locus. nano-ID enables studies of RNA metabolism on the level of single RNA molecules and isoforms in different cell states and conditions.
2020-05-06 | GSE127890 | GEO