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MetabolomicsThe telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous trans...

2024-04-02 | MTBLS8679 | MetaboLights
TranscriptomicsMeasure transcript integrity using RNA-seq data
Achieved biospecimens annotated with patient clinical characteristics are unique resources for translational research. However, RNA extracted from the achieved tissues is often degraded. RNA degradation can have a significant impact on the measure of transcript abundance that can lead to an increase...
ORGANISM(S): Homo sapiens 
2016-02-19 | E-GEOD-70285 | biostudies-arrayexpress
TranscriptomicsAssessment of genome integrity with array CGH of cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple round...
ORGANISM(S): Bos taurus 
2011-05-23 | E-GEOD-26132 | biostudies-arrayexpress
TranscriptomicsIntegrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (PAR-CLIP)
We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, for AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total ...
ORGANISM(S): Homo sapiens 
2014-11-05 | E-GEOD-52971 | biostudies-arrayexpress
TranscriptomicsHistone H3.3 maintains genome integrity during mammalian development
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans, and has been implicated in many important biological processes including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components, or in H3.3 encoding genes,...
ORGANISM(S): Mus musculus 
2015-06-12 | E-GEOD-69771 | biostudies-arrayexpress
ProteomicsThe Greatwall kinase safeguards the genome integrity by balancing the kinome activity in mitosis.
Mastl is commonly overexpressed in cancer, appearing as an alternative therapeutic anticancer target. Loss of Mastl induces multiple chromosomal mitotic errors that lead to the accumulation of micronuclei and multilobulated cells with polyploidy. Our detailed analyses display that loss of Mastl quic...
ORGANISM(S): Mus Musculus (mouse) 
2020-10-15 | PXD019297 | JPOST Repository
TranscriptomicsThe age and genomic integrity of neurons after cortical stroke in humans
It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA-rearrangements in the human neocortex. We show here that neither is the case, using immunohistochemistry, transcriptome-, genome- and ploidy-analyses, and determination of nuclear bomb test-derived 14C-concentration in ...
ORGANISM(S): Homo sapiens 
2014-03-28 | E-GEOD-56267 | biostudies-arrayexpress
ProteomicsJAK2-CHK2 signaling safeguards the integrity of the mitotic spindle assembly checkpoint and genome stability
Checkpoint kinase 2 (CHK2) plays an important role in safeguarding the mitotic progression, specifically the spindle assembly, though the mechanism of regulation remains poorly understood. Here, we identified a novel mitotic phosphorylation site on CHK2 Tyr156, and its responsible kinase JAK2. Expre...
ORGANISM(S): Homo sapiens (Human) 
2024-10-16 | PXD056821 | Pride
Phosphorylation Chk2 Lc-ms/ms 
ProteomicsPRMT5 activity sustains histone production to maintain genome integrity
Histone proteins package DNA into nucleosomes, forming chromatin and thereby safeguarding genome integrity. Proper histone expression is essential for cell proliferation and chromatin organization, yet the upstream regulators of histone supply remain in-completely understood. PRMT5—a cell essential ...
ORGANISM(S): Homo sapiens (Human) 
2026-09-08 | PXD065294 | Pride
Histone transcription Prmt5 Arginine methylation Arginine methyltransferase Genome integ-rity Post-translational modifications 
TranscriptomicsMapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type
Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially i...
ORGANISM(S): Arabidopsis thaliana 
2011-11-06 | E-GEOD-21781 | biostudies-arrayexpress
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