Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

ABSTRACT: A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

INSTRUMENT(S):

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Leaf

SUBMITTER: Wanchao Zhu

LAB HEAD: Lin Li

PROVIDER: PXD026111 | Pride | 2021-05-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	WA285LQ_R_6_Slot1-45_1_1690.d.zip	Other
	WA285LQ_R_7_Slot1-46_1_1692.d.zip	Other
	WA285LQ_R_8_Slot1-47_1_1694.d.zip	Other
	search_result_rice.zip	Other

Items per page:

1 - 4 of 4

Similar Datasets

A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

Project description:A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

2021-05-30 | PXD019635 | Pride

A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

2021-05-30 | PXD026112 | Pride

A new cost-effective ribosome profiling technique complements the functional genome annotation and reveals a key role of genic 3’ untranslated region in plant translatomic variation

2021-05-30 | PXD026096 | Pride

A Comparative Proteome and Phosphoproteome Reveal the Molecular Mechanism of the Difference between Imitative Wild Variety and Cultivated Variety of Dendrobium huoshanense C. Z. Tang et S. J. Cheng

Project description:This project intends to conduct comparative proteomics research on wild and cultivated varieties of Dendrobium huoshanense that are similar in plant shape and in the same growth and development stage through proteomics and protein modification omics combined with the differences in metabolites in Dendrobium huoshanense. Full-scan proteomic data of Dendrobium; compare the protein expression levels of wild and cultivated varieties to find relevant candidate proteins, and perform functional annotation and KEGG analysis of metabolic pathways for candidate proteins with different expressions to further analyze the material basis differences between wild and cultivated varieties Provide research objects of molecular biology.

2022-06-24 | PXD022337 | Pride

Comparative TSS-seq analysis among Arabidopsis natural variations revealed genetic stability of genic and non-genic promoters

Project description:In our previous study, more than 300K promoters were identified in the Arabidopsis genome, including many non-genic promoters that do not transcribe gene bodies. Although some functional non-genic promoters have been reported, the biological importance of many others remains unclear. In this study, we evaluated their genetic stability by analysis of promoter sequence and peak positions of TSS clusters using Arabidopsis natural variations. Canonical genic promoters showed high conservation of sequence and TSS peak positions. Moreover, they were well structured in terms of the presence of core elements, promoter context, and epigenetic features. These data revealed that the genic promoters are genetically stable and well-structured, which is consistent with their biological significance for the expression of genes. On the other hand, non-genic promoters showed low stability of TSS peak position and low structured features. Therefore, We concluded that most non-genic promoters are biologically insignificant with some exceptions. Interestingly, the genetic stability of promoters has a positive relation with the expression level. This suggests weak promoters like most non-genic promoters are results of leaky transcription, which supports the concept of “transcriptional noise”.

2025-12-30 | GSE298979 | GEO

The evolution of genic piRNA cluster loci expression patterns

2015-11-01 | GSE62556 | GEO

Genome-wide identification and characterization of small peptides in maize

Project description:Small peptides (sPeptides), a class of biological molecules of less than 100 amio acids encoded by small open reading frames (sORFs), play important roles in multiple biological process. Here, we conducted a comprehensive study using mRNA-seq, Ribo-seq, and Mass Spectrometry (MS) on six tissues (each with at least two replicates) of maize, set up a bioinformatic pipeline, and performed a genome-wide scan of sORFs and sPeptides in maize. Our study sets up a guildline for the genome-wide scan of sORFs and sPeptides in plants by integrating Ribo-seq, and MS data, provides a more comprehensive resource of functional sPeptides in maize, and sheds light on the complex biological system of plants in a new perspective.

2021-05-30 | PXD025997 | Pride

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

Project description:The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are sensed remain poorly understood. Here we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1&2) functioning as the R-loops sensor of genic regions in higher plant Arabidopsis thaliana. AtALBA1 and 2 form a heterodimer protein complex and localize in the nucleus. While AtALBA1 binds to the DNA-RNA hybrid strand, AtALBA2 associates with single-stranded DNA in the R-loops. AtALBA1&2 preferentially binds to the genic R-loop regions that are associated with active epigenetic marks. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. Our results demonstrate the AtALBA1&2 protein complex is the Arabidopsis genic R-loops sensor for maintaining genome stability in Arabidopsis.

2019-04-17 | GSE121683 | GEO

The evolution of genic piRNA cluster loci expression patterns

Project description:This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts. By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species. We dissected gonad tissues consisting of ovaries from wildtype adult Drosophilids (D.melanogaster, D.erecta, D.yakuba, D.virilis) and testes from wildtype pre-pubsecent and adult mouse and rats. Adult testes from rabbits were purchased from Pel-Freez Biologicals. Total or immunopreciptated RNAs were extracted from the pulvirized gonad tissues of Drosophilids and Glires. Small RNAs were purified from these samples, converted into cDNA libraries, and sequenced on an Illumina HiSeq2000.

2015-11-01 | E-GEOD-62556 | biostudies-arrayexpress