Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Lepidium perfoliatum and Lepidium apetalum Chloroplast Genome sequencing and assembly

PROVIDER: PRJNA682689 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13213155_1.fastq.gz	Fastqsanger.gz
	SRR13213155_2.fastq.gz	Fastqsanger.gz
	SRR13213156_1.fastq.gz	Fastqsanger.gz
	SRR13213156_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Project description:The complete chloroplast genome of Silphium perfoliatum L.

| PRJNA686806 | ENA

RNA-seq of Arabidopsis thaliana wild-type and a putative chloroplast ribosome biogenesis mutant AtRsgA homozygous knockout

Project description:In this study, we have characterized a putative chloroplast ribosome assembly factor. To elucidate transcriptional responses caused by decreased chloroplast function, we have measured the transcriptome of wild-type and knock-down seedlings.

2018-08-16 | E-MTAB-6866 | biostudies-arrayexpress

ddLepDidy1

Project description:Lepidium didymum genome assembly, ddLepDidy1

| PRJEB71486 | ENA

The comparison for the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants

Project description:We found that thylakoid-anchored protein PBF8 is a key regulator for Photosystem I (PSI) biogenesis. To explore the role of PBF8 in regulating chloroplast gene expression, we performed the RNA-seq to compare the the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants. To this end, we isolated the total RNA form 12-day-old wild type and pbf8 seedlings grown on the MS medium under long-day conditions (14 h light, 10 h dark) at 22 ºC and with a light intensity of 80 µmol m-2 s-1. The rRNAs were deleted using the Ribo-Zero Kit (Epicentre). The resulting rRNA-depleted RNA was used for preparing the sequencing library with NEBNext Single Cell/Low input library Prep Kit. The libraries were pooled and sequenced on an Illumina Nova 6000 system with 150-bp pair-end reads. Finally, our results show that the transcript accumulation for chloroplast-encoded PSI subunit and assembly factor genes between the wild type (Col-0) and pbf8 samples, suggesting PBF8 may not affect the transcript levels of chloroplast-encoded PSI subunits and assembly factors in chloroplasts.

2024-01-24 | GSE239827 | GEO

Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [ChIP-seq]

Project description:The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.

2022-12-13 | GSE220489 | GEO

Lepidium campestre isolate:EHA205

Project description:Lepidium campestre isolate:EHA205 Genome sequencing and assembly

| PRJNA587432 | ENA

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

Chloroplast-genome-wide maps of small RNAs in Chinese cabbage (Brassica rapa) and Arabidopsis thaliana (Ler).

Project description:Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3â-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5â-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast.

2012-03-31 | GSE28281 | GEO

Project description:The complete chloroplast genome of Lepidium latifolium and phylogenetic analysis of Brassicales

| PRJNA673799 | ENA

Coordination of nuclear and plastid transcription for chloroplast biogenesis requires H4 acetylation by the NuA4 complex

Project description:Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.

2022-07-26 | GSE180614 | 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