GEO DataSets

(Submitter supplied) Cuscuta campestris is an obligate parasitic plant that attaches to the stems of host plants to obtain water and nutrients. C. campestris produces a specialized set of microRNAs specifically at the host-parasite interface. Many of these interface-induced microRNAs target mRNAs from the host. This experiment was designed to capture full-length primary transcripts that give rise to C. campestris interface-induced microRNAs. more...

Organism:

Cuscuta campestris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32961

9 Samples

Download data: TSV

(Submitter supplied) Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. more...

Organism:

Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28300

6 Samples

Download data: TXT

(Submitter supplied) To gain an understanding of the regulatory role of PilG and PilH in Xcc a set of global gene expression profiles,we performed transcriptome analysis.Transcriptome analyses that showed PilG and PilH regulating many genes involved chemotaxis and flagellar biosynthesis.Taken this data together it is clear the impact of PilG and PilH on the expression of specific genes at the transcriptional level accounts for the phenotypes seen in the ΔpilG and ΔpilH strains.

Organism:

Xanthomonas campestris pv. campestris str. 8004

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25598

6 Samples

Download data: XLSX

(Submitter supplied) Parasitism is a successful life strategy that has evolved independently in several families of Higher Plants. In parasitic plants, nutrients and water are obtained from their hosts through specifically adapted haustoria. The genera Cuscuta and Orobanche represent examples for the two profoundly different groups of parasites, one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs (sRNome) from Cuscuta campestris and compared it to an exploratory sRNome from Orobanche aegyptiaca. more...

Organism:

Cuscuta campestris

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30483

13 Samples

Download data: FASTA, TXT

(Submitter supplied) The parasitic plant Cuscuta campestris produces specialized microRNAs that are specifically expressed at the haustorial interface. Some of these "Interface-Induced MicroRNAs" function to target host mRNAs. C. campestris haustoria can be induced in the absence of any host tissues using a combination of light and physical pressure. This experiment tested with such in vitro, host-free haustoria produced interface-induced microRNAs. more...

Organism:

Cuscuta campestris

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32307

9 Samples

Download data: CSV

(Submitter supplied) Cuscuta campestris is an obligate stem parasite which uses an organ called the haustoria to divert water and photosynthates from the host.  Previously, we have identified that at the haustorial interface between Cuscuta campestris and Arabidopsis thaliana, miRNAs generated by the parasite are able to move into the host and regulate host gene expression.  This study identifies how long after attachment does trans-species miRNA transcription begin in Arabidopsis thaliana and Solanum lycopersicum, as well as identifying which stage of haustoria development they become detectable.  A time course was performed by harvesting interfaces every 24 hours post attachment, and samples were subjected to RNA extraction and sRNA sequencing. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL29032

42 Samples

Download data: CSV

(Submitter supplied) Cuscuta campestris is an obligate stem parasite which uses an organ called the haustoria to divert water and photosynthates from the host.  Previously, we have identified that at the haustorial interface between Cuscuta campestris and Arabidopsis thaliana, miRNAs generated by the parasite are able to move into the host and regulate host gene expression.  This study identifies how long after attachment does trans-species miRNA transcription begin in Arabidopsis thaliana and Solanum lycopersicum, as well as identifying which stage of haustoria development they become detectable.  A time course was performed by harvesting interfaces every 24 hours post attachment, and samples were subjected to RNA extraction and sRNA sequencing. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24270

50 Samples

Download data: CSV

(Submitter supplied) Cuscuta campestris is an obligate parasitic plant that requires a host to complete its lifecycle. Parasite-host connections occur via an haustorium, a unique organ that acts as a bridge for the uptake of water, nutrients and macromolecules. Research on Cuscuta is often complicated by host influences, but comparable systems for growing the parasite in the absence of a host do not exist. We developed an axenic method to grow C. more...

Organism:

Cuscuta campestris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30290

8 Samples

Download data: TXT

(Submitter supplied) Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. more...

Organism:

Brassica rapa subsp. pekinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24709

2 Samples

Download data: TXT

(Submitter supplied) Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. more...

Organism:

Brassica rapa subsp. pekinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29989

2 Samples

Download data: TXT

(Submitter supplied) The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. more...

Organism:

Brassica rapa subsp. pekinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24709

6 Samples

Download data: TXT

(Submitter supplied) The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. more...

Organism:

Brassica rapa subsp. pekinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29989

6 Samples

Download data: TXT

(Submitter supplied) We performed a transcriptomic analysis of the necrotrophic bacteria Xanthomonas campestris pv. campestris exposed to two different isothiocyanates (allyl-isothiocyanate and indol-3-carbinol), searching for mechanisms of adaptation and detoxification of these chemicals.

Organism:

Xanthomonas campestris pv. campestris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24162

6 Samples

Download data: TXT

(Submitter supplied) Vascular plant diseases, such as rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) and crucifer black rot caused by Xanthomonas campestris pv. campestris (Xcc), cause huge yield loss of crops worldwide. However, how plants operate vascular defense against these obligate pathogens remains elusive. In this study, we used both Arabidopsis and rice pathosystems to address the long-standing question. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: XLS

(Submitter supplied) The tripartite ParA-ParB-parS complex ensures faithful chromosome segregation in the majority of bacterial species. ParB nucleates on the centromere-like parS site and spreads to neighboring DNA to form a network of protein-DNA complexes. This nucleoprotein network in turn interacts with ParA to partition the parS locus, hence the chromosome to each daughter cell. Here, we determine the co-crystal structure of the C-terminal domain truncated ParB-parS complex from Caulobacter crescentus, and show that its N-terminal domain is inherently flexible and adopts multiple different conformations. more...

Organism:

Caulobacter vibrioides NA1000; Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26943 GPL18133

27 Samples

Download data: TXT

(Submitter supplied) We investigated the transcriptome dynamics of Brassica oleracea in response to Xcc race 1 infection at 3 and 12 days after inoculation by using Massive Analysis of 3′-cDNA Ends (MACE) technology

Organism:

Brassica oleracea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16360

12 Samples

Download data: TXT

(Submitter supplied) Specific interactions between proteins and DNA are essential to many biological processes. Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18133

30 Samples

Download data: TXT

(Submitter supplied) The hybrid seed production was performed using the male sterility line, which is an important way of heterosis utilization in Chinese cabbage. A stably inherited male sterile mutant msm was obtained from a Chinese cabbage DH line ‘FT’ using the isolated microspore culture combined with 60Co γ-rays mutagenesis. Compared to the wild type ‘FT’, the msm exhibited completely degenerated stamens and no pollen phenotype, and other characters had no significant difference except for stamen. more...

Organism:

Brassica rapa subsp. pekinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17788

6 Samples

Download data: TXT

(Submitter supplied) ChIP-seq database identifies genes with promoter regions bound by VgrR in X. campestris pv. campestris grown under osmostress conditions

Organism:

Xanthomonas campestris pv. campestris str. 8004

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25598

2 Samples

Download data: WIG

(Submitter supplied) Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. more...

Organism:

Arabidopsis thaliana; Cuscuta pentagona

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL22255 GPL22256 GPL17639

6 Samples

Download data: TXT