txid4479[Organism:exp] - GEO DataSets

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Items: 1 to 20 of 67046

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Select item 2002242281.

A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development [scRNA-seq]

(Submitter supplied) Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome divergent regulation in the context of cellular differentiation. more...

Organism:: Triticum aestivum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25409
2 Samples

Download data: MTX, TSV

Series

Accession:: GSE224228

ID:: 200224228

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2002541772.

ZmICE1a regulates defense-storage trade-off in maize endosperm [RNA-seq]

(Submitter supplied) The endosperm of cereal grains feeds the entire world as major food supply, however little is known for its defense responses during endosperm development. Inducer of CBF Expression 1 (ICE1) is a known regulator of cold tolerance in plants. ICE1 has a monocot-specific homologue that is preferentially expressed in cereal grains but with an unclear regulatory function. Here, we characterized the function of monocot-specific ZmICE1 (ZmICE1a) in maize (Zea mays) kernel. more...

Organism:: Zea mays

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25410
24 Samples

Download data: TXT

Series

Accession:: GSE254177

ID:: 200254177

Select item 2002540663.

ZmICE1a regulates defense-storage trade-off in maize endosperm [CUT&Tag]

Organism:: Zea mays

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL25410
4 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE254066

ID:: 200254066

Select item 2002424604.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platform:: GPL24468
29 Samples

Download data

Series

Accession:: GSE242460

ID:: 200242460

Select item 2002424595.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [RNA-Seq]

(Submitter supplied) Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24468
8 Samples

Download data: TXT

Series

Accession:: GSE242459

ID:: 200242459

Select item 2002424556.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [ChIA-PET]

Organism:: Oryza sativa

Type:: Other

Platform:: GPL24468
8 Samples

Download data: BW

Series

Accession:: GSE242455

ID:: 200242455

Select item 2002424537.

H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [ChIP-Seq]

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL24468
13 Samples

Download data: BW

Series

Accession:: GSE242453

ID:: 200242453

Select item 2002771278.

Evaluating the effect of secreted ribonucleases from Ustilago maydis on the extracellular RNA profile/repertoire of Zea mays during corn smut disease

(Submitter supplied) The apoplast of host plants serves as a dynamic interface during invasion and subsequent establishment of disease by a microbial pathogen. In the recent past, host plant apoplasts have been demonstrated to harbour small membrane bound vesicles called extracellular vesicles (EVs) that contain both RNA and protein. EVs are considered to play a significant role in cell-cell communication between the host and the pathogen during infection. more...

Organism:: Zea mays

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34900
36 Samples

Download data: GTF

Series

Accession:: GSE277127

ID:: 200277127

Select item 2002768949.

Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq II

(Submitter supplied) The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs), enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. more...

Organism:: Arabidopsis thaliana; Homo sapiens; Oryza sativa Indica Group

Type:: Other

Platforms:: GPL26667 GPL23157 GPL20795
12 Samples

Download data: TXT

Series

Accession:: GSE276894

ID:: 200276894

Select item 20026237110.

Transcriptomic and metabolomic reveal OsCOI2 as the jasmonate-receptor master switch in rice root

(Submitter supplied) Jasmonate is an essential phytohormone involved in plant development and stress responses. Jasmonate perception occurs through the COI nuclear receptor allowing to target the JAZs repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of JA-responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. more...

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
18 Samples

Download data: TXT

Series

Accession:: GSE262371

ID:: 200262371

Select item 20023185611.

Rice amino acid transporter OsMP1 is involved in amino acid homeostasis and mediates broad-spectrum resistance to blast fungus and bacterial blight through upregulating JA signaling pathway

(Submitter supplied) To investigate the molecular mechanisms about how OsMP1 regulates rice blast resistance, we established the CR4 line in which target gene has been knocked down by CRISPR-Cas9 gene editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of CR4 and wild-type Hei.

Organism:: Oryza sativa

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27660
6 Samples

Download data: TXT

Series

Accession:: GSE231856

ID:: 200231856

Select item 20026890212.

A Spatiotemporal Transcriptome Revealed Stalk Development in Pearl Millet

(Submitter supplied) Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance, however, the molecular mechanisms governing stalk development in pearl millet remained to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. more...

Organism:: Cenchrus americanus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL34549
40 Samples

Download data: BW, TXT

Series

Accession:: GSE268902

ID:: 200268902

Select item 20024400913.

An improved terminal ribose-modified small RNA sequencing (TRM-sRNA-seq) reveals novel features of miRNA modification and identifies HEN1-independent 2’-O-modified sRNAs derived from tRNAs

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:: Arabidopsis thaliana; Solanum lycopersicum; Zea mays; Oryza sativa

Type:: Non-coding RNA profiling by high throughput sequencing

4 related Platforms
54 Samples

Download data: TXT

Series

Accession:: GSE244009

ID:: 200244009

PubMed Full text in PMC Similar studies

Select item 20027596214.

Nitrogen source effect (ammonium and nitrate) on Brachypodium distachyon B21 root transcriptome

(Submitter supplied) Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. more...

Organism:: Brachypodium distachyon

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17337
6 Samples

Download data: CSV

Series

Accession:: GSE275962

ID:: 200275962

Select item 20025204015.

A cis-regulatory atlas of rice single cells

(Submitter supplied) Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. more...

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27660
18 Samples

Download data: TXT

Series

Accession:: GSE252040

ID:: 200252040

Select item 20026206216.

Untargeted mutagenesis of brassinosteroid receptor SbBRI1 confers drought tolerance by altering phenylpropanoid metabolism in Sorghum bicolor

(Submitter supplied) Drought is a critical issue in modern agriculture, therefore there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signaling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. more...

Organism:: Sorghum bicolor

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34319
12 Samples

Download data: TXT

Series

Accession:: GSE262062

ID:: 200262062

Select item 20027391817.

The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity

(Submitter supplied) Some pathogen-derived effectors reprogram mRNA splicing in their host plant to regulate plant immune responses. The fungus Exserohilum turcicum is the causal agent of northern corn leaf blight, a damaging maize (Zea mays) disease. However, the low efficiency of genetic transformation of E. turcicum has hampered research on its effectors and whether E. turcicum effectors interfere with RNA splicing remained unknown. more...

Organism:: Zea mays

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25410
27 Samples

Download data: TXT

Series

Accession:: GSE273918

ID:: 200273918

Select item 20025442718.

Fumarylacetoacetate hydrolase targeted by a Fusarium graminearum effector positively regulates wheat FHB resistance and yield and promotes heading

(Submitter supplied) Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. more...

Organism:: Triticum aestivum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25409
6 Samples

Download data: TXT

Series

Accession:: GSE254427

ID:: 200254427

Select item 20027440319.

Induced variation in BRASSINOSTEROID INSENSITIVE 1 (BRI1) confers a compact wheat architecture

(Submitter supplied) The brassinosteroid (BR) plant hormones regulate numerous developmental processes, including those determining stem height, leaf angle, and grain size that have agronomic relevance in cereals. Indeed, barley (Hordeum vulgare) varieties containing uzu alleles that impair BR perception through mutations in the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) exhibit a semi-dwarf growth habit and more upright leaves suitable for high-density planting. more...

Organism:: Triticum aestivum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23509
23 Samples

Download data: CSV

Series

Accession:: GSE274403

ID:: 200274403

Select item 20018180920.

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

(Submitter supplied) INO80, one member of ATP-ase remodeler factor, play a role on chromatin dynamic modulation. OsINO80 (LOC_Os03g22900) is identified as a homologue of INO80 in rice. To study the function of OsINO80 on H2A.Z, we analyzed the distribution of OsINO80 and H2A.Z in 14-week-old seedling of Oryza stative Japanese rice plant through ChIP assay following by high through sequencing (ChIP-seq).Integrated analysis showed that OsINO80 regulate the H2A.Z level.

Organism:: Oryza sativa

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27660
12 Samples

Download data: BIGWIG

Series

Accession:: GSE181809

ID:: 200181809

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