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Functional Genomics Studies

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Select item 2002438061.

aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. more...

Organism:: Brassica napus; Glycine max; Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Citrus sinensis; Zea mays; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum

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

11 related Platforms
160 Samples

Download data: BROADPEAK, NARROWPEAK

Series

Accession:: GSE243806

ID:: 200243806

PubMed Similar studies

Select item 2002438042.

aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs [ChIP-Seq]

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:: Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum; Citrus sinensis; Populus; Oryza sativa; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Glycine max

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

11 related Platforms
152 Samples

Download data: BROADPEAK, NARROWPEAK

Series

Accession:: GSE243804

ID:: 200243804

Select item 2002187253.

Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation (Dianthus caryophyllus L.)

(Submitter supplied) Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, involvement of histone methylation in regulating petal senescence is still largely unknown. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during the ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). more...

Organism:: Dianthus caryophyllus

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

Platform:: GPL32881
18 Samples

Download data: BW

Series

Accession:: GSE218725

ID:: 200218725

Select item 2000989564.

RNA sequencing of plant microRNAs precipitated by the tombusviral suppressor of RNA silencing p19.

(Submitter supplied) Viral suppressors of RNA silencing, VSRs, counteract the antiviral RNA silencing of host plants by sequestration of virus-derived siRNAs. A central question concerns whether and how VSRs associate cellular miRNAs and thus modulate plant gene expression during a viral infection. In this study we characterize the binding behaviour of the tombusviral p19 protein to miRNAs by performing an RNA-pull down experiment with bead-associated p19 protein from carnation italian ringspot virus. more...