GEO DataSets

(Submitter supplied) Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the total RNA sequencing.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

5 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) RNA sequencing of progenies of Rutgers CV. Wild type grafted on Rutgers transgenic MSH1-RNAi ; Rutgers CV. Wild type grafted on Rutgers Wild type

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21762

6 Samples

Download data: TXT

(Submitter supplied) Bisulfite (methylome) sequencing of progenies of Rutgers CV. Wild type grafted on Rutgers MSH1-RNAi line; Rutgers CV. Wild type grafted on Rutgers Wild type

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25655

6 Samples

Download data: TXT

(Submitter supplied) Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the small RNA sequencing. Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the small RNA sequencing.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24025

12 Samples

Download data: TXT

(Submitter supplied) Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1) and on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on 0.5M MS growth medium and root tissue was collected after 12 days and used for the RNA sequencing.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(Submitter supplied) Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

15 Samples

Download data: TXT

(Submitter supplied) apical meristem tissues from 4-week-old wild type, epiF3, MSH1 gene mutant including (mild-DR and dwarf-DR) plants were used in this experiment.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19694

12 Samples

Download data: CSV

(Submitter supplied) Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24025

6 Samples

Download data: TXT

(Submitter supplied) Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. Memory plants were self pollinated for six generations and plants from generation 1 and 5 were sequenced for RNASeq.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

15 Samples

Download data: TXT

(Submitter supplied) Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. Memory plants were self pollinated for six generations and plants from each generations were Bisulfite sequenced.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

48 Samples

Download data: TXT

(Submitter supplied) Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. While rest transgene null plants displayed normal phenotype termed as non-memory.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

13 Samples

Download data: TXT

(Submitter supplied) Germination of the memory line and isogenic Col-0 wild type on media containing 100 uM 5-azacytidine alleviated the phenotype differences between the two lines, resulting in similar growth rates. Here we generate methylome profile for wild type and msh1 memory line under 100 uM 5-azacytidine treatment to investigate the effect of 5-azacytidine on msh1 memory line methylation profile.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

12 Samples

Download data: TXT

(Submitter supplied) We grafted Transcriptional Gene Silencing (TGS)-inducing wild type Arabidopsis and a mutant that is compromised in 24 nucleotide (nt) small RNA (sRNA) production onto a wild type reporter line. We observed that 21-24 nt sRNAs were transmitted across a graft union yet only the 24 nt sRNAs directed RNA-dependent DNA methylation (RdDM) and TGS of a transgene promoter in meristematic cells.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

10 Samples

Download data: GFF3

(Submitter supplied) Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: TXT

(Submitter supplied) The Arabidopsis msh1 mutant show various growth phenotype. We use microarray analysis to characterize gene expression pattern for two of the phenotypes - variegation and stunted growth.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

9 Samples

Download data: CEL

(Submitter supplied) Using siRNA-Seq to provide siRNA accumulation status in fve mutant.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

2 Samples

Download data: BW

(Submitter supplied) Using ChIP-seq to study the deposition of FVE on the chromatin

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: BW

(Submitter supplied) Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0 WT, nrpd1-3, nrpe1-11 and fve-4.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21785

4 Samples

Download data: BW

(Submitter supplied) The small RNA mediated DNA methylation (RdDM) is highly elaborated in Arabidopsis as an important epigenetic pathway controls expression of genes and multiple developmental processes. RDR2 and DCL3 are necessary factors to the 24-nt siRNA biogenesis and the RdDM pathway. Here, we find that IBM1 (increase in BONSAI methylation 1), a conserved JmjC family histone demethylase, could directly associated with the chromatin of RDR2 and DCL3. more...

Organism:

Arabidopsis thaliana

Type:

Other; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT