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Links from GEO DataSets

Items: 20

1.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...
Organism:
Phytophthora infestans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17596
2 Samples
Download data: GFF3
Series
Accession:
GSE50030
ID:
200050030
2.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Phytophthora infestans; Phytophthora sojae; Phytophthora ramorum
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL17596 GPL17597 GPL17598
4 Samples
Download data: GFF3
Series
Accession:
GSE50033
ID:
200050033
3.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora sojae small RNA

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...
Organism:
Phytophthora sojae
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17598
1 Sample
Download data: GFF3
Series
Accession:
GSE50032
ID:
200050032
4.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora ramorum small RNA

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...
Organism:
Phytophthora ramorum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17597
1 Sample
Download data: GFF3
Series
Accession:
GSE50031
ID:
200050031
5.

Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Phytophthora infestans
Type:
Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL21069 GPL19416
13 Samples
Download data: TSV, TXT
Series
Accession:
GSE75282
ID:
200075282
6.

Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (RNA-Seq)

(Submitter supplied) The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). more...
Organism:
Phytophthora infestans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19416
2 Samples
Download data: TXT
Series
Accession:
GSE75281
ID:
200075281
7.

Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (small RNA-Seq)

(Submitter supplied) The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). more...
Organism:
Phytophthora infestans
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL21069
11 Samples
Download data: TSV
Series
Accession:
GSE74370
ID:
200074370
8.

small RNA-seq of Physcomitrella patens small RNA mutants

(Submitter supplied) To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.
Organism:
Physcomitrium patens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17793
30 Samples
Download data: TXT
Series
Accession:
GSE51419
ID:
200051419
9.

Small RNA genes of Physcomitrella patens

(Submitter supplied) Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times. Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT". Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)
Organism:
Physcomitrium patens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16754
10 Samples
Download data: TXT
Series
Accession:
GSE44900
ID:
200044900
10.

Divergent Patterns of Endogenous Small RNA Populations From Seed and Vegetative Tissues of Glycine max

(Submitter supplied) An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean
Organism:
Glycine max
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL10267
4 Samples
Download data: TXT
Series
Accession:
GSE36728
ID:
200036728
11.

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Citrullus lanatus
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL23842 GPL20225
15 Samples
Download data: TXT
Series
Accession:
GSE102030
ID:
200102030
12.

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [degradome]

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...
Organism:
Citrullus lanatus
Type:
Other
Platform:
GPL23842
1 Sample
Download data: TXT
Series
Accession:
GSE102029
ID:
200102029
13.

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [miRNA-Seq]

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...
Organism:
Citrullus lanatus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL20225
14 Samples
Download data: TXT
Series
Accession:
GSE102028
ID:
200102028
14.

Characterization of small RNA-generating regions targeted by RNA polymerase V in Arabidopsis

(Submitter supplied) In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (Pol) Pol IV and Pol V. Pol IV plays a major role in siRNA biogenesis, while Pol V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions which are dependent on both Pol IV and Pol V have been identified previously, the genomic loci targeted Pol V for siRNA accumulation and silencing have not been described extensively. more...
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11221
13 Samples
Download data: TXT
Series
Accession:
GSE36424
ID:
200036424
15.

Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and their Association with Stress Responses

(Submitter supplied) we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina.
Organism:
Avicennia marina
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16535
1 Sample
Download data: TXT
Series
Accession:
GSE43669
ID:
200043669
16.

Coupling of microRNA-directed phasiRNA generation with alternative splicing in small RNA-mediated gene silencing

(Submitter supplied) Purpose:We aimed to characterize genome-widely the miRNA population and phasiRNA-generating genes/loci in litchi (Litchi chinensis). Multiple high throughput sequencing strategies, including sRNA sequencing, parallel analysis of RNA ends (PARE) sequencing, and strand-specific RNA-seq, were applied in combination with thorough bioinformatics analyses using a variety of computational methods.
Organism:
Litchi chinensis
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL19467 GPL23452
12 Samples
Download data: TXT
Series
Accession:
GSE98698
ID:
200098698
17.

Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

(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
Series
Accession:
GSE41755
ID:
200041755
18.

Control of agricultural traits by hc-siRNA associated MITEs in rice

(Submitter supplied) Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9 methylation and histone H3K4 demethylation, respectively. Miniature inverted repeat transposable elements (MITEs) are one of the most high-copy-number DNA transposons, which are interspersed around rice genome and might influence nearby gene expression. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13160 GPL9147
6 Samples
Download data: BIGWIG, WIG
Series
Accession:
GSE50778
ID:
200050778
19.

Transcriptomes of two phytophthora species at mycelium stage

(Submitter supplied) Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. more...
Organism:
Phytophthora infestans; Phytophthora sojae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL25218 GPL25217
7 Samples
Download data: GTF, XLSX
Series
Accession:
GSE116090
ID:
200116090
20.

MeDIP-seq of two phytophthora species at mycelium stage

(Submitter supplied) We report the 6mA methylation profiling in two Phytophthora species and one psdamt3 mutant. Genomic DNA of Phytophthora sojae P6497 mycelium (3-days old), Phytophthora infestans T30-4 mycelium and psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was extracted and sonicated to 200-400bp using Biorupter UCD-600. The antibody sysy 202003 was used to immunoprecipitation. We find that 6mA is associated with lowly expressed genes in two Phytophthora species. more...
Organism:
Phytophthora infestans; Phytophthora sojae
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL25217 GPL25218
12 Samples
Download data: BED
Series
Accession:
GSE116089
ID:
200116089
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