GEO DataSets

(Submitter supplied) Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL28728 GPL20257

134 Samples

Download data: XLSX

(Submitter supplied) Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL28728 GPL20257

136 Samples

Download data: XLSX

(Submitter supplied) Heat stress is a major limiting factor for grain yield and grain quality in wheat production. In crops, abiotic stresses have transgenerational effects and the mechanistic basis of stress memory is associated with epigenetic regulation. The current study presents the first systematic analysis of the transgenerational effects of post-anthesis heat stress in tetraploid wheat. Genotype-dependent response patterns to parental and progeny heat stress were found for the leaf physiological traits, harvest components, and grain quality traits measured. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL20257 GPL28728

24 Samples

Download data: XLSX

(Submitter supplied) Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. more...

Organism:

Triticum turgidum subsp. durum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20257

96 Samples

Download data: TAB

(Submitter supplied) Water-deficit stress negatively affects wheat yield and quality. Abiotic stress on the parental plants during reproduction could have transgenerational effects on the progenies. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in the progenies. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL20257 GPL28728

24 Samples

Download data: XLSX

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

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL17701 GPL15632

6 Samples

Download data: TXT

(Submitter supplied) We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains.

Organism:

Triticum aestivum

Type:

Other

Platform:

GPL15632

2 Samples

Download data: TXT

(Submitter supplied) We aimed to identify differentially expressed miRNAs during wheat grain development by using high-throughput sequencing approach. Four small RNA libraries were constructed from wheat grains collected at 7, 14, 21 and 28 days post anthesis (DPA). A total of 165 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

4 Samples

Download data: TXT

(Submitter supplied) Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

72 Samples

Download data: XLS

(Submitter supplied) The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10467

2 Samples

Download data: TXT

(Submitter supplied) The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10467

7 Samples

Download data: TXT

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

Organism:

Triticum aestivum

Type:

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

Platforms:

GPL24909 GPL17701 GPL23509

72 Samples

Download data

(Submitter supplied) Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24909

24 Samples

Download data: XLSX

(Submitter supplied) Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. more...

Organism:

Triticum aestivum

Type:

Other

Platform:

GPL17701

24 Samples

Download data: XLSX

(Submitter supplied) Sequencing of 24 small RNA libraries produced 55.2M reads while 404M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23509

24 Samples

Download data: XLSX

(Submitter supplied) Background: MicroRNAs regulate various biological processes in plants. Considerable data are available on miRNAs involved in the development of rice, maize and barley. In contrast, little is known about miRNAs and their functions in the development of wheat. In this study, five small RNA (sRNA) libraries from wheat seedlings, flag leaves, and developing seeds were developed and sequenced to identify miRNAs and understand their functions in wheat development. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

5 Samples

Download data: FA

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

Organism:

Phaseolus vulgaris

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19961

7 Samples

Download data: TXT

(Submitter supplied) Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. more...

Organism:

Phaseolus vulgaris

Type:

Other

Platform:

GPL19961

2 Samples

Download data: TXT

(Submitter supplied) Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. more...

Organism:

Phaseolus vulgaris

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19961

5 Samples

Download data: TXT

(Submitter supplied) Two independent small RNA (sRNA) libraries from male and female asparagus plants were sequenced, generating 4.13 and 5.88 million final cleaned reads, respectively. A total of 154 conserved miRNA belonging to 26 families, and 40 novel miRNA candidates that seemed to be specific to asparagus were identified, among them, 63 miRNAs exhibited significant differential expression between male and female plants, and 36 target mRNAs representing 44 conserved and fournovel miRNA in asparagus by high-throughput degradome sequencing analysis.

Organism:

Asparagus officinalis

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL20875

3 Samples

Download data: XLS