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GEO DataSets

Functional Genomics Studies

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Select item 2001691981.

Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes

(Submitter supplied) Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. more...

Organism:: Aegilops tauschii

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

Platform:: GPL26494
6 Samples

Download data: TXT

Series

Accession:: GSE169198

ID:: 200169198

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001296952.

The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis

(Submitter supplied) we present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species.

Organism:: Triticum monococcum; Triticum aestivum; Triticum turgidum; Aegilops speltoides; Aegilops tauschii

Type:: Expression profiling by high throughput sequencing

5 related Platforms
110 Samples

Download data: XLSX

Series

Accession:: GSE129695

ID:: 200129695

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000986843.

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

(Submitter supplied) Polyploidy occurs in some animals and all flowering plants including important crops such as wheat. The consequences of polyploidy on crops remain elusive partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids SSAA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. more...

Organism:: Triticum urartu; Triticum urartu x Aegilops tauschii; Aegilops longissima; Aegilops longissima x Triticum urartu; Aegilops tauschii

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

5 related Platforms
45 Samples

Download data: FASTA, FPKM_TRACKING, GTF, TXT

Series

Accession:: GSE98684

ID:: 200098684

PubMed Similar studies SRA Run Selector

Select item 2000476174.

Transcriptome modification to the BBAA subgenomes of common wheat since allohexaploidization is largely irreversible

(Submitter supplied) The three subgenomes (B, A and D) of common wheat (2n=6x=42) are largely intact, which makes extraction of the BBAA subgenomes as organismally independent genomes possible. Availability of such novel extracted tetraploid wheat (Extracted-tetra) provides a unique opportunity to study whether and to what extent the BBAA subgenomes of common wheat have been irreversibly modified, as well as its attendant biological consequences, during their evolutionary trajectory as allohexaploidy. more...

Organism:: Triticum turgidum subsp. durum; Triticum dicoccoides; Triticum aestivum; Triticum turgidum; Triticum carthlicum; Aegilops tauschii

Type:: Expression profiling by array

Platform:: GPL3802
33 Samples

Download data: CEL

Series

Accession:: GSE47617

ID:: 200047617

Analyze with GEO2R

Select item 2000711905.

High-density deletion bin map of wheat D genome

(Submitter supplied) A NimbleGen array containing both gene-based and RJM repeat junction probe sequences derived from Ae. Tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes.

Organism:: Triticum aestivum; Aegilops tauschii

Type:: Genome variation profiling by genome tiling array

Platform:: GPL20725
96 Samples

Download data: PAIR

Series

Accession:: GSE71190

ID:: 200071190

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000586786.

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

(Submitter supplied) To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized

Organism:: Triticum aestivum; Triticum urartu; Aegilops speltoides; Aegilops tauschii; Secale cereale

Type:: Expression profiling by array

Platform:: GPL18847
12 Samples

Download data: PAIR, TXT

Series

Accession:: GSE58678

ID:: 200058678

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000565877.

mRNA and sRNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation for Allopolyploid Heterosis in Nascent Hexaploid Wheat

(Submitter supplied) Nascent allohexaploid wheat may represent the initial genetic state for the evolution and domestication of common wheat, which arose by combining the AB genomes of tetraploid Triticum turgidum with the D genome from Aegilops tauschii and out-competed its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA expression analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring, with the assistance of newly released A and D genome sequences. more...

Organism:: Triticum aestivum; Triticum turgidum; Aegilops tauschii

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

Platforms:: GPL17701 GPL18540 GPL18539
50 Samples

Download data: TXT

Series

Accession:: GSE56587

ID:: 200056587

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000298828.

Global transgenerational gene expression dynamics in two nascent allohexaploid wheat lines analogous in genome constitution to common wheat (Triticum aestivum)

(Submitter supplied) Alteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat. We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array. more...

Organism:: Triticum aestivum; Aegilops tauschii; Triticum turgidum subsp. durum; Triticum carthlicum

Type:: Expression profiling by array

Platform:: GPL3802
18 Samples

Download data: CEL

Series

Accession:: GSE29882

ID:: 200029882

Analyze with GEO2R

Select item 2000292439.

High through put screen of small RNA in parental, hybrid and allopolyploid wheat

(Submitter supplied) Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses

Organism:: Aegilops tauschii; Triticum aestivum; Triticum turgidum subsp. durum

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

Platforms:: GPL13525 GPL10467 GPL15035
4 Samples

Download data: TXT

Series

Accession:: GSE29243

ID:: 200029243

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20002016910.

[hexa-] Transcriptomic changes in synthetic hexaploid wheat

(Submitter supplied) affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. more...