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Setaria viridis

ABSTRACT: Gene expression in green millet (Setaria viridis): developmentally regulated genes, transcription start sites, and stimulating introns

PROVIDER: PRJNA354250 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5020970_1.fastq.gz	Fastqsanger.gz
	SRR5020970_2.fastq.gz	Fastqsanger.gz
	SRR5020980_1.fastq.gz	Fastqsanger.gz
	SRR5020980_2.fastq.gz	Fastqsanger.gz
	SRR5020990_1.fastq.gz	Fastqsanger.gz

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Gene expression in green millet (Setaria viridis): developmentally regulated genes, transcription start sites, and stimulating introns

Project description:Setaria viridis (green millet) is gaining popularity as a model C4 monocot due to its small size, rapid life cycle, and compact, sequenced genome. To analyze the structure and regulation of genes throughout development, the transcriptomes of 13 tissues at different stages of development were determined by RNA sequencing, and transcription start sites were mapped. Genes were identified that are differentially expressed in different developmental stages within the leaf, as well as in the apical meristem before and after the transition from vegetative to reproductive growth, and in panicles before and after anthesis. In a majority of genes, transcription initiated at the sequence YR within a narrow peak 20 – 40 nt downstream of a TATA box. Genes expressed in multiple tissues generally use the same transcription start site across all tissue types. Several introns were identified that increase gene expression. These results will increase understanding of plant development, improve the annotation of the Setaria genome, and provide tissue-specific or constitutive promoters for use in transgenic applications.

2017-11-14 | GSE89855 | GEO

Leaf transcriptome analysis of Setaria viridis MPA1 RNAi plants

Project description:This experiment was conducted to investigate the effect of RNAi of MPA1 on the global leaf transcriptome of Setaria viridis.

2022-01-01 | E-MTAB-8907 | biostudies-arrayexpress

Sorghum bicolor and Setaria viridis PARE-seq

Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.

2020-05-19 | GSE150798 | GEO

Setaria viridis (A10.1) circadian expression after light or temperature entrainment

Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment

2017-07-01 | GSE97739 | GEO

Setaria viridis small RNAs from panicle tissues

Project description:A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).

2018-07-28 | GSE111490 | GEO

Grasses suppress shoot-borne roots to conserve water during drought

2016-07-22 | GSE78054 | GEO

Grasses suppress shoot-borne roots to conserve water during drought

Project description:Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments. RNA from Lower region (crown) or Upper region (stem) of watered (W) or drought (D) treated Setaria plants were harvested at 6 or 9 days after sowing; there are 8 samples per biological repeat, 3 biological repeats.

2016-07-22 | E-GEOD-78054 | biostudies-arrayexpress

Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

Project description:RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

2017-12-23 | GSE100423 | GEO

Transcriptome sequencing of Foxtail millet Setaria italica for different tissues

Project description:Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues.

2012-03-31 | GSE36391 | GEO

A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

Project description:Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

2018-08-17 | GSE118673 | GEO

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