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Ribosome profiling in mitochondria from flowers of wildtype Arabidopsis thaliana and DWEORG1 (At3g15590) mutant

ABSTRACT: Ribosome profiling in mitochondria from flowers of wildtype Arabidopsis thaliana and DWEORG1 (At3g15590) mutant

PROVIDER: PRJEB54714 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9951986.fastq.gz	Fastqsanger.gz
	ERR9951987.fastq.gz	Fastqsanger.gz
	ERR9951988.fastq.gz	Fastqsanger.gz
	ERR9951989.fastq.gz	Fastqsanger.gz

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RNA-Seq from flowers of wildtype Arabidopsis thaliana and DWEORG1 (At3g15590) mutant

Project description:As one of the largest protein family in landplants pentatricopeptide repeat (PPR) proteins offer a wide research array. They are mostly involved in the RNA processing steps in Chloroplasts and Mitochondria. Recently it has been shown, that they are not only involved in the RNA processing steps, but are also part of the mitoribosome (rPPRs) as regulators of translation and ribosome stabilizers. This experiment focuses on a non-previously reported rPPR protein. The RNA-Seq data are needed for a ribosome profiling experiment that aimed to analyze DWEORG1's impact on mitochondrial translation. Arabidopsis mutants are compared to the wild type using duplicates for the RNA-Seq experiment. RNASEQ (determining the transcript abundance) and RIBOSEQ ( for detecting ribosome occupancy on each transcript) of wild type and mutants were conducted to determine the translational efficiency of mitochondrial transcripts in the mutant and wild type. The plants were grown in the Greenhouse under long day conditions. Flowers were harvested simultaneously for all genotypes, snap-frozen in liquid nitrogen and stored at -80°C until use.Total RNA was prepared from a mix of flower buds and open flowers.For total RNA extraction from flowers Trizol was used. Total RNA were treated with Dnase and depleted of rRNAs using the RiboMinusTM Plant Kit for RNA-Seq (invitrogen), following the manufacturer’s instructions.The sequencing libraries of two biological repeats per genotype were prepared using the NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific) following the manufacturer's instructions. For sequencing Illumina NextSeq 500 75 bp single reads were used. The reads were than mapped to the Col-0 mitochondrial genome of Arabidopsis thaliana acccession JF729201.

2022-07-13 | E-MTAB-11928 | biostudies-arrayexpress

RNA-Seq from flowers of wildtype Arabidopsis thaliana and DWEORG1 (At3g15590) mutant

Project description:RNA-Seq from flowers of wildtype Arabidopsis thaliana and DWEORG1 (At3g15590) mutant

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Transcription profiling of flowers from Arabidopsis Col-4 plants

Project description:As part of the CAGE consortium, fully opened flowers from Arabidopsis thaliana Col-4 plants at the developmental stage 6.50 (Boyes stage) were hybridized against the oligo reference labeled with Cy3. The flower samples in addition to the leaf, whole shoot, and roots samples from other CAGE members provide a basal/normal genomic expression pattern for the Col-4 wildtype plants.

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Ribosome profiling of whi3 mutant yeast

Project description:In general, RNA-binding proteins act to modulate gene expression at transcript level through degradation or at protein level through translation. To elucidate the effect of Whi3, a yeast RNA binding protein, on gene expression, we performed ribosome profiling experiment on whi3 mutant and wildtype cells. Comparison ribosome profiling and RNA-seq data between whi3 mutant and wildtype cells

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RNA-Seq of et mutant flowers in Arabidopsis thaliana

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Small RNA (sRNA) sequencing from A. thaliana flowers

Project description:Purpose: To study small RNAs expressed in A. thaliana flowers Methods: sRNA libraries were constructed as previously described (C Lu et al. 2007) and sequenced on an Illumina GAIIx or Illumina HiSeq 2000 instrument at the Delaware Biotechnology Institute. These libraries were prepared between 2010 and 2012.

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Ribosome profiling of whi3 mutant yeast

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Transcriptional profiling of Persea americana flowers

Project description:The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, sterile perianth organs surrounding stamens (male reproductive organs) and carpels (female reproductive organs) constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure, of floral organs, while the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. As such, regulatory mechanisms underlying the archetypal floral plan, for instance that of the eudicot genetic model Arabidopsis thaliana, are unlikely to apply to the original flowers. Here we show that broadly overlapping transcriptional programs characterise the floral transcriptome of the basal angiosperm Persea americana (avocado), while floral gene expression domains are typically organ-specific in Arabidopsis. Our findings extend the “fading borders” model for basal angiosperms from organ identity genes to the downstream floral transcriptome, and suggest that the combinatorial mechanism for organ identity may not operate in basal angiosperms as it does in Arabidopsis. Furthermore, fading expression of components of the stamen transcriptome in central and peripheral regions of Persea flowers resembles the developmental program of the hypothesized gymnosperm “floral progenitor”. Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.

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