txid57918[Organism] - GEO DataSets

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Select item 2002608251.

N6-methyladenosine RNA methylomes in diploid strawberry fruit of wild-type and Fvalkbh10b mutant at 27 DPA

(Submitter supplied) To decipher the mechanisms by which FvALKBH10B regulates fruit ripening, we performed m6A sequencing (m6A-seq) using mRNA from fruits of wild type and Fvalkbh10b mutant. The libraries for sequencing were prepared with 3 replicates, in which the mRNA samples were independently prepared. FvALKBH10B mutation leads to a delay in fruit ripening and causes global m6A hypermethylation of 1859 genes.

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL32944
12 Samples

Download data: CSV

Series

Accession:: GSE260825

ID:: 200260825

Select item 2002608242.

DAP-seq reveals FvSEP3 directly targets downstream genes relevant to strawberry fruit ripening

(Submitter supplied) To better understand FvSEP3-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to uncover FvSEP3 directly binding sites at the genome level. For DAP-seq analysis, the recombinant FvSEP3 fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.

Organism:: Fragaria vesca

Type:: Other

Platform:: GPL32944
3 Samples

Download data: CSV

Series

Accession:: GSE260824

ID:: 200260824

Select item 2002086403.

High-throughput sequencing of strawberry fruits

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

Organism:: Fragaria vesca

Type:: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL32497 GPL32494
41 Samples

Download data: BED, BW

Series

Accession:: GSE208640

ID:: 200208640

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Select item 2002086384.

ChIP-seq of Fragaria.vesca

(Submitter supplied) Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. more...

Organism:: Fragaria vesca

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL32497
39 Samples

Download data: BED, BW

Series

Accession:: GSE208638

ID:: 200208638

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Select item 2002086095.

small RNA sequencing of mature diploid strawberry

(Submitter supplied) Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.

Organism:: Fragaria vesca

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

Platform:: GPL32494
2 Samples

Download data: BW

Series

Accession:: GSE208609

ID:: 200208609

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Select item 2002207866.

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening

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

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL32944
12 Samples

Download data: BW

Series

Accession:: GSE220786

ID:: 200220786

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Select item 2002207857.

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

(Submitter supplied) To better understand FvRIF-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to unravel FvRIF binding sites at the genome level. For DAP-seq analysis, the recombinant FvRIF fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA ‘input’ negative control libraries were prepared and submitted for deep sequencing.

Organism:: Fragaria vesca

Type:: Other

Platform:: GPL32944
3 Samples

Download data: BW

Series

Accession:: GSE220785

ID:: 200220785

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Select item 2002207688.

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [RNA-seq]

(Submitter supplied) To identify genes that are transcriptionally regulated by FvRIF during fruit ripening, we performed comparative transcriptome analysis through RNA sequencing (RNA-seq) using fruits of the wild type and the mutant lines (FvRIF-cr-6 and FvRIF-cr-13) at 28 DPA. Three independent biological replicates were applied for the RNA-seq analysis.

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing

Platform:: GPL32944
9 Samples

Download data: XLSX

Series

Accession:: GSE220768

ID:: 200220768

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Select item 2002255429.

Ectopic expression of FvVND4c promotes secondary cell wall thickening and flavonoid accumulation in Fragaria vesca

(Submitter supplied) Secondary cell wall thickening (SCW) has a significant effect in the growth and development of plants, as well as in the resistance to various biotic and abiotic stresses. It is regulated by a multilevel transcriptional regulatory network, in which VASCULAR-RELATED NAC-DOMAINs (VNDs) act as key regulators. Lignin is an important component of SCW, it has a cooperative regulation with the biosynthesis of flavonoids which also originate from phenylpropanoid pathway. more...

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing

Platform:: GPL32944
8 Samples

Download data: XLSX

Series

Accession:: GSE225542

ID:: 200225542

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Select item 20020725410.

Transcriptomic analysis of CO2-treated strawberries with enhanced resistance to softening and oxidative stress

(Submitter supplied) Identification of molecular determinants underlying the firming effect and protection gainst senescence of high CO2 using diploid strawberries: One of the greatest threats to strawberries is rapid softening, however firmness increases during or following high CO2 levels. Firmness at consumption is an obvious target for preventing fruit loss and to gain eating quality. Therefore, we performed RNA-seq analysis, construcing a weighted gene co-expression network analysis (WGCNA) to identify which molecular determinants play a role in cell wall integrity , using strawberries under storage conditions. more...

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26365
12 Samples

Download data: CSV

Series

Accession:: GSE207254

ID:: 200207254

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Select item 20016718311.

N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

(Submitter supplied) For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.

Organism:: Fragaria vesca

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL25277
18 Samples

Download data: TSV

Series

Accession:: GSE167183

ID:: 200167183

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016637412.

RNASEQ based transcriptome profiling of cold responsive genes in Fragaria vesca genotypes with differing sensitivity to cold

(Submitter supplied) By using high through put Illumina based sequencing approach, we generated RNASEQ data for leaves and crowns of Alta and NCGR1363 at 0H and 42D exposure to temperature stress. We present the expression profile of 896 putative candidate genes identified within a QTL associated with freezing tolerance. Expression profiles revealed genotype specific cold responsive expression patterns in one group of candidates and expression differences between genotypes prior to treatment for many of the genes.

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing

Platform:: GPL25278
24 Samples

Download data: TXT

Series

Accession:: GSE166374

ID:: 200166374

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012903213.

Genome-wide study the fruit ripening associated lncRNAs in strawberry

(Submitter supplied) With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. more...

Organism:: Fragaria vesca

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26365
18 Samples

Download data: FA, GTF, TXT

Series

Accession:: GSE129032

ID:: 200129032

SRA Run Selector

Select item 20011658114.

fruitENCODE: An encyclopedia of DNA elements for fruit ripening

(Submitter supplied) Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. more...

Organism:: Carica papaya; Prunus persica; Oryza sativa; Fragaria vesca; Pyrus x bretschneideri; Citrullus lanatus; Cucumis melo; Cucumis sativus; Arabidopsis thaliana; Malus domestica; Solanum lycopersicum; Musa acuminata AAA Group; Vitis vinifera

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

18 related Platforms
282 Samples

Download data: BW, NARROWPEAK, TBI, TXT

Series

Accession:: GSE116581

ID:: 200116581

PubMed Similar studies SRA Run Selector

Select item 20007952615.

Widespread natural variation of DNA methylation within angiosperms

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...

Organism:: Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis

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

30 related Platforms
34 Samples

Download data: TSV

Series

Accession:: GSE79526

ID:: 200079526

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006179816.

Deep small RNA and degradome sequencing identifies new miRNAs-target pairs and novel PhasiRNAs in F-box regulatory networks in diploid strawberry

(Submitter supplied) The wild strawberry Fragaria vesca has recently emerged as an excellent model for investigating flower and fruit traits in economically important fruit crops. Its history of physiological studies combined with sequenced genome and full complements of molecular genetic tools facilitate investigations into mechanisms of its unique biological processes such as fleshy fruit development from the enlarged stem tip called receptacle. more...