GEO DataSets

(Submitter supplied) Comparative analysis of nascent transcription among plant species

Organism:

Physcomitrium patens; Hordeum vulgare; Drosophila melanogaster; Selaginella moellendorffii; Carica papaya; Chlamydomonas reinhardtii; Zea mays; Arabidopsis thaliana

Type:

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

17 related Platforms

68 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) To uncover a suit of genes related to the consumer preferred flavours, whole RNA sequencing followed by de novo genome assembly was performed on extreme flavoured papaya varieties RB1 (preferred with sweet flavour and floral aroma) and 1B (non-preferred with bitter flavour and musty aroma) fruits at ripe and unripe stages. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different papaya varieties at ripe and unripe stages.

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32671

12 Samples

Download data: FASTA, TXT

(Submitter supplied) The aim of this research was to study the effects of cis-element differences between the X, Y and Yh alleles on the expression of CpMDAR4, a potential candidate gene for sex differentiation in papaya, using a transcriptional reporter system in a model species Arabidopsis thaliana. Possible effects of a retrotransposon insertion in the Y and Yh alleles on the transcription and expression of CpMDAR4 alleles in papaya flowers were also examined. more...

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26326

55 Samples

Download data: TXT

(Submitter supplied) We report the application of NGS-derived transcriptome profile to elucidate a temporal line of both control and ethylene-induced ripening process of papaya fruit focusing on ripening-induced transcripts that act directly on plant cell wall disassembling

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26326

15 Samples

Download data: TSV

(Submitter supplied) The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways.

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26326 GPL27469

12 Samples

Download data: FA, TXT

(Submitter supplied) The freeze-thaw awakening is a method in which seeds or germ cells prior to germination are slowly cooled, stored, and thawed to promote growth. To further test the validity of this method, we applied freeze-thaw awakening treatment on papaya seeds. When the seed was grown under room temperature (15-25C), the germination rate increased by more than 40% compared to those that were not subjected to the method. more...

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26326

2 Samples

Download data: FASTA, TXT

(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

(Submitter supplied) The tissues of male flowers, female flowers and hermaphrodite are collected and stored in liquid nitrigen immediately. Total RNA was isolated from male, hermaphrodite, and female flowers using the Trizol reagent (Invitrogen USA). Low molecular weight RNA was enriched from the total RNA by precipitating with 0.4M NaCl and polyethylene glycol (PEG). The enriched low molecular weight RNA was then separated on a denaturing 15% polyacrylamide gel. more...

Organism:

Carica papaya

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13438

6 Samples

Download data: TXT

(Submitter supplied) For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences.

Organism:

Carica papaya

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13809

6 Samples

Download data

(Submitter supplied) Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. more...

Organism:

Carica papaya; Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

7 Samples

Download data: CEL

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

Organism:

Citrus sinensis; Ginkgo biloba; Carica papaya; Capsicum annuum; Lactuca sativa; Zea mays; Amborella trichopoda; Gossypium arboreum; Chlamydomonas reinhardtii; Volvox carteri; Picea abies; Cucurbita maxima; Solanum lycopersicum; Sorghum bicolor; Silene latifolia; Panicum virgatum; Chara corallina; Populus trichocarpa; Nicotiana tabacum; Erythranthe guttata; Hordeum vulgare; Triticum aestivum; Zostera marina; Aristolochia fimbriata; Miscanthus x giganteus; Persea americana; Petunia x hybrida; Solanum tuberosum; Setaria italica; Musa acuminata; Marsilea quadrifolia; Vitis vinifera; Cycas rumphii; Nuphar advena

Type:

Non-coding RNA profiling by high throughput sequencing

34 related Platforms

99 Samples

Download data: TXT

(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Carica papaya tissues (including leaves and flowers). more...

Organism:

Carica papaya

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13438

3 Samples

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