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| Status |
Public on Feb 08, 2021 |
| Title |
P_9_150 |
| Sample type |
SRA |
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| Source name |
Pedicel of fruit (150 Days after pollination, DAP) without abscission zone (AZ), and treated with ethylene for 9 hours
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| Organism |
Elaeis guineensis |
| Characteristics |
tissue: Pedicel from fruit
developmental stage: 150 DAP (150 Days after pollination)
treatment: Treated with ethylene for 9 hours
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| Treatment protocol |
For each sample group, independent bunches were collected from distinct individuals of the same genotype. Spikelets were then collected in the centre of each bunch and sets of 6 spikelets were randomly sampled from them and put in individual hermetically sealed 50 l volume boxes. In absence of ethylene treatment, ethylene absorber (ETHYL-GONE, http://www.biosafer.com/ethyl-gone.php) was added in the box. All the boxes were kept at ambient temperature (approximately 30°C), and after 24 h of treatment the number of fruit separating from the spikelets were counted. Using the concentration of ethylene (10 μl l-1) that induced and synchronized the highest amount of fruit shedding (Roongsattham et al., 2012), fruit from 30 and 150 DAP were treated with ethylene. Spikelets were treated with or without ethylene, and every 3 h, treated or untreated spikelets were collected and shedding was quantified for each stage of development. For each time point, the pedicel and the base of the fruit containing the primary and adjacent AZs were isolated and frozen immediately in liquid nitrogen. Samples from two independent experiments were collected immediately after bunches were harvested.
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| Growth protocol |
Oil palm (Elaeis guineensis Jacq.) cultivated at Krabi Golden Tenera plantation, from a tenera clone (clone C) produced in Thailand.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extractions, the fruit bunches were collected and the base of fruits containing the AZ were sampled as follows: the spikelets were removed from the bunches, rinsed in water, then individual fruit containing the base of the fruit containing the AZ were removed with scalpel, then the base of the fruit containing the AZ were dissected (approximately 50 AZ pieces were collected per sample), weighed at approximately 3 grams then froze immediately in liquid nitrogen. Backcross material were cleaned and processed with the same procedure. Total AZ weights were approximately 3-6 grams. Total RNA from mesocarp, pedicel and the base of the fruit enriched in AZs, treated or not with ethylene was extracted as previously described [Morcillo F et al.,Tree Physiol. 2006;26(5):585-594].
Total RNA (1 μg) was used to synthesize cDNA using the first-strand cDNA synthesis kit (ImProm-IITM Reverse Transcription System, Promega). The titanium kit was used (according to Roche GS FLX Titanium manual) and cDNAs derived from the different tissues and different ethylene treatment time points were tagged independently and then mixed together in one sample for 454 pyrosequencing carried out by the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand. Sequencing of the three natural abscission samples (AZ30, AZ120 and AZ160) collected in Thailand was complete by the company GATC Biotech (www.gatc-biotech.com).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
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| Data processing |
The 454 pyrosequence analysis, de novo assembly performed following the methods described previously using an automated pipeline previously described and with support of the SouthGreen Bioinformatics Platform (http://southgreen.cirad.fr/), and the high performance cluster of the Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (Argout et al., 2008; Tranbarger et al., 2011).
For the Illumina samples, low quality reads were removed using Cutadapt. Trimmed reads were mapped using the BWA-MEM package with default parameters (Li 2012). Samtools was used to count mapped reads and the number of reads per kilobase and million reads (RPKM) were then calculated (Li et al., 2009]). The oil palm predicted transcripts used for mapping was downloaded from the NCBI website (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/, GCF_000442705.1_EG5_rna.fna; January 2015).
Supplementary_files_format_and_content: xlsx; RPKM read counts
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| Submission date |
Feb 07, 2021 |
| Last update date |
Feb 09, 2021 |
| Contact name |
Timothy John TRANBARGER |
| E-mail(s) |
timothy.tranbarger@ird.fr
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| Phone |
0467416472
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| Organization name |
Institut de Recherche pour le Développement
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| Department |
Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)
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| Lab |
DIADE, IRD Centre de Montpellier
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| Street address |
911 avenue agropolis BP 64501
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| City |
Montpellier |
| ZIP/Postal code |
34394 |
| Country |
France |
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| Platform ID |
GPL29704 |
| Series (1) |
| GSE166314 |
Oil Palm Fruit Abscission Zone Transcriptome |
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| Relations |
| BioSample |
SAMN17831621 |
| SRA |
SRX10045598 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5068450_Pedicel_9_150_contigs.xlsx |
773.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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