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SRX692840: GSM1496866: 13d_leaf_stress_br2; Jatropha curcas; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 78.1M spots, 3.9G bases, 2.4Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptomics and physiological analyses reveal coordinated alteration of metabolic pathways in Jatropha curcas drought tolerance
show Abstracthide Abstract
Jatropha curcas, a multipurpose plant attracting much attention due to its high oil content and quality for biofuel, is recognized as a drought tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, with the use of a combined approach of transcriptional profiling and morphophysiological characterization along a period of water withholding (49 days) followed by rewatering (7 days). Morphophysiological measurements evidenced that J. curcas plants presented different adaptations to withstand moderate and severe drought. Thus, RNA-Seq was performed for samples collected at moderate and severe stress followed by rewatering, for both roots and leaves. Transcriptomic analysis revealed organ-specific adaptations across all investigated conditions, except under severe stress, in which the drought response of J. curcas surpassed organ-specificity by dramatic transcriptomic reorganization. These changes in gene expression were clearly evidenced by the down-regulation of genes involved in growth and water uptake, and up-regulation of osmotic adjustments and cellular homeostasis related genes. However, organ-specific variations were also detected, such as strong up-regulation of chlorophyll and trehalose metabolism in leaves. Functional validation further corroborated the differentially expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway. Overall design: Two Jatropha curcas accessions were submitted to moderate and severe drought stress (water withholding) followed by recovery (3d re-watering), transcriptomic profiles were assessed by RNA-Seq.
Sample: 13d_leaf_stress_br2
SAMN03019553 • SRS694566 • All experiments • All runs
Organism: Jatropha curcas
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: Root tips and young leaves were collected along the drought assay and subsequent re-watering period. In detail, one leaf (≤2cm in length) per plant was cut with a scalpel blade from the apical tip of the plants and immediately frozen in liquid nitrogen. For root collection, plants were gently removed from the pot. Root tips (≤ 1 cm in length) were retracted with forceps from different parts of the root system and carefully brushed to remove any attached soil, the process never extended more than 30 seconds until samples were flash-frozen in liquid nitrogen. A pool of six plants for days 0 and 49, and three plants for days 13 and 52 were sampled per treatment and accession. Samples were stored at – 80ºC until further use. Before extraction the frozen material was grind in liquid nitrogen with a mortar and pestle into a fine powder. Total RNA was extracted using the RNeasy plant mini kit (Qiagen, Germany) according to the manufacturer's instructions, however for leaf samples the lysis buffer was supplemented with 0.2% of PEG 20000, as suggested by Gehrig et al. (2000). After the extraction, samples were treated with DNAse (Turbo DNA-free Kit, AM1907, Ambion, USA) according to the manufacturer's instructions to minimize genomic contaminants. RNA quality and quantity was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips, following manufacturer's protocol; RNA integrity numbers (RIN) ranged from 8.3 - 9.9. cDNA libraries were prepared using an initial amount of 400 ng of total RNA, and the Illumina's TruSeqTM RNA Sample Preparation v2 protocol. Indexed barcodes were used for pooling, and sequencing was performed on an Illumina HiSeqTM 2000. To assess concentration and ensure an appropriate size distribution (between 200-570 bp) the cDNA libraries were checked using Bioanalyzer DNA 1000 chips. The sequencing run was carried out on a fully loaded flow cell with single-end 50 bp reads following manufacturer's instructions with a loading amount of 9 pmol cDNA per lane. On average, each sample was covered by about 82 million reads.
Experiment attributes:
GEO Accession: GSM1496866
Runs: 1 run, 78.1M spots, 3.9G bases, 2.4Gb
Run# of Spots# of BasesSizePublished


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