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| Status |
Public on Feb 09, 2017 |
| Title |
Deep sequencing-based characterization of transcriptome and transcriptional profiling of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress |
| Organism |
Citrus trifoliata |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
A large number of high-quality transcripts were fistly obtained by sequencing the pooled RNAs from trifoliate orange under different stress treatments (cold, salt, drought). Four cold-treated libraries were further mapped to the assembled transcriptome, leading to identification of more 5,000 DEGs. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were most significantly enriched in the DEGs. A total of 60 transcription factors were revealed to be cold responsive.n addition, a number of genes involved in catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were either up- or down-regulated under cold stress. These data provide valuable information for elucidating transcriptomic reprogramming and underlying mechanisms of trifoliate orange in response to cold and underpin exploitation of genes of interest in the future.
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| Overall design |
High-throughput RNA sequencing of pooled library derived from trifoliate orange under different stress treatments (cold, salt, drought) and four cold-treated libraries.In detail,three-month-old trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings were collected from an experimental nursery at Huazhong Agricultural University. After a full wash, the plants were incubated in glass beakers filled with tap water and kept for 5 d at 25°C in a growth chamber. In order to enrich stress-responsive genes, the seedlings were treated with different stresses, including cold, salt, and drought. For cold treatment, the plants were placed at 4°C; the leaves were harvested at indicated time points (0, 6, 24, and 72 h). Salinity treatment was applied by placing the seedlings in 200 mM NaCl solution for same time schedule as cold. For drought treatment, the seedlings were placed on filter papers and dehydrated at ambient environment; the whole plants were sampled at 0, 0.5, 3, and 6 h. These tissues were immediately frozen in liquid nitrogen after sampling and stored at -80 °C
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| Contributor(s) |
Wang M, Liu J |
| Citation(s) |
26219960 |
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| Submission date |
Mar 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wang Min |
| E-mail(s) |
510178941@qq.com
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
| GPL19968 |
Illumina HiSeq 2000 (Citrus trifoliata) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA279929 |
| SRA |
SRP056728 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67439_RAW.tar |
14.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE67439_pooled-Unigene.fa.gz |
15.2 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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