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| Status |
Public on Apr 25, 2011 |
| Title |
Control |
| Sample type |
SRA |
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| Source name |
normal growth condition
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| Organism |
Populus euphratica |
| Characteristics |
tissue: leaves
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| Treatment protocol |
In the drought stress treatment, P. euphratica plants were submitted to soil water deficiency in four RSMC levels for two months according to previous research (Hasio, 1973). They were Group A with RSMC 70-75%; Group B with RSMC 50-55%; Group C with RSMC 35-40% and Group D with RSMC 15-20%. Soil with sufficient irrigations everyday kept RSMC at 70-75% because of transpiration, so Group A was used as control sample. Leaf water potential was measured by PsyPro water potential data logger (WescorTM). Net photosynthetic rate and transpiration rate were measured by Li-6400 Photosynthesis System (LI-COR TM). All data were statistically analyzed by one-way ANOVA using SPSS (SPSS statistical package 10.1, Chicago, IL, USA).
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| Growth protocol |
One year-old seedlings of P. euphratica, obtained from the Xinjiang Uygur Autonomous Region of China, were planted in individual pots (15 L) containing loam soil and placed in a greenhouse at Beijing Forestry University. Each pot contained three individuals. Potted plants were well irrigated according to evaporation demand and watered with 1 L full-strength Hoagland nutrient solution every 2 weeks for two months before drought stress treatment. The temperature in the greenhouse was 20 ℃ to 25 ℃ with a 16 hour photoperiod (4 AM-8 PM).
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| Extracted molecule |
total RNA |
| Extraction protocol |
For material harvest, mature leaves from the same position of eight different plants in each treatment were mixed and ground immediately in liquid nitrogen. Total RNA was extracted from mixed leave tissues by standard CTAB method for plants (Chang, 1993). Then the total RNA was used for high through-put sequencing and microarray profiling.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
sRNA
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| Data processing |
Sequencing reads were first aligned against the P. trichocarpa genome (JGI P. trichocarpa genome V 1.1) by SOAP software (Li et al., 2008). Sequences with perfect match were retained for further analysis. By comparing the existing sRNA database, all small RNAs were annotated in the order of the following categories: 1. rRNAetc: rRNA, tRNA, snRNA, scRNA and snoRNA deposited at Genebank (http://www.ncbi.nih.gov/Genbank/); Rfam (http://rfam.sanger.ac.uk/) database. In this category, RNA sequences based on structural conservation were also considered. GtRNAdb (http://lowelab.ucsc.edu/GtRNAdb/Ptric/popTri2-tRNAs.fa), a highly confidential Populus tRNA database predicted by tRNAscan based on structure (Schattner et al., 2005), was also used for excluding tRNA. 2. known miRNA: previously discovered miRNAs in miRBase13.0; 3. exon_sense/antisense: genomic exon sequences in sense/antisense direction; 4. intron_sense/antisense: genomic intron sequences in sense/antisense direction. Both of the exon_sense/antisense and intron_sense/antisense were classified by the Populus genome data from P. trichocarpa genome V 1.1 (http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html). 5. unknown sRNA.
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| Submission date |
Dec 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
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| Organization name |
SUSTC (current, may different with previous institution )
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| Department |
MCDB
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| Street address |
SUStech Huiyuan #1 406
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
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| Platform ID |
GPL11262 |
| Series (1) |
| GSE25747 |
A Genome-Wide Characterization of New and Drought Stress Responsive MicroRNAs in Populus euphratica |
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| Relations |
| SRA |
SRX033028 |
| BioSample |
SAMN00139640 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM632660_Control.fasta.gz |
7.1 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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