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| Status |
Public on Sep 26, 2022 |
| Title |
M28-4h-rep2 |
| Sample type |
SRA |
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| Source name |
Seeds of M28,drought 4 hour,rep2
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: leaf
genotype: EMS mutant
treatment: drought 4h
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| Treatment protocol |
At the five full leaves stage, each pot with 3 similar sized seedlings was fully watered, and then all pots for K326 or M28 were randomly divided into 3 parts for drought treatment, natural drought (ND) treatment and 200 mM mannitol for simulated drought (SD) treatment.Total RNA was extracted using collected leaves with ND and SD at 0, 1, 2, 4 and 8h.
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| Growth protocol |
Seeds of K326 and its derived EMS mutant, M28 with enhanced drought resistance, were sterilized and pretreated in 4℃ for 2 days. The pretreated seeds were put in pot with nutrient soil for germination. The germinated seedlings with fully expanded cotyledons were transferred into small pots. Each pot contained the exact same amount (120g) of nutrient soil, 10 seedlings per pot for each replicate, total three replicates for K326 or M28. All pots were randomly put in the incubator to grow under 22±1℃,16h/8h light-dark cycle and 70% humidity.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using collected leaves with ND and SD at 0, 1, 2, 4 and 8h. After completely removal of genomic DNA contamination, mRNA was enriched for RNA-seq library preparation following the kit instruction.
After completely removal of genomic DNA contamination, mRNA was enriched for RNA-seq library preparation following the kit instruction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
the quality of raw read was processed using FastQC
Adapter contamination and poor-quality bases were removed using Trimmomatic
Hisat2 was used to align clean reads to the tobacco reference genome.
FeatureCounts was used for counting number of reads and FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values, representing gene expression levels.
Assembly: Nitab-v4.5
Supplementary files format and content: tobacco_FPKM.txt( FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values)
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| Submission date |
Sep 23, 2022 |
| Last update date |
Sep 26, 2022 |
| Contact name |
Zexue He |
| E-mail(s) |
hezexue@stu.njau.edu.cn
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| Organization name |
Nanjing Agricultural University
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| Department |
Agricultural College
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| Street address |
Xuanwu District,1 Weigang
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| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210018 |
| Country |
China |
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| Platform ID |
GPL22345 |
| Series (1) |
| GSE214048 |
Drought induced transcriptomic changes in tobacco |
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| Relations |
| BioSample |
SAMN30985559 |
| SRA |
SRX17682393 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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