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| Status |
Public on Mar 31, 2024 |
| Title |
AtPIN5-BY2_EST_1588 |
| Sample type |
SRA |
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| Source name |
suspension cell culture
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| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Bright Yellow 2
biological replicates: 2
cell type: suspension cell culture
treatment: EST
treatment time: 48h
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| Treatment protocol |
AtPIN5 expression was induced by 1 µM β-estradiol (diluted in DMSO) added at the beginning of the subculture interval. DMSO-treated cells used as a non-induced control.
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| Growth protocol |
Tobacco cell line BY-2 (Nicotiana tabacum L. cv. Bright Yellow 2) was maintained in liquid Murashige and Skoog (MS) medium (3% sucrose (w/v), 4.3 g/l MS salts, 100 mg/l myo-inositol, 1mg/l thiamin, 0.2 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), and 200 mg/l KH2PO4; pH 5.8), in the dark, at 27°C, under continuous shaking (150 rpm; orbital diameter 30 mm) and sub-cultured every 7 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (Institute of Applied Biotechnologies or Novogene)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
IAB
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| Data processing |
reads were quality filterred by rcorrector and trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Nicotiana tabacum v1 Edwards 2017 (https://solgenomics.net/ftp/genomes/Nicotiana_tabacum/edwards_et_al_2017/)
Supplementary files format and content: sf files generated by Salmon software, include TPM values
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| Submission date |
Mar 05, 2024 |
| Last update date |
Mar 31, 2024 |
| Contact name |
Karel Muller |
| E-mail(s) |
muller@ueb.cas.cz
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| Organization name |
Institute of Experimenal Botany of the Czech Academy of Sciences
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| Department |
Lab. of hormonal regulations in plants
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| Street address |
Rozvojová 263
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| City |
Praha 6 |
| ZIP/Postal code |
16502 |
| Country |
Czech Republic |
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| Platform ID |
GPL29390 |
| Series (1) |
| GSE260945 |
RNA-seq of AtPIN5 overexpressing tobacco BY-2 cells |
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| Relations |
| BioSample |
SAMN40272668 |
| SRA |
SRX23844250 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8128522_1588_quant.sf.gz |
998.3 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
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