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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 30, 2020 |
| Title |
ctrl BY-2 rep3 |
| Sample type |
SRA |
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| Source name |
suspension cell culture
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| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Bright Yellow 2
cell line: BY-2
growth cycle stage: exponential growth phase
cultivation conditions: auxin (2,4-D) supplemented conditions
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| Treatment protocol |
Auxin free culturred BY-2 cells were innoculated into MS medium without 2,4-dichlorophenoxyacetic acid.
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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 |
Total RNA was isolated using RNeasy Plant Mini kit (Qiagen) from 50-100 mg of BY-2 cells and treated with DNA-Free kit (Thermo Fischer Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols by GATC Biotech service company.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
rough reads processed using Trimmomatic (parameters: leading:3, trailing:3, slidingwindow:4:20, minlen:40)
transcript quantification and normalization done by Salmon with parameters –seqBias, --gcBias, --numBootstraps 30
Genome_build: Nicotiana tabacum v1.0 cDNA (Edwards, K.D., Fernandez-Pozo, N., Drake-Stowe, K., et al. (2017) A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics, 18, 448)
ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017
Genome browser available at: https://solgenomics.net
Supplementary_files_format_and_content: sf files generated by Salmon software, include TPM values
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| Submission date |
Oct 29, 2020 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Karel Muller |
| E-mail(s) |
[email protected]
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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 |
GPL25653 |
| Series (1) |
| GSE160438 |
A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis |
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| Relations |
| BioSample |
SAMN16595832 |
| SRA |
SRX9401156 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4873392_772quant.sf.txt.gz |
959.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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