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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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