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Sample GSM4873392 Query DataSets for GSM4873392
Status Public on Oct 30, 2020
Title ctrl BY-2 rep3
Sample type SRA
 
Source name suspension cell culture
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
Treatment protocol Auxin free culturred BY-2 cells were innoculated into MS medium without 2,4-dichlorophenoxyacetic acid.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
Submission date Oct 29, 2020
Last update date Oct 30, 2020
Contact name Karel Muller
E-mail(s) [email protected]
Organization name Institute of Experimenal Botany of the Czech Academy of Sciences
Department Lab. of hormonal regulations in plants
Street address Rozvojová 263
City Praha 6
ZIP/Postal code 16502
Country Czech Republic
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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