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| Status |
Public on Feb 24, 2021 |
| Title |
21RNAwt.3 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Xanthi NN
transgenic line: wild type
replicate: 3
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| Growth protocol |
Tobacco transgenic lines corresponding to the T4 generation of our previously published DcLCYB1-expressing lines were used in this work (Moreno et al., 2016). Tobacco (Nicotiana tabacum cultivar Xanthi NN) wild type and transgenic lines were raised from seeds germinated in Petri dishes containing MS medium supplemented with 30 g/L sucrose (Murashige and Skoog, 1962) and kanamycin (100 mg/mL).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen powder of tobacco leaves of 5-week-old T3 plants using the Nucleo Spin RNA extraction kit (Macherey-Nagel, Germany). Genomic DNA traces were eliminated by a 15 min DNase I treatment.
QuantSeq 3’ mRNA-Seq services were performed for the wild type and transgenic DcLCYB1 line L14, L15 and L16, at Lexogen GmbH (Vienna, Austria). 500 ng total RNA were used as input for generating sequencing-ready libraries using the QuantSeq FWD 3’ mRNA-Seq library preparation kit (Lexogen, Vienna, Austria; SKU 015). Libraries were characterized by microcapillary electrophoresis and fluorometry prior to pooling and sequencing.
A sequencing yield of 572,9M-demultiplexed reads was obtained from a single run on a NextSeq 500 device in SR75 HO mode
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Integrated data analysis was performed by Lexogen (STAR aligner) where reads were mapped against the Nitab 4.5 reference genome and read-counts were determined.
Differential expression was computed using DESeq2 in R (Love et al., 2014).
Genome_build: Nitab 4.5 reference genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017/)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)
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| Submission date |
Sep 05, 2020 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Juan Camilo Moreno Beltran |
| E-mail(s) |
juankmilo86@gmail.com
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| Organization name |
MPI for Molecular Plant Physiology
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| Department |
Molecular Physiology
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| Lab |
Skirycz
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| Street address |
Am Muehlenberg 1
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| City |
Potsdam |
| State/province |
Brandenburg |
| ZIP/Postal code |
14476 |
| Country |
Germany |
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| Platform ID |
GPL23495 |
| Series (1) |
| GSE157541 |
A multiOMICs approach shed light on the higher yield phenotype and abiotic stress tolerance in tobacco lines expressing the carrot lycopene β-cyclase1 |
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| Relations |
| BioSample |
SAMN16066983 |
| SRA |
SRX9081907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4769706_21RNAwt.3.gene_id_count.tab.gz |
147.3 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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