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| Status |
Public on Apr 17, 2023 |
| Title |
1658265PMT2root |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: root
genotype: PMT RNAi suppresion
treatment: untopped
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| Extracted molecule |
total RNA |
| Extraction protocol |
With use of liquid nitrogen, tobacco samples were grinded to fine powder in mortars, and 200-mg samples were taken for RNA extraction. RNA extraction was performed by RNeasy® Plant Mini Kit (© QIAGEN N.V., Venlo, the Netherlands).
Subsequenlt sequencing library preparation was performed (no fragmentation) by TruSeq® Stranded Total RNA Gold (© Illumina, Inc., San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
PMT2 root sample bio rep 7
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| Data processing |
The generated sequencing data were demultiplexed by Illumina BaseSpace® Clarity LIMS (© Illumina, Inc.) and subsequently imported to Qiagen CLC Genomics Workbench version 11.0.1 (CLC bio, a QIAGEN Company). Transcriptome reads were mapped to updated version the N. tabacum reference genome [49] using the ‘RNA-Seq Analysis’ 2.16 tool with similarity of 0.95 (S=0.95) and fraction length of 0.95 (L=0.95) as mapping criteria. The mismatch, insertion, and deletion costs were set to 2, 3, and 3, respectively.
Global alignment was not performed, and paired distances were detected automatically. The maximum number of read hits was set to 10, and paired reads were counted as 2. RPKM values were retrieved for each gene in the reference genome, including for those without transcript models. A fusion gene table was not created.
For each sample principal component analysis (PCA) was performed with the CLC ‘PCA for RNA-Seq’ tool. Gene expression analysis was performed with the ‘Empirical Analysis of DGE’ tool, where RPKM values for each gene were retrieved and compared by empirical analysis of DGE, which employs the ‘exact test’ developed by Robinson and Smyth [50] that was incorporated into the EdgeR Bioconductor package [51]. Genes with pairwise comparison p-values ≤0.05 and an absolute fold change ≥2 were regarded as significantly different.
Assembly: Transcriptome reads were mapped to updated version the N. tabacum reference genome by Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV: The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 2014, 5:3833.
Supplementary files format and content: Sample-specific mapping statistics are provided in Supporting Table 1.xlsx
Supplementary files format and content: A total of 2075 genes with statistically different expression were present in at least one of these comparisons and their expression for each samples is presented in Supporting Table 2.xlsx
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| Submission date |
Apr 12, 2023 |
| Last update date |
Apr 17, 2023 |
| Contact name |
Kacper Piotr Kaminski |
| E-mail(s) |
[email protected]
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| Phone |
0787088883
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| Organization name |
Philip Morris International
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| Street address |
Rue Fleury 5
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| City |
Neuchâtel |
| ZIP/Postal code |
2000 |
| Country |
Switzerland |
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| Platform ID |
GPL25653 |
| Series (1) |
| GSE229462 |
Suppression of pyrrolidine ring biosynthesis and its effects on gene expression and subsequent accumulation of anatabine in leaves of Tobacco (N. tabacum L.) |
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| Relations |
| SRA |
SRX19940280 |
| BioSample |
SAMN34153879 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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