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| Status |
Public on Jun 09, 2023 |
| Title |
RNA-Seqoftobacco:Stalk [Basma_Sb_1] |
| Sample type |
SRA |
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| Source name |
Stalk
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: Stalk
cell line: After topping
genotype: Basma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Stalk_exp.txt
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| Data processing |
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM (http://deweylab.github.io/RSEM/) establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 15 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.
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| Submission date |
May 23, 2023 |
| Last update date |
Jun 09, 2023 |
| Contact name |
kai pi |
| E-mail(s) |
pekyhome@outlook.com
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| Organization name |
Guizhou University
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| Department |
Key Laboratory for Tobacco Quality Research Guizhou Province
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| Lab |
Tobacco College
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| Street address |
None
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| City |
Guiyang |
| State/province |
Guizhou |
| ZIP/Postal code |
550000 |
| Country |
China |
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| Platform ID |
GPL29390 |
| Series (1) |
| GSE233199 |
Transcriptome analysis of different tissues in different materials |
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| Relations |
| BioSample |
SAMN35325762 |
| SRA |
SRX20474535 |
| 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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