|
| Status |
Public on Jun 30, 2022 |
| Title |
Tobacco leaf tissue - G70×GDH11_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Tobacco leaf tissue
|
| Organism |
Nicotiana tabacum |
| Characteristics |
developmental stage: growing for 70 days
tissue: Middle leaf
genotype: G70XGDH11
|
| 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)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
hybrid G70×GDH11
S19
|
| 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) in a reference-based approach
The software RSEM was used to quantitatively analyze the expression levels of genes and transcripts
Assembly: https://solgenomics.net/organism/Nicotiana_tabacum/genome
Supplementary files format and content: tab-delimited text files include FPKM values for 18 Samples
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
kai pi |
| E-mail(s) |
pekyhome@outlook.com
|
| Phone |
+8613299960523
|
| Organization name |
Guizhou University
|
| Department |
Key Laboratory for Tobacco Quality Research Guizhou Province
|
| Lab |
Tobacco College
|
| Street address |
None
|
| City |
Guiyang |
| State/province |
Guizhou |
| ZIP/Postal code |
550000 |
| Country |
China |
| |
|
| Platform ID |
GPL29390 |
| Series (1) |
| GSE198555 |
Overdominant expression of related genes of ion homeostasis improves K+ content advantage in hybrid tobacco leaves |
|
| Relations |
| BioSample |
SAMN26653937 |
| SRA |
SRX14459988 |
