|
| Status |
Public on Aug 26, 2022 |
| Title |
Cigar tobacco plants under 50 μmol m-2 s-1 light intensity [T50_3] |
| Sample type |
SRA |
| |
|
| Source name |
Cigar tobacco plants under 50 μmol m-2 s-1 light intensity
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: H382
tissue: Leaf
developmental stage: Seedling stage
treatment: Cigar tobacco plants under 50 μmol m-2 s-1 light intensity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cigar leaves were taken and quickly frozen in liquid nitrogen to collect RNA.The sequencing library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and 3ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumnia CASAVA 1.7 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Hisat software was used to carry out genome localization analysis on filtered sequencing sequences. Hisat default parameters were used. Ntab-K326 AWOJ-SS.fa.gz was used as a reference genome.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs) (Trapnell et al., 2010) is the number of fragments per million fragments from a gene per kilobase length. It is the most commonly used method for estimating gene expression level. HTseq software was used to analyze the gene expression level.
Assembly: Ntab-K326 AWOJ-SS.fa.gz
Supplementary files format and content: tab-delimited text files include FPKM values of genes for each sample
|
| |
|
| Submission date |
Aug 23, 2022 |
| Last update date |
Aug 26, 2022 |
| Contact name |
ying xiao wu |
| E-mail(s) |
wuxiaoying2021@yeah.net
|
| Organization name |
Tobacco Research Institute, Chinese Academy of Agricultural Sciences
|
| Department |
Cultivation and nutrition center
|
| Lab |
Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture
|
| Street address |
China and South Korea the street
|
| City |
qingdao |
| State/province |
shangdong |
| ZIP/Postal code |
266000 |
| Country |
China |
| |
|
| Platform ID |
GPL29390 |
| Series (1) |
| GSE211923 |
Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco during different light intensities |
|
| Relations |
| BioSample |
SAMN30470971 |
| SRA |
SRX17238171 |
