|
| Status |
Public on Aug 03, 2022 |
| Title |
Yanyan97_1h_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yanyan97
|
| Organism |
Nicotiana tabacum |
| Characteristics |
developmental stage: five-leaf stage
tissue: seedlings
treatment: 1h cold treatment at 4 degrees centigrade
genotype: Yanyan97
|
| Treatment protocol |
Tobacco seedlings at the five-leaf stage were used for cold treatment at 4℃. Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.
|
| Growth protocol |
Two cultivated tobacco (Nicotiana tabacum L.) varieties, Taiyan8 tobacco (TT) and Yanyan97 tobacco (YT), were used in this study. The seeds were sterilized in 75% ethanol for 30 s and washed with sterile water for five times. Sterilized seeds were germinated and grown in 1/2 MS medium in an illuminated incubator (16 h/8 h day/night light cycle, 22/20℃day/night temperature setting with 65% relative humidity).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The raw sequence data were processed to remove low-quality reads using FastQC (v0.11.5) and Trim_Galore (v0.6.4). The filtered high-quality reads were mapped on the Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/) using HISAT2 (v2.0.5) with default parameters.
Reads with a mapping quality below twenty were excluded from further analyses using SAMtools (v1.9).(-q 20)
StringTie (v1.3.4d) and FeatureCounts (v1.6.4) were used to obtain transcripts per million (TPM) and read counts for all annotated genes in the tobacco genome.
Genome_build: Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcripts Per Million) values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene read counts for every gene and every sample
|
| |
|
| Submission date |
Apr 26, 2021 |
| Last update date |
Aug 03, 2022 |
| Contact name |
zhenyu luo |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Department |
College of Agricuture
|
| Lab |
Zhanglab
|
| Street address |
Xuanwu
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL25653 |
| Series (1) |
| GSE173352 |
Transcriptomic insights into differential cold tolerance of two tobacco cultivars |
|
| Relations |
| BioSample |
SAMN18872727 |
| SRA |
SRX10681856 |
