|
| Status |
Public on Oct 30, 2017 |
| Title |
LK |
| Sample type |
SRA |
| |
|
| Source name |
tobacco_low potassium
|
| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: seedings
growth condition: low potassium treatment for 6h,12h, and 24h
|
| Treatment protocol |
then transfer to low potassium medium for, 6h, 12h and 24h treatment.
|
| Growth protocol |
The tobacco seeds were surface sterilized and germinated on MS medium for 20 days,
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from roots of alligator weed using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Statistical analysis of the quality information was performed and the raw sequence reads were cleaned using fastx (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/index.html). Bases with low quality at 3'3 end and fuzzy N bases in reads were removed from raw sequences. All low quality reads, such as short reads (<20 nt), empty reads, and ncRNA reads, were removed
A total Pool of Reads was generated with each samples’ reads and de novo assembly was performed using the Scaffolding Contig Algorithm of CLC GenomicsWorkbench (version 5.5).
Statistical analysis was performed to identify differentially expressed genes between the two libraries. RPKM (Reads perKilo bases per Million reads) quantitative criteria was applied to calculate the expressed amount of the reads coverage
Fisher’s test for difference was conducted according to the RPKM of the contigs and internal reference of the total expression amount in each sample
we used a stringent FDR value <0.05 and the fold change ≥2 or ≤0.5 as a threshold to judge the significant difference of gene expression. The DEGseq analysis was performed to count the differential gene expression.
Supplementary_files_format_and_content: RPKM values for each Sample and comparison between two samples; details in 'readme.txt'
|
| |
|
| Submission date |
Nov 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
li li qin |
| E-mail(s) |
liliqin88@163.com
|
| Phone |
+86-28-8629-0978
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
wenjiang district huiming 211road
|
| City |
Chengdu |
| State/province |
sichuan province |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL13760 |
| Series (1) |
| GSE63692 |
De Novo Transcriptome of tobacco seedlings and Identification of early response gene network under low potassium stress |
|
| Relations |
| BioSample |
SAMN03224264 |
| SRA |
SRX769756 |
