|
| Status |
Public on Dec 31, 2018 |
| Title |
T24_3 |
| Sample type |
SRA |
| |
|
| Source name |
T24 leaves
|
| Organism |
Andrographis paniculata |
| Characteristics |
tissue: leaf
induction stage: T24
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from leaves induced for 0, 12, 24 and 48 hours with three biological replicates were extracted using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions. Highly purified and intact mRNAs were enriched from total RNAs using Dynabeads® mRNA purification kit (Ambion, 61006). RNAs were fragmented into ~ 300 nt fragments by 1 min incubation at 94℃ in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0). The fragmentation reaction was stopped with 50 mM EDTA, followed by standard ethanol precipitation and collected for sequencing and expression validation.
For the strand-specific RNA-seq, fragmented RNAs were re-suspended in H2O and used for library generation with mRNA sequencing kit (Illumina Inc. San Diego, CA). Sequencing was carried out on Illumina HiSeq 4000 sequencer (Illumina Inc. San Diego, CA) according to the manufacturer’s instructions and 150 nt paired-end sequencing reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
T24_3
MeJA induce for 24 hours
|
| Data processing |
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
Clean reads from all samples were pooled together and feeded to de novo RNA-seq assembly software Trinity (v2.0.6) with default parameters.
The expression of assembled transcripts and genes were quantified using RSEM (v1.2.19).
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of each transcript for all samples.
|
| |
|
| Submission date |
Jun 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tong Chen |
| E-mail(s) |
chentong_biology@163.com
|
| Phone |
86-15210822685
|
| Organization name |
China Academy of Chinese Medical Sciences
|
| Department |
State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica
|
| Lab |
Luqi Huang's lab
|
| Street address |
No 16 Nan-xiao-jie Dong-zhi-men-nei
|
| City |
Beijing |
| ZIP/Postal code |
100700 |
| Country |
China |
| |
|
| Platform ID |
GPL22087 |
| Series (1) |
| GSE83775 |
Time-serialized expression profile of MeJA induced Andrographis paniculata leaves |
|
| Relations |
| BioSample |
SAMN05296545 |
| SRA |
SRX1880254 |
