|
| Status |
Public on Jan 30, 2023 |
| Title |
S_pif7_2 |
| Sample type |
SRA |
| |
|
| Source name |
6-day-old white light-grown treated with 1 hr shade seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
age: 6-day-old
genotype: pif7
treatment: shade
|
| Treatment protocol |
With 1 hr shade (R/FR=0.4) treatment
|
| Growth protocol |
6-day-old white light-grown Col-0 (WT), pif7, asf1ab, and hira seedlings treated with 1 hr shade.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to TAIR10 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: The expression levels (FPKM) of differentially expressed genes after shade treatment.
|
| |
|
| Submission date |
Nov 27, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Chuanwei Yang |
| E-mail(s) |
yangchuanwei@fudan.edu.cn
|
| Organization name |
Fudan university
|
| Department |
school of life sciences
|
| Street address |
2005 Songhu Road, Yangpu District
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE189669 |
Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance syndrome of Arabidopsis |
|
| Relations |
| BioSample |
SAMN23470237 |
| SRA |
SRX13242208 |
