|
| Status |
Public on Jul 29, 2024 |
| Title |
N_SH_WT_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedling
genotype: Col-0
condition: naive
treatment: 1 hr shade
|
| Treatment protocol |
Shade treatment (R/FR≈0.5).
|
| Growth protocol |
Seedlings were grown under N (4-day-old seedlings + 8 h white light + 40 h recovering white light + 1 h triggering shade) and P (4-day-old seedlings + 8 h priming shade + 40 h recovering white light + 1 h triggering shade) conditions.
|
| 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 |
| |
|
| Description |
Naïve_SH_WT_replicate1
|
| 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.
Assembly: TAIR10
Supplementary files format and content: all_genes_expression_TPM.txt: The expression levels (TPM) of differentially expressed genes after shade treatment.
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Qican Cheng |
| E-mail(s) |
20110700031@fudan.edu.cn
|
| Phone |
+86155104563045
|
| Organization name |
Fudan university
|
| Department |
school of life sciences
|
| Street address |
2005 Songhu Road, Yangpu District
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE226745 |
Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance memory of Arabidopsis |
|
| Relations |
| BioSample |
SAMN33603889 |
| SRA |
SRX19578262 |
