|
| Status |
Public on May 03, 2022 |
| Title |
CK_Os-2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: leaf
genotype: WT
treatment: CK
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 μg/mg doxycycline treated and control check leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Assembly: TAIR10;IRGSP-1.0; SL3.0
Supplementary files format and content: tab-delimited text files include count for each Sample
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
May 03, 2022 |
| Contact name |
Moyang Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Agriculture and Biology
|
| Street address |
dongchuan road 800
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE201607 |
Machine learning accelerates the dissection of mitostasis as a cross-species central biological hub for leaf senescence |
|
| Relations |
| BioSample |
SAMN27783501 |
| SRA |
SRX15004686 |
