|
| Status |
Public on Apr 10, 2024 |
| Title |
osino80_rep1, RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
14-day-old seedlings
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: 14-day-old seedlings
cultivar: Nipponbare
genotype: osino80-2
treatment: no treatment
|
| Growth protocol |
Rice were grown in artificial growth chambers under an SD photoperiod for 14 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an RNAprep pure Plant Kit (Tiangen Biotech).
The strand-specific RNA-seq libraries were constructed by following the KAPA stranded mRNA-seq Kit instructions (Illumina® Platforms, KR0960-v5.17), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Oryza sativa Nipponbare
osino80_rep1
|
| Data processing |
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The reads with high quality score were aligned to the rice reference genome (MSU7) using Hisat2.
Reads mapped to the nuclear genome were preserved and SAMtools was used to obtain high quality alignments.
FeatureCounts was used to calculate the reads count of genes.
Differentially expressed TEs (Transposable Elements) were identified using TEtranscripts.
Assembly: MSU7
Supplementary files format and content: Binary bw files (bigwig).
Supplementary files format and content: Tab-delimited text files including featureCounts value and TPM (Transcripts per million) for each Sample.
|
| |
|
| Submission date |
Apr 05, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Wenhao Xie |
| E-mail(s) |
20210700089@fudan.edu.cn
|
| Phone |
18005879367
|
| Organization name |
Fudan University
|
| Department |
School of Life Science
|
| Street address |
No. 2005, Songhu Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (2) |
| GSE225485 |
RNAseq for WT and osino80 |
| GSE263341 |
ChIP-seq, RNA-seq and BS-seq for WT and osino80 |
|
| Relations |
| BioSample |
SAMN40763872 |
| SRA |
SRX24172767 |
