|
| Status |
Public on May 04, 2024 |
| Title |
RNA-seq_12ON_phyB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seeds
developmental stage: seeds at 12 h of dark incubation after light treatment under the phyB-on condition
genotype: phyB mutant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Spectrum Plant Total RNA Kit (STRN50, Sigma). Three biological replicates for each sample were subjected to RNA-seq.
Poly(A) RNA from 1 μg total RNA was used to generate each cDNA library according to the TruSeq RNA Sample Prep Kit (Illumina) protocol. All libraries were then sequenced on a HiSeq 2500 System (Illumina) with paired-end 150-bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using HISAT2 (version 2.1.0) with parameters “--dta --min-intronlen 50 --max-intronlen 6000”. Only unique mapping and MAPQ score > 20 reads were kept using SAMtools version 1.6 for subsequent analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 30, 2022 |
| Last update date |
May 04, 2024 |
| Contact name |
Yangyang Fan |
| E-mail(s) |
fanyangyang123456@126.com
|
| Organization name |
Peking University
|
| Street address |
No.5 Yiheyuan Road Haidian District,
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE195745 |
Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA [RNA-seq] |
| GSE195748 |
Noncoding RNA HID1 promotes phyB-dependent seed germination by repressing the biosynthesis of ABA. |
|
| Relations |
| BioSample |
SAMN25509364 |
| SRA |
SRX13991813 |
