|
| Status |
Public on Sep 26, 2023 |
| Title |
lowP_12SIII-3 |
| Sample type |
SRA |
| |
|
| Source name |
3-week-old root tissues
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: 3-week-old root tissues
cultivar: cv. Nipponbare
genotype: max1-1400
treatment: Low Pi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total rice root RNA was extracted with TRIzol (Invitrogen, https://www.thermofisher.com/de/de/home.htmL) using a Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA).
The cDNA libraries were constructed following standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
gene_fpkm
lowP_12SIIIvslowP_WT_deg
|
| 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 containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly (ensemblplants_oryza_sativa_japonica_group_irgsp_1_0_gca_001433935_1). Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Differential gene expression was examined using DESeq2
Assembly: ensemblplants_oryza_sativa_japonica_group_irgsp_1_0_gca_001433935_1
Supplementary files format and content: FPKM, DESeq2 output
|
| |
|
| Submission date |
Dec 28, 2022 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Jian You Wang |
| E-mail(s) |
jianyou.wang@kaust.edu.sa
|
| Phone |
0543907951
|
| Organization name |
KAUST
|
| Street address |
4700 King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia
|
| City |
Thuwal |
| State/province |
Not Specified |
| ZIP/Postal code |
4700 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE221837 |
Transcriptome analysis of rice max1-1400 mutant |
|
| Relations |
| BioSample |
SAMN32429329 |
| SRA |
SRX18863316 |
