|
| Status |
Public on Dec 18, 2024 |
| Title |
P6497-24hpi-RNA-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
24hpi Phytophthora sojae infected soybean
|
| Organism |
Phytophthora sojae |
| Characteristics |
tissue: 24hpi Phytophthora sojae infected soybean
strain: P6497
Stage: 24hpi
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the E.Z.N.A.® Total RNA Kit I (Omega BIO-TEK) according to the product manual.
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-seq library preparation and construction services were provided by BGI.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Data processing |
Clean reads were aligned to Phytophthora sojae whole genome using hisat2 v2.1.0 with default parameters
TPM was calculated using stringtie v1.3.3b with default parameters
Assembly: Phytophthora sojae V1.1
Supplementary files format and content: Excel file with gene expression matrix (TPM value of all genes)
Supplementary files format and content: gtf files include FPKM,TPM,and coverage values for each Sample
|
| |
|
| Submission date |
Mar 03, 2024 |
| Last update date |
Dec 18, 2024 |
| Contact name |
Haidong Shu |
| E-mail(s) |
2018202004@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Department |
Department of Plant Pathology
|
| Lab |
The Lab of Pathogenomics
|
| Street address |
Weigang NO.1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL34270 |
| Series (1) |
| GSE260751 |
Chromatin dynamics of Phytophthora during host infection [RNA-seq] |
|
| Relations |
| BioSample |
SAMN40241153 |
| SRA |
SRX23820084 |
