|
| Status |
Public on May 12, 2021 |
| Title |
les4-wt-3 |
| Sample type |
SRA |
| |
|
| Source name |
les4-wt
|
| Organism |
Zea mays |
| Characteristics |
genotype: les4-wt
tissue: leaf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sample using the Trizol reagent
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s manual and index codes were added to attribute sequences to each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
G4-3
|
| Data processing |
Clean reads were derived after removal of low quality regions and adapter sequences from raw reads. Then clean reads were aligned to the maize reference genome (B73 RefGen_v4, available online: https://www.maizegdb.org/assembly/) using HISAT2
Aligned reads from HISAT2 mapping were subjected to String Tie for DeNovo Transcript assembly
The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples. The R package “DESeq2” were used to identify differentially expressed genes with fold changes (FC) above 2 and False Discovery Rate (FDR) lower than 0.05
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: FPKMs
|
| |
|
| Submission date |
Apr 07, 2020 |
| Last update date |
May 12, 2021 |
| Contact name |
xiaohuan mu |
| E-mail(s) |
muxiaohuan@cau.edu.cn
|
| Phone |
+8615824830720
|
| Organization name |
Henan Agricultural University
|
| Street address |
zhengzhou long zi hu
|
| City |
zheng zhou |
| ZIP/Postal code |
450002 |
| Country |
China |
| |
|
| Platform ID |
GPL25842 |
| Series (1) |
| GSE148220 |
New insights into the maize disease lesion mimics-conferred defense response revealed by integrated transcriptomics and metabolomics analysis |
|
| Relations |
| BioSample |
SAMN14548874 |
| SRA |
SRX8073313 |
