|
| Status |
Public on Dec 25, 2023 |
| Title |
RHW1-crispr-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ear
|
| Organism |
Zea mays |
| Characteristics |
tissue: Ear
genotype: RHW1 knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAprep Pure Plant Plus kit,treated with RNase-free DNaseI and purified using the RNAclean Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
crispr2
|
| Data processing |
Sequencing reads were processed with trimmomatic-0.35 to remove adaptor sequence and low-quality sequence, and then mapped to B73.v4 reference genome using HISAT2 (version: 2.1.0).
Uniquely mapped reads were kept for subsequent gene expression quantification using HTSeq-count.
DEGs analysis was performed using the edgeR package (version: 3.32.1)in R-project.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie.
Assembly: B73.v4
Supplementary files format and content: tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Nov 14, 2022 |
| Last update date |
Dec 25, 2023 |
| Contact name |
Aiai Xia |
| E-mail(s) |
sumlove@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
Plant Genetics and Breeding
|
| Lab |
Yan He Lab
|
| Street address |
NO2 Yuanmingyuan West Road, Haidian, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE217926 |
The RHW1-ZCN4 regulatory pathway confers natural variation of husk leaf width in maize |
|
| Relations |
| BioSample |
SAMN31712458 |
| SRA |
SRX18249874 |
