|
| Status |
Public on Feb 09, 2024 |
| Title |
MSH7-crispr-aa-14DAP-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Seed (14 DAP)
|
| Organism |
Zea mays |
| Characteristics |
tissue: Seed (14 DAP)
genotype: MSH7 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 |
MSH7-aa-14-rep2
MSH7-14DAP-genecounts.txt
|
| Data processing |
Sequencing reads were processed with trimmomatic-0.39 to remove adaptor sequence and low-quality sequence, and then mapped to B73 RefGen_v4 reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-50/plants/fasta/zea_mays/dna/) using HISAT2 (version: 2.2.1).
Uniquely mapped reads were kept for subsequent gene expression quantification using featureCounts (v1.6.4).
DEGs analysis was performed using the DESeq2 R package.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie (version: 1.3.6).
Assembly: B73 RefGen_v4 reference genome
Supplementary files format and content: tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Feb 09, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Luguang Jiang |
| Organization name |
China Agricultural University
|
| Street address |
No.2 Yuanmingyuan West Road, Haidian, Beijing
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE224891 |
MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize |
|
| Relations |
| BioSample |
SAMN33219565 |
| SRA |
SRX19319765 |
