|
| Status |
Public on May 14, 2024 |
| Title |
TraPR small RNA-seq: ago18HM-5mm-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
anther
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
cell type: anther
genotype: mostly B73
group: ago18HM-5mm
molecule subtype: Small RNA - Argonaute loaded
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TraPR Small RNA Isolation kit (Lexogen)
sRNA-seq libraries were prepared using a Somagenics RealSeq-AC miRNA library kit following the manufacturer’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
library strategy: TraPR (Trans-kingdom, rapid, affordable Purification of RNA-induced silencing complexes (RISCs)) small RNA-seq
To quantify phasiRNA abundance, sRNA-seq reads were mapped to the respective Zea genomes using Bowtie v1.3.1.Reads mapped to PHAS loci were counted using featureCounts v1.6.3 and normalized to counts per million (CPM) using edgeR v4.0.2. Differential expression analyses were performed using edgeR with a generalized linear model-based method.
Assembly: B73 RefGen_v5
Supplementary files format and content: CPM tables
|
| |
|
| Submission date |
Jan 30, 2024 |
| Last update date |
May 14, 2024 |
| Contact name |
Junpeng Zhan |
| E-mail(s) |
zhan@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
1 Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL34147 |
| Series (2) |
| GSE254583 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq] |
| GSE254584 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. |
|
| Relations |
| SRA |
SRX23452216 |
| BioSample |
SAMN39674183 |
