|
| Status |
Public on May 14, 2024 |
| Title |
nanoPARE: HP301-2mm-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
anther
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
group: HP301-2mm
cell type: anther
genotype: HP301
molecule subtype: polyA RNA - 5' end
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TRI reagent (Sigma-Aldrich).
RNA-seq (Smart-seq2) and nanoPARE libraries were prepared from 5 ng total RNA per sample using the nanoPARE library preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
cleavage_sites_miRNA_HP301_2mm_1.tsv.gz
cleavage_sites_phasiRNA_HP301_2mm_1.tsv.gz
|
| Data processing |
Small RNA-transcript interactions in each anther sample were identified using the previously published nanoPARE analysis pipeline.
Assembly: Respective reference genomes of Zea varieties
Supplementary files format and content: Tables of cleavage sites
|
| |
|
| 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) |
| GSE254582 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [Smart-seq2+nanoPARE] |
| GSE254584 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. |
|
| Relations |
| SRA |
SRX23452107 |
| BioSample |
SAMN39673928 |
