|
| Status |
Public on May 14, 2024 |
| Title |
small RNA-seq: HP301-0.4mm-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
anther
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
group: HP301-0.4mm
cell type: anther
genotype: HP301
molecule subtype: small RNA - total
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TRI reagent (Sigma-Aldrich) or the TraPR Small RNA Isolation kit (Lexogen; for TraPR sRNA-seq only)
sRNA-seq libraries were prepared from ~100 ng total RNA per sample using a Somagenics RealSeq-AC miRNA library kit following the manufacturer’s protocol. RNA-seq (Smart-seq2) and nanoPARE libraries were prepared from 5 ng total RNA per sample using the nanoPARE library preparation protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
To quantify phasiRNA abundance, sRNA-seq reads were mapped to the respective Zea genomes using Bowtie v1.3.1; to quantify miRNA abundance, sRNA-seq reads were mapped to a FASTA file of all mature miRNAs annotated for each genome using bowtie; and to quantify mRNA abundance, Smart-seq2 reads were mapped to the respective Zea genomes (B73 RefGen_v5 was used for the ago18 mutant data) using HISAT v2.1.0. Reads mapped to PHAS loci or miRNAs 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. Small RNA-transcript interactions in each anther sample were identified using the nanoPARE analysis pipeline (Schon et al., 2018). The sRNA-target pairs with adjusted P value < 0.05 at the EndCut step and are detected in at least two biological replicates were considered positive.
Assembly: Respective reference genomes of Zea varieties
Supplementary files format and content: CPM tables for sRNA-seq and RNA-seq, cleavage-site tables for nanoPARE
|
| |
|
| 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) |
| GSE254581 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [small_RNA] |
| GSE254584 |
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function. |
|
| Relations |
| BioSample |
SAMN39674288 |
| SRA |
SRX23452286 |
