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Sample GSM8046627 Query DataSets for GSM8046627
Status Public on May 14, 2024
Title TraPR small RNA-seq: ago18HT-5mm-rep1
Sample type SRA
Source name anther
Organism Zea mays subsp. mays
Characteristics cell type: anther
genotype: mostly B73
group: ago18HT-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
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.
SRA SRX23452220
BioSample SAMN39674179

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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