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Sample GSM8439566 Query DataSets for GSM8439566
Status Public on Aug 29, 2024
Title ZmEIP_2_14d
Sample type SRA
 
Source name leaves
Organism Zea mays
Characteristics tissue: leaves
cell line: LH244
cell type: leaves
genotype: ZmEIP
time: 14d
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol reagent
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw reads were filtered using ht2-filter in the HTQC package (1.92.1) with default parameters to remove low-quality reads. The filtered reads were compared to the reference maize genome (Zea mays RefGen_V4) using TopHat (2.0.11) to remove host genome sequences. The mapped reads were assembled, and fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks.
Assembly: Zea mays RefGen_V4
Supplementary files format and content: FPKM
 
Submission date Aug 04, 2024
Last update date Aug 29, 2024
Contact name Haiyue Yu
E-mail(s) yuhaiyueo@126.com
Organization name Chinese Academy of Agricultural Sciences
Street address Yuanmingyuanxilu No.2
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL25410
Series (1)
GSE273918 The Exserohilum turcicum effector EtEC81 reprograms alternative splicing in maize and activates immunity
Relations
BioSample SAMN43024986
SRA SRX25595219

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

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