|
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.
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|
|
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
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|
|
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 |