|
| Status |
Public on Aug 29, 2024 |
| Title |
ZmEIP_1_10d |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Zea mays |
| Characteristics |
tissue: leaves
cell line: LH244
cell type: leaves
genotype: ZmEIP
time: 10d
|
| 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 |
SAMN43024996 |
| SRA |
SRX25595209 |
