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| Status |
Public on Dec 04, 2023 |
| Title |
RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi rep1 |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Fusarium graminearum PH-1 |
| Characteristics |
cell type: Mycelium
genotype: WT
time: 120 hour post-inoculation
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extraction using TRIZOL reagent following the manufacturer’s instructions.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
For RNA-seq analysis, all of the raw reads were filtered by Fastp (version 0.18.0) software to remove adapters and low quality reads (quality score≤20).
Clean reads were aligned to the Fg reference genome using Hisat2 (v1.3.3).
Expression levels for each sample were quantified to TPM
Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1
Supplementary files format and content: Genes displaying log2 [fold change] ≥ 1.5 and an adjusted (false discovery rate) p value < 0.05 were classified as differentially expressed genes (DEGs) by using DESeq2 package.
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| Submission date |
Sep 22, 2022 |
| Last update date |
Dec 04, 2023 |
| Contact name |
zhao xiao zhen |
| E-mail(s) |
zhaoxiaozhen@ahau.edu.cn
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| Phone |
17768116791
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| Organization name |
Anhui Agricultural University
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| Street address |
Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China
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| City |
Hefei |
| ZIP/Postal code |
230036 |
| Country |
China |
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| Platform ID |
GPL32260 |
| Series (2) |
| GSE213960 |
Bivalent histone modification of BCG1 enables fungal pathogen to evade host immunity (RNA-Seq) |
| GSE213962 |
Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion |
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| Relations |
| BioSample |
SAMN30964042 |
| SRA |
SRX17676013 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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