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| Status |
Public on Jun 29, 2022 |
| Title |
RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi, 2 |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Fusarium graminearum PH-1 |
| Characteristics |
tissue: Mycelium
genotype: WT
infection: YES
treatment: 48 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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| Description |
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 48hpi_2
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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 FPKM (fragment per kilobase of transcript per million mapped reads) using Stringtie (v1.2.0).
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.
Genome build: ASM24013v3 (reference genome of F. graminearum strain PH-1)
FPKMs, counts
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| Submission date |
May 16, 2022 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Yujie Wang |
| E-mail(s) |
2019202005@njau.edu.cn
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| Organization name |
Nanjing Agricultural University
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| Street address |
No. 1, Weigang, Xuanwu District
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL32260 |
| Series (1) |
| GSE203093 |
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress |
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| Relations |
| BioSample |
SAMN22064444 |
| SRA |
SRX12728877 |
| 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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