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| Status |
Public on Jul 13, 2023 |
| Title |
Vd171_rep 1 |
| Sample type |
SRA |
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| Source name |
fungal mycelia
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| Organism |
Verticillium dahliae |
| Characteristics |
tissue: fungal mycelia
genotype: wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a Nucleospin® RNA Plant Kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA or by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
Results of gene expression include gene expression levels and differential expression analysis.
Further, we perform Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis.
Assembly: GCA_000723945.1Ni_benscaffolds:100,480contigs:100,480N50:776L50:22,990
Supplementary files format and content: .xls file containing all the gene expression reads and relative expression levels
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| Submission date |
Jul 06, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Chenlei Hua |
| E-mail(s) |
chenlei.hua@zmbp.uni-tuebingen.de
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| Organization name |
University of Tübingen
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| Department |
Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP)
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| Lab |
PRR Lab
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| Street address |
Auf der Morgenstelle 32
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| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
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| Platform ID |
GPL24077 |
| Series (1) |
| GSE236729 |
The transcriptional landscape of Nicotiana benthamiana and Verticillium dahliae interaction |
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| Relations |
| BioSample |
SAMN36344529 |
| SRA |
SRX20929699 |
| 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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