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| Status |
Public on Sep 02, 2024 |
| Title |
S.lycopersicum rep3, parasitized |
| Sample type |
SRA |
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| Source name |
Roots
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Roots
cell line: Formula
treatment: Orobanche ramosa-parasitized
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tomato roots, using the NucleoSpin RNA kit (MACHEREY-NAGEL, Germany) according to the manufacturer’s instructions. Thermo Scientific NanoDrop ND-1000 Spectrophotometer UV/Vis was used to determine the concentration and quality of the RNA.
Samples were subjected to cDNA library preparation (poly-A selection) and sequenced (150nt paired-end reads) on an Illumina NovaSeq 6000 system (Novogene Europe, Cambridge, UK). On average 13.9 million reads were obtained per library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Read quality was assessed with FastQC from the Babraham Institute. In order to remove adapter sequences and trim low-quality reads from the raw sequencing data, Cutadapt tool was utilized. Pre-processed reads were subjected to splice-aware genomic alignment and quantification, using STAR (v2.7.10) and RSEM (v1.3.1), respectively. Differential expression analysis was performed using the programming language R (version 4.2.2) and the R package edgeR. The limma R package was used for pathway enrichment analysis, employing the kegga() function and the KEGG database.
Assembly: GCF_000188115.5_SL3.1_genomic.fna, GCF_001406875.1_SPENNV200_genomic.fna
Supplementary files format and content: RSEM output files
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| Submission date |
Oct 16, 2023 |
| Last update date |
Sep 02, 2024 |
| Contact name |
Vasiliki Kotsira |
| E-mail(s) |
vasilikikotsira@hotmail.com
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| Phone |
6948742823
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| Organization name |
Department of Computer Science and Biomedical Informatics
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| Street address |
Papasiopoulou 2-4
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| City |
Galaneika – Lamia |
| ZIP/Postal code |
35131 |
| Country |
Greece |
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| Platform ID |
GPL27957 |
| Series (1) |
| GSE245472 |
Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism |
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| Relations |
| BioSample |
SAMN37846059 |
| SRA |
SRX22102144 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7843167_Fp3.genes.results.gz |
111.0 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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