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Status |
Public on Sep 02, 2024 |
Title |
IL6-3 rep3, control |
Sample type |
SRA |
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Source name |
Roots
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Organism |
Solanum lycopersicum x Solanum pennellii |
Characteristics |
tissue: Roots cell line: IL6-3 treatment: non treated (control)
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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 |
GPL33844 |
Series (1) |
GSE245472 |
Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism |
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Relations |
BioSample |
SAMN37846050 |
SRA |
SRX22102153 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7843176_IL6-3_c4_penn.genes.results.gz |
164.1 Kb |
(ftp)(http) |
RESULTS |
GSM7843176_IL6-3_c4_slyc.genes.results.gz |
183.7 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
Raw data are available in SRA |
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