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Sample GSM7843170 Query DataSets for GSM7843170
Status Public on Sep 02, 2024
Title IL6-2 rep3, control
Sample type SRA
 
Source name Roots
Organism Solanum lycopersicum x Solanum pennellii
Characteristics tissue: Roots
cell line: IL6-2
treatment: non treated (control)
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Oct 16, 2023
Last update date Sep 02, 2024
Contact name Vasiliki Kotsira
E-mail(s) vasilikikotsira@hotmail.com
Phone 6948742823
Organization name Department of Computer Science and Biomedical Informatics
Street address Papasiopoulou 2-4
City Galaneika – Lamia
ZIP/Postal code 35131
Country Greece
 
Platform ID GPL33844
Series (1)
GSE245472 Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism
Relations
BioSample SAMN37846056
SRA SRX22102147

Supplementary file Size Download File type/resource
GSM7843170_IL6-2_c3_penn.genes.results.gz 163.9 Kb (ftp)(http) RESULTS
GSM7843170_IL6-2_c3_slyc.genes.results.gz 185.0 Kb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA

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