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Sample GSM8091761 Query DataSets for GSM8091761
Status Public on Jul 22, 2024
Title WT_DMSO_rep1
Sample type SRA
 
Source name whole seedlings
Organism Solanum lycopersicum
Characteristics tissue: whole seedlings
genotype: WT
treatment: 0.1% DMSO
Treatment protocol the medium was refreshed, and it was supplemented with 0.1% DMSO (mock) or 10 μM ABA or 20 μM iSB09 . Samples were collected after 3 hours of incubation
Growth protocol Solanum lycopersicum seedlings (3 d.a.g.) were transferred from plates to flashes with liquid media during 8 days
Extracted molecule total RNA
Extraction protocol RNA was harvested using E.Z.N.A.® Plant RNA Kit (Omega Biotek).
The library was constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description SlycopMock.1
Data processing After quality analysis with FastQC and read cleaning and adaptor trimming with cutadapt, clean reads were mapped to reference genome of Solanum lycopersicum SL4.0 using STAR. Read counts table produced by STAR was used to perform the differential expression analysis with DESeq2.
Assembly: SL4.0 (https://solgenomics.net/ftp/tomato_genome/assembly/build_4.00/)
Supplementary files format and content: tab-delimited text fille includes raw counts for each sample
 
Submission date Feb 21, 2024
Last update date Jul 22, 2024
Contact name Pedro L. Rodriguez
E-mail(s) prodriguez@ibmcp.upv.es
Organization name IBMCP
Street address C/ Ingeniero Fausto Elio, s/n
City Valencia
State/province Valencia
ZIP/Postal code 46011
Country Spain
 
Platform ID GPL28981
Series (1)
GSE256238 iSB09 elicits ABA-responsive gene expression in Solanum lycopersicum seedlings
Relations
BioSample SAMN40018595
SRA SRX23682406

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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