|
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 |