|
| Status |
Public on Jan 30, 2018 |
| Title |
callus 24h DEX 1 |
| Sample type |
SRA |
| |
|
| Source name |
callus
|
| Organism |
Solanum lycopersicum |
| Characteristics |
agent: induced with DEX
tissue: callus
time point: 24h
|
| Treatment protocol |
Dexamethason was added to a concetration of 10 mg/L
|
| Growth protocol |
ambient temperature, 16h light, 8h dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy plant minikit (Qiagen)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)
Equimolar amounts of libraries were pooled and diluted towards 6pM concentrations for paired end clustering on one lanes of a flow cell V4 (Illumina) and analyzed paired end on a HiSeq2500 instrument using a 126,7,126 flow cycle pattern.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
callus 24h DEX 1
|
| Data processing |
De-multiplexing of obtained sequences was done using CASAVA 1.8.1. software.
Reads were mapped with CLC Genomics Workbench 8.0 (Qiagen)
Genome_build: Solanum lycopersicon ITAG2.4
Supplementary_files_format_and_content: reads were mapped on the tomato genome version ITAG2.4 (gene models). Gene expression ratios for DEX samples compared to control samples were determined for each timepoint
" processed data.xlsx". The columns in this file called " raw CLC output" provide ratios between expression levels: so column D: callus 3h DEX/callus control; column E: callus 24h DEX/callus control; column F: root 3h DEX/root control; column G: root 24h DEX/root control.
|
| |
|
| Submission date |
Jan 29, 2018 |
| Last update date |
Jan 30, 2018 |
| Contact name |
Jules Beekwilder |
| E-mail(s) |
jules.beekwilder@wur.nl
|
| Organization name |
Wageningen Plant Research
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE109772 |
Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues of Tomato |
|
| Relations |
| BioSample |
SAMN08428577 |
| SRA |
SRX3615322 |
