|
Status |
Public on Jan 30, 2018 |
Title |
root control 3 |
Sample type |
SRA |
|
|
Source name |
root
|
Organism |
Solanum lycopersicum |
Characteristics |
agent: not induced tissue: root
|
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 |
root control 3
|
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 |
SAMN08428593 |
SRA |
SRX3615327 |