|
| Status |
Public on Mar 04, 2022 |
| Title |
LR-5-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Section of primary root - lateral root stage 5
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Section of primary root containing lateral roots at Stage 5 - when the root primorida reaches the epidermis, but before emergence
|
| Treatment protocol |
N/A
|
| Growth protocol |
Tomato M82 DR5::VENUSx3-NLS seedlings were germinated on agar plates (1/2 strengh MS, 0.5% sucrose, 0.8% agar)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each plant lateral root stage was determine by DR5 flourescene under a stereoscope and a section of the primary root containing the lateral root primorida was microdissected and flash frozen. RNA was extracted usin QIAGEN microRNA extraction kit and treated with DNase I.
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
7089-LR-st-5
|
| Data processing |
Reads were aligned to the tomato genome ITAG4 and expression quantified using salmon 1.3.0. As the library is 3’ biased, we extended all genes to cover 500 additional base pairs downstream. Parameters for salmons were: --noLengthCorrection --noEffectiveLengthCorrection --validateMappings
Expression data were normalized using Deseq2
Genome_build: Solanum lycopersicum ITAG4
Supplementary_files_format_and_content: Raw expression reads for all replicates
|
| |
|
| Submission date |
Oct 05, 2020 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Idan Efroni |
| E-mail(s) |
idan.efroni@mail.huji.ac.il
|
| Organization name |
Hebrew University
|
| Department |
Plant Sciences
|
| Street address |
POB 12
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL21762 |
| Series (1) |
| GSE159050 |
Developmental series of tomato lateral root development |
|
| Relations |
| BioSample |
SAMN16374860 |
| SRA |
SRX9245766 |
