|
| Status |
Public on Jun 05, 2015 |
| Title |
Mock 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole-plant Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Colombia 0
treatment: Mock
sample time: 3 hours post treatment
|
| Treatment protocol |
Treatment was performed with OG-containing suspensions of either 200 µM trimeric OGs (Sigma-Aldrich, trimers) or a 2 mM mixture of short (DP<10) OGs (short OG-mix). 1/2 MS medium was used as a mock treatment. Plants were subjected to the suspensions for 3 hours.
|
| Growth protocol |
For the growth inhibition assay, Arabidopsis seedlings were placed in individual wells with 1 ml of liquid 1/2MS medium in 12-well plates (Gómez-Gómez et al., 1999). The plates were sealed with Parafilm to minimize evaporation. Seeds were stratified for 3 days then allowed to grow in a 12 h light cycle at 20°C. After 8 days the medium was replaced with fresh liquid 1/2MS and the seedlings were grown for 2 more days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from seedlings as described by Ferrari et al. (2007). Briefly, the protocol for treating plants was similar to that used in growth inhibition studies with the difference that 12 seeds were placed in each well for germination. For each biological replicate, plants were harvested from 3 wells, rinsed in MQ and blotted dry before freezing in liquid nitrogen. The plant material was crushed by using metal beads in a shaker. The RNA was extracted using the GeneJET Plant RNA Purification mini kit (ThermoScientific) following the manufacturer’s protocol. Sample quality was assessed by gel electrophoresis and measured using a NanoDrop (ThermoScientific). 2 µg of total RNA was treated with DNAseI, Rnase-free (ThermoScientific) and used for cDNA synthesis using Maxima Reverse Transcriptase and Ribolock Rnase Inhibitor (ThermoScientific) following the manufacturer’s protocol. Primers used for cDNA synthesis were random hexamers and oligo dT primers.
The library was constructed using the standard protocols for the ABI SOLiD system. Two pools containing all samples were made and run on seperate lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
The SOLiD™ Software platform was used for basecalling, read trimming and quality control.
Mapping to the Arabidopsis genome TAIR9 was performed using SHRiMP v. 2.2.3 using the parameters -N 8 -m 20 -i -25 -g -40 -e -10 -E
Read counts were summarized and analyzed using HT-Seq version 0.6.0 and subsequent relative gene expression between treatments was calculated using DESeq 2 version 1.10
Genome_build: tair9
Supplementary_files_format_and_content: read count tab delimited csv tables contains read counts for each sample
|
| |
|
| Submission date |
Jun 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Broberg |
| E-mail(s) |
martin.broberg@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Department |
Biosciences
|
| Street address |
Viikinkaari 5D
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL16033 |
| Series (1) |
| GSE69538 |
Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock |
|
| Relations |
| BioSample |
SAMN03760845 |
| SRA |
SRX1047872 |
