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Sample GSM1703560 Query DataSets for GSM1703560
Status Public on Jun 05, 2015
Title Mock 3
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
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
BioSample SAMN03760847
SRA SRX1047874

Supplementary file Size Download File type/resource 718.9 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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