|
| Status |
Public on Jan 15, 2021 |
| Title |
M. albugensis + A. laibachii + SynCom Peeled Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Latex-peeled microbes from plant leaves, 4dpi
|
| Organisms |
Arabidopsis thaliana; Albugo laibachii; Moesziomyces sp. GD-2020a |
| Characteristics |
host plant cultivar: Col-0
biotic interaction: M. albugensis, A. thaliana, A. laibachii, bacterial SynCom
tissue: Latex-peeled microbes from plant leaves
|
| Treatment protocol |
3-weeks old seedlings were spray inoculated, each with 500µl of M. albugensis/ SynCom members (OD600 0.6) solved in MgCl2. After two days plants are challenged with the oomycete pathogen A. laibachii. Therefore zoospores were harvested from infected plants, washed and set to a spore number of 16*10^4 spores/ml. 500µl are evenly sprayed to each plant. Plants that are not infected with the pathogen were sprayed with MgCl2. All samples were incubated at 4°C over night with 100% humidity and moved to the growth chamber on the next day. 24h after moving samples were harvested.
|
| Growth protocol |
For axenic culture samples and prior to inoculation M. albugensis was grown in liquid YEPSlight medium at 22°C and 200rpm. Bacterial SynCom member were grown in KingsB media under the same conditions. A. thaliana seedlings were grown under short day conditions (22°C/18°C 8h day/16h night).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Four weeks old A. thaliana plants were fixed and liquid latex was applied to the leaf surface. The latex was dried using the cold air option of a hair dryer, carefully peeled off and immediately frozen in liquid nitrogen. Afterwards the frozen latex pieces were grinded with liquid nitrogen and the RNA was isolated by using Trizol® Reagent (Invitrogen) according to the manufacturer’s instructions.DNA contaminations were removed by using Turbo DNA-Free™ Kit (Ambion).
RNA libraries were prepared by the CCG (Cologne genome center) using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing read quality control was performed using FastQC version 0.11.5
Sequenced reads were mapped to the genome of M. albugensis using tophat v2.0.10
Read counts per gene were extracted by using HTSeq version 0.9.0
Genome_build: Moesziomyces albugensis WT v.2 (currently in submission).
Supplementary_files_format_and_content: tab delimited .txt file with raw read counts for each predicted M. albugensis transcript, samples in columns
|
| |
|
| Submission date |
Apr 14, 2020 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Gunther Doehlemann |
| E-mail(s) |
g.doehlemann@uni-koeln.de
|
| Organization name |
University of Cologne
|
| Department |
CEPLAS / Institute of Botany
|
| Lab |
Terrestrial Microbiology
|
| Street address |
Zülpicher Straße 47a
|
| City |
Cologne |
| ZIP/Postal code |
50674 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28398 |
| Series (1) |
| GSE148670 |
Transcriptome of Moesziomyces albugensis in response to different biotic factors (A. laibachii & SynCom) on A. thaliana leaves |
|
| Relations |
| BioSample |
SAMN14598702 |
| SRA |
SRX8117158 |
