|
| Status |
Public on Nov 03, 2021 |
| Title |
At-Mp_3_4426.U |
| Sample type |
SRA |
| |
|
| Source name |
roots,mycelium
|
| Organisms |
Arabidopsis thaliana; Macrophomina phaseolina |
| Characteristics |
developmental stage: 28 days post seed inoculation
strain: Col-0,MPI-SDFR-AT-0080
culture medium: 100µM Pi MS-Agar
inoculation: Mycelium-inoculated seeds
|
| Treatment protocol |
Prior to growth, plant seeds were inoculated with fungal mycelium or mock solution. For the control conditions, fungal inoculum were grown on the same agar-based culture medium.
|
| Growth protocol |
Seven A. thaliana seeds (or 16 drops of 10µL crushed mycelium solution) were grown in a sterile plate gnotobiotic system filled with an agar medium (described in Gruber et al. 201 - 100µM inorganic Phosphate). Culture was carried out in growth cabinets for 28 days at 21 °C for 10 hours with light (intensity 4), and at 19 °C and 14 hours in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from plant roots or mycelium grown on medium using Qiagen RNEasy Plant Mini Kit
An RNAseq library was prepared with the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and then sequenced in single read mode on a HiSeq 3000 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Pair of genomes mapped: Mp+At
Mp_fungalTranscriptome.csv
Mp_plantTranscriptome.csv
|
| Data processing |
Raw-RNASeq reads were trimmed with Trimmomatic and parameters TRAILING:20 AVGQUAL:20 HEADCROP:10 MINLEN:100
Trimmed reads were mapped onto pairs of reference genomes using HiSat2
Per-gene read counts were retrieved from HiSat2 alignments using FeatureCounts
RPKM values were calculated from FeatureCounts data
Differential gene expression analyses were conducted with DESeq2, independently for plant and fungal transcriptomes
Genome_build: TAIR10.1
Genome_build: https://mycocosm.jgi.doe.gov/Chame1/Chame1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Parch1/Parch1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Phapo1/Phapo1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Truan1/Truan1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Macpha1/Macpha1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Zalva1/Zalva1.home.html
Supplementary_files_format_and_content: Files '_fungalTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of fungal genes in planta vs. on medium. This file also provide RPKM values in control (mycelium grown on medium) and test (fungus in planta) conditions
Supplementary_files_format_and_content: Files '_plantTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of A. thaliana genes mock-inoculated vs. inoculated with mycelium. This file also provide RPKM values in control (mock-treated plants) and test (plant inoculated with mycelium) conditions
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Fantin Mesny |
| E-mail(s) |
mesny@mpipz.mpg.de
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Department |
Plant-Microbes interaction
|
| Lab |
Hacquard group
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL29931 |
| Series (1) |
| GSE169629 |
Genetic determinants of endophytism in the Arabidopsis root mycobiome |
|
| Relations |
| BioSample |
SAMN18491087 |
| SRA |
SRX10444271 |
