|
| Status |
Public on Apr 26, 2021 |
| Title |
Leaf187_vitro_3 TN_B_041 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria isolated from Arabidopsis thaliana
|
| Organism |
Exiguobacterium sp. Leaf187 |
| Characteristics |
strain: Leaf187
host genotype: Col-0
replicate: 3
|
| Treatment protocol |
Commensal strains were grown in the liquid 50% TSB medium. For each strain, multiple cultures were prepared with different bacterial density to ensure that unsaturated cultures are used for experiments. Bacterial cells were harvested by centrifugation, washed twice with sterile water, and resuspended in sterile water to OD600 of 0.5 (∼2.5 × 108 cfu/mL). For bacterial RNA-seq, 80–100 A. thaliana leaves (four fully expanded leaves per plant) were syringe-inoculated with bacterial suspensions using a needleless syringe. For plant RNA-seq, approximately six leaves (two fully expanded leaves per plant) were treated. Mock control (water infiltration) was included in every experiment. Leaves were harvested at 6 hours after inoculation. Sampling was conducted for each plant genotype at a time, and it took approximately 5 min per genotype. Leaves were immediately frozen in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from bacterial cells using FastRNA PRO™ BLUE KIT (MP Biomedicals). For plant RNA-seq, RNA was extracted with FastRNA PRO™ KIT with Lysing Matrix E (MP Biomedicals) and DNA was digested with TURBO DNase (Ambion). RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, USA). 500 ng total RNA has initially been used for polyA enrichment with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For bacterial RNA-seq, cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN). For plant RNA-seq, cDNA libraries were generated from polyA enriched RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Leaf187_vitro_3
Firmicutes
L187_combined.txt
|
| Data processing |
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the genome of corresponding commensal strain using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Apr 26, 2021 |
| Contact name |
Tatsuya Nobori |
| E-mail(s) |
tnobori@salk.edu
|
| Phone |
+49-(0)221-5062-302
|
| Organization name |
Max-Planck Institute for Plant Breeding Research
|
| Street address |
Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28526 |
| Series (1) |
| GSE150422 |
Dissecting the co-transcriptome landscape of plants and microbiota |
|
| Relations |
| BioSample |
SAMN14906292 |
| SRA |
SRX8332986 |
