|
| Status |
Public on Jun 04, 2020 |
| Title |
Hybrid_verbena_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Sinorhizobium meliloti |
| Characteristics |
strain: BM806
treatment: verbena root exudate
|
| Treatment protocol |
10 uM of luteolin or one of the three alfalfa root exudates normalised to the total organic carbon present was added to each of the cultures and incubated for additiona 4 hours at 30°C with shaling at 130 rpm.
|
| Growth protocol |
Overnight cultures of S. meliloti, grown in M9-succinate medium at 30°C at 130 rpm were diluted to an OD600 of 0.05 in 5 ml of M9-succinate and incubated untill an OD of 0.4 was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After incubation, cells were blocked with RNAprotect Bacteria (Qiagen) and total RNA was extracted using RNeasy Mini kits (Qiagen) from 0.5 ml of culture following the manufacturer’s instructions, including on column DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
overall_collapsed.tsv
Hybrid_raw_counts.tsv
|
| Data processing |
Basecalls and demultiplexing performed using bcl2fastq2 version 2.20
Trimming performed using StreamingTrim algorithm version 1.0 (with a quality threshold of 20)
Reads quantification with SALMON version 1.1
Normalization and analyses conducted using DESeq2 version 1.18
Genome_build: ASM696v1 (Sinorhizobium meliloti 1021); ASM34606v1 (Sinorhizobium meliloti 2011); ASM14779v3 (Sinorhizobium meliloti AK83)
Supplementary_files_format_and_content: Stats file generated by bcl2fastq2; raw count files are tab separated matrices reporting SALMON quantification
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Giovanni Bacci |
| E-mail(s) |
djbrh83@gmail.com
|
| Phone |
+393395614857
|
| Organization name |
University of Florence
|
| Department |
Department of Biology
|
| Street address |
via Madonna del Piano, 6
|
| City |
Sesto Fiorentino |
| State/province |
FI |
| ZIP/Postal code |
50019 |
| Country |
Italy |
| |
|
| Platform ID |
GPL28622 |
| Series (1) |
| GSE151705 |
Dissecting transcriptomic signatures of genotype x genotype interactions during the initiation of plant-rhizobium symbiosis |
|
| Relations |
| BioSample |
SAMN15091836 |
| SRA |
SRX8463225 |
