|
| Status |
Public on May 17, 2021 |
| Title |
Glucose_rep_E2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Xanthomonas citri pv. citri |
| Characteristics |
strain: 306
carbon source: Glucose
biological replicate: 6
|
| Growth protocol |
X. citri was cultivated in LB-medium without sodium chloride (LB ON) with 100 µg/mL of ampicillin, being maintained at 30 °C and 200 rpm for 16 hours. The bacterial cultures were centrifuged and washed with XVM2m medium once, and then inoculated in the XVM2m medium containing glucose or xylooligosaccharides as sole carbohydrate source with an initial optical density at 600 nm of 0.01. Bacteria were grown with constant shaking at 200 rpm and 30 °C and were harvested when reached the mid-exponential phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from X. citri cultures at mid-exponential phase using the Trizol/chloroform protocol. Genomic DNA was then removed, followed by purification of the samples with the RNeasy Mini Kit (Qiagen). Then, 2-2.5 µg of RNA was used for depletion of rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria - Epicenter Biotechnologies).
The preparation of the cDNA libraries was achieved with the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol. Libraries were sequenced on the Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Glucose_rep_E2
|
| Data processing |
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.38 and rRNA reads were filtered using SortmeRNA v. 2.0.
QC reads were mapped into the Xanthomonas citri pv. citri str. 306 genome using Bowtie2 algorithm.
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparison against the control (Glucose) condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the control condition (Glucose) were determined by applying p-ajusted ≤ 0.05 as the threshold.
Genome_build: Xanthomonas
Genome_build: European Nucleotide Archive ASM716v1
Genome_build: genome-build-accession GCA_000007165.1
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results
|
| |
|
| Submission date |
Oct 09, 2020 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Gabriela F Persinoti |
| E-mail(s) |
[email protected]
|
| Phone |
551935175165
|
| Organization name |
Brazilian Center for Research in Energy and Materials CNPEM
|
| Department |
Brazilian Biorenewables National Laboratory LNBR
|
| Street address |
Rua Giuseppe Máximo Scalfaro, 10.000
|
| City |
Campinas |
| State/province |
São Paulo |
| ZIP/Postal code |
13083-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL29238 |
| Series (1) |
| GSE159288 |
Xyloglucan processing by Xanthomonas plant pathogens and its role in the activation of virulence factors. |
|
| Relations |
| Reanalyzed by |
GSE234477 |
| BioSample |
SAMN16403203 |
| SRA |
SRX9269484 |
