|
| Status |
Public on Sep 26, 2023 |
| Title |
Cellobiose_D2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Xanthomonas citri pv. citri |
| Characteristics |
strain: 306
carbon source: Cellobiose
biological replicate: 4
|
| Treatment protocol |
For growth curve analysis, X. citri 306 strain was cultured in LBON medium (1% m/v bacto peptone and 0.5% m/v yeast extract) containing 100 µg. mL−1 ampicillin at 30 °C and 200 rpm until mid-exponential phase. Then, the cultures were centrifuged for 5 minutes at 6000 g and the harvested cells were washed once with the modified minimal medium XVM2 (40) (XVM2m, without sucrose and fructose) supplemented with glucose, cellobiose or starch (5 mg. mL-1), and transferred to a 20 mL culture medium for an initial OD600 nm = 0.01. Growth analyses were performed at 30 °C and 200 rpm, being monitored through OD600 nm readings at times 0h, 8h, 14h, 20h, 26h, 32h, 36h, 44h and 52h in triplicate (Supplementary Figure 1).
|
| Growth protocol |
Strains and plasmids used in this study are listed in Supplementary Table 5. E. coli cells were cultured in Lysogeny broth (LB) medium or LB agar plates at 37℃. X. citri 306 strains were cultured in LBON medium (1% m/v bacto peptone and 0.5% m/v yeast extract) and on LBON agar plates at 28℃. When required, media were supplemented with antibiotics: ampicillin (100 µg/ml) or kanamycin (50 µg/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted from 15 mL X. citri 306 cultures grew at mid-exponential phase (as described above) using the TRIzol/chloroform protocol (41). Genomic DNA was removed by treatment with DnaseI (Invitrogen™) and then then the samples were treated with RNaseOUT (Invitrogen™), followed by purification with the Rneasy Mini Kit (Qiagen), according to the manufacturer’s recommendations. The absorbance analyzes were performed in a NanoDrop spectrophotometer (Thermo Scientific) and the integrity of the samples evaluated in the Agilent 2100 Bioanalyzer (Agilent Technologies). Prior to the tests, the samples were quantified on a Qubit® 2.0 Fluorometer using the RNA BR assay kit (Life Technologies).
For cDNA library preparation, only RNA samples free of genomic DNA contamination and with values of RIN (RNA Integrity Number) greater than 7 were used. 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 performed using the TruSeq Stranded mRNA kit (Illumina Inc.) according to the manufacturer’s protocol. Samples quality was accessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and libraries were quantified via qPCR using the KAPA Library Quantification Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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
Assembly: European Nucleotide Archive ASM716v1
Assembly: 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 |
Jun 08, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Joaquim Martins Junior |
| E-mail(s) |
[email protected]
|
| Phone |
+551135182420
|
| Organization name |
Brazilian Center for Research in Energy and Materials CNPEM
|
| Department |
Brazilian Biorenewables National Laboratory LNBR
|
| Street address |
Rua Giuseppe Maximo Scolfaro 10000
|
| City |
Campinas |
| State/province |
SP |
| ZIP/Postal code |
13083-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL29238 |
| Series (1) |
| GSE234477 |
Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens |
|
| Relations |
| BioSample |
SAMN35574072 |
| SRA |
SRX20581301 |
