|
| Status |
Public on Aug 19, 2024 |
| Title |
4-hydroxybenzoate, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Xanthomonas citri subsp. citri 306 |
| Characteristics |
cell type: bacterial cells
genotype: WT
treatment: 4-hydroxybenzoate
|
| Growth protocol |
Cells were grown at 30 ºC, 200 rpm in 40 mL XVM2m minimal medium supplemented with six lignin-related aromatic compounds (coniferyl alcohol, 4-hydroxybenzoate, 4-hydroxybenzaldehyde, vanillin, syringaldehyde, and benzaldehyde), three complex mixtures of lignin-derived compounds (LM lignin, Light Bio-oil, and aldehydes mix), or glucose (as a reference). Samples were collected at the mid-exponential phase (OD600 = 0.05-0.1) from four biological replicates. The cells were pelleted, resuspended in 1.2 mL TRIzol™, and stored at -80 ºC until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol™/chloroform method. Samples were treated with RNase-free DNaseI (Invitrogen) and RNaseOUT (Invitrogen) for 30 min, at 37 °C, and purified with the RNeasy Mini Kit (Qiagen), following manufacturer’s recommendations. RNA samples integrity was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies). The rRNA was depleted with Ribo-Zero Plus rRNA Depletion Kit (Illumina Inc.).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina Inc.), following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
4HBA_1
|
| Data processing |
The raw reads generated in the RNA-seq were filtered to remove adapters or low-quality sequences using the fastp tool, and contaminant rRNA reads were removed using sortmeRNA.
High-quality reads were mapped in the X. citri 306 genome (GI: 21240769) using the Bowtie2 tool
Samtools program was used to process the alignment files viewed using the Integrative Genome viewer program
The mapped reads in the X. citri 306 transcripts were counted using the featureCounts tool
The data processed were summarized and plotted by multiQC package
Assembly: GI: 21240769
Supplementary files format and content: TPM_counts.xlsx (tab-delimited TPM counts)
Supplementary files format and content: Raw_counts.xlsx (tab-delimited raw counts)
Supplementary files format and content: DE.table_edgeR.xlsx (tab-delimited differentially expressed genes)
|
| |
|
| Submission date |
Jan 05, 2024 |
| Last update date |
Aug 19, 2024 |
| Contact name |
Joaquim Martins Junior |
| E-mail(s) |
martins.jr.bio@gmail.com
|
| 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 |
GPL34065 |
| Series (1) |
| GSE252662 |
Metabolic pathways for lignin-related aromatic compounds elucidated in a Xanthomonas phytopathogen |
|
| Relations |
| BioSample |
SAMN39275602 |
| SRA |
SRX23114760 |
