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Sample GSM8004961 Query DataSets for GSM8004961
Status Public on Aug 19, 2024
Title syringaldehyde, biol rep 3
Sample type SRA
 
Source name bacterial cells
Organism Xanthomonas citri subsp. citri 306
Characteristics cell type: bacterial cells
genotype: WT
treatment: syringaldehyde
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 SYALD_3
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) [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 GPL34065
Series (1)
GSE252662 Metabolic pathways for lignin-related aromatic compounds elucidated in a Xanthomonas phytopathogen
Relations
BioSample SAMN39275570
SRA SRX23114793

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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