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Sample GSM8004950

Query DataSets for GSM8004950

Status

Public on Aug 19, 2024

Title

glucose, reference condition, biol rep 4

Sample type

SRA

Source name

bacterial cells

Organism

Xanthomonas citri subsp. citri 306

Characteristics

cell type: bacterial cells
genotype: WT
treatment: glucose, reference condition

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

Gluc_4

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