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Status |
Public on Jan 25, 2024 |
Title |
cmasB, R1 |
Sample type |
SRA |
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Source name |
Bacteria
|
Organism |
Bacteroides thetaiotaomicron |
Characteristics |
strain: VPI-5482 cell type: Bacteria genotype: masB+ condition: masB control
|
Growth protocol |
Growth assays in the presence of diverse carbon sources were carried out in minimal medium (MM), supplemented with 0.5% of a suitable carbon source. Stress response assays were performed in TYG medium containing the indicated concentration of a stressor and incubated for a further 2 h. MS2 affinity purification was performed on cultures grown in TYG medium until an OD of 2.0, followed by 2 h incubation with inducer, anhydrotetracycline (aTC).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated by the hot phenol method. Traces of genomic DNA were removed by treatment with DNase I (Fermentas) and Superase-In RNase Inhibitor (Ambion) For conventional RNA-seq, libraries were prepared with the NEBNext Multiplex Small RNA Library Prep kit for Illumina according to the manufacturer’s instructions. For differential RNA-seq (dRNA-seq) and MS2 affinity purification and sequencing, libraries were prepared with the TruSeq Library Prep kit for Illumina.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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|
Description |
c201_R1_mapped_sorted.bam (column name in MS2_counts.csv)
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Data processing |
Generated reads were quality-checked using FastQC (v0.11.8) and adapters were trimmed using Cutadapt (v1.16) with Python (v3.6.6), using the following parameters: -j 6 -a Illumina Read 1 adapter=AAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -a Poly A=AAAAAAAAAAA --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --minimum-length=20 --nextseq-trim=20 3_1. For the both sequencing data types (dRNA-seq and conventional RNA-seq), READemption (v0.4.5) was used to map reads. ANNOgesic pipeline (v0.7.33) was used to annotate transcriptomic features prior to manual curation. Assembly: B. thetaiotaomicron VPI-5482 reference genome (NC_004663.1) and plasmid (NC_004703.1) Supplementary files format and content: Count tables as excel files
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Submission date |
Jun 14, 2023 |
Last update date |
Jan 25, 2024 |
Contact name |
Alexander J. Westermann |
E-mail(s) |
alexander.westermann@helmholtz-hiri.de
|
Organization name |
Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI),
|
Street address |
Josef-Schneider-Straße 2/D15
|
City |
Würzburg |
ZIP/Postal code |
97080 |
Country |
Germany |
|
|
Platform ID |
GPL28094 |
Series (1) |
GSE234958 |
An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity |
|
Relations |
BioSample |
SAMN35739680 |
SRA |
SRX20683804 |