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| Status |
Public on Jul 16, 2024 |
| Title |
Strain TC_KPN15_rep 1 |
| Sample type |
SRA |
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| Source name |
Enterobacteria
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| Organism |
Klebsiella pneumoniae |
| Characteristics |
cell type: Enterobacteria
genotype: pOXA-48 transconjugant
dataset batch: First dataset
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| Growth protocol |
We grew the cells in LB medium with continuous shaking. When cultures reached a turbidity of 0.5 (first dataset) or 0.2-0.3 (second dataset) at 600 nm, we collected the cells at 4ºC, pelleted them by centrifugation at 4ºC 12,000 g or 11,000 g for 1 min and immediately froze them at -70ºC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
We purified the total RNA from each sample using the NZY Total RNA Isolation kit (NZYTECH) (first dataset) or the Total RNA Mini Kit (BioRad’s Aurum) (second dataset). Then, we determined RNAs concentration using the Qubit RNA Broad-Range Assay following the manufacturer's instructions. Additionally, the quality of the RNA was examined using the Tape-Station system (Agilent).
We ribodepleted the RNA and sequenced it at the Wellcome Trust Centre for Human Genetics (WTCHG; Oxford, UK) using the Illumina's NovaSeq6000 platform, resulting in >8 million reads per sample (first dataset), or at SeqCoast Genomics (Portsmouth, NH, USA) with Illumina NextSeq2000, generating >6 million reads per sample (second dataset).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
TC_KPN15.1
KPN15_featureCounts.tsv
KPN15_DE_results_raw.tsv
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| Data processing |
We trimmed and adapter-removed the reads with Trim Galore v0.6.4 (-q 20 --length 50 --illumina). We assessed the quality of the reads before and after trimming with FastQC v.0.11.9 and MultiQC v1.11.
After annotating the reference genomes with PGAP v2021-07-01.build5508, we mapped the trimmed reads to their corresponding reference genome with BWA-MEM v0.7.17.
We inspected the mappings to confirm the appropriate presence or absence of pOXA-48 in the replicates.
We obtained the raw counts of reads mapping to each genomic feature (including CDS, ncRNA, tRNA, tmRNA, antisense RNA, RNase P and SRP RNA) with featureCounts from the Rsubread v2.14.2 package.
We performed the DE analysis from raw counts using DESeq2 v1.40.1 by comparing the pOXA-48-carrying strain against the pOXA-48-free strain (first dataset) or the pOXA-48ΔlysR-carrying strain (second dataset).
Assembly: SAMN39826502, SAMN32542096, SAMN32542113, SAMN32542116, SAMN32542119, SAMN32542124, SAMN32542126, SAMN14640123, SAMN14640085, SAMN14640188, SAMN14640320, SAMN14640201
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (<strain>_featureCounts.tsv)
Supplementary files format and content: tab-delimited text files include log2FoldChanges, padj and other values for each differential expression analysis (<strain>_DE_results_raw.tsv or <strain>_DE_results_pOXA-48-vs-pOXA-48DlysR_raw.tsv)
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| Submission date |
Jun 14, 2024 |
| Last update date |
Jul 16, 2024 |
| Contact name |
Alvaro San Millan |
| E-mail(s) |
asanmillan@cnb.csic.es
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| Organization name |
Centro Nacional de Biotecnología-CSIC
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| Department |
Biotecnología Microbiana
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| Lab |
Plasmid Biology and Evolution
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| Street address |
Darwin, 3
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| City |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
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| Platform ID |
GPL28669 |
| Series (1) |
| GSE269852 |
Plasmid-chromosome transcriptional crosstalk in multidrug resistant clinical enterobacteria |
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| Relations |
| BioSample |
SAMN39826556 |
| SRA |
SRX23531575 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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