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| Status |
Public on Jul 17, 2024 |
| Title |
arcZ_mutant-pJV300-2 |
| Sample type |
SRA |
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| Source name |
Bacterial cells
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| Organism |
Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 |
| Characteristics |
cell type: Bacterial cells
genotype: arcZ_mutant-pJV300
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| Growth protocol |
K. pneumoniae strains were grown in LB media containing IPTG (final concentration 1 mM) as sRNA expression inducer with 220 rpm at 37 °C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells at OD600 3 were harvested by addition of 0.2 volumes of stop mix (95% ethanol, 5% (v/v) phenol) and snap-frozen in liquid nitrogen.
Total RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER® enzyme digestion, amplification, and purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Clean reads were generated from raw sequencing reads by removing adaptor sequences (5' Adapter: 5'-AATGATACGGCGACCACCGAGATCTACAC(i5Index)ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; 3' Adapter: 5'-CAAGCAGAAGACGGCATACGAGAT(i7Index reversed)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3') and low-quality sequences using cutadapt (Version 2.10) and FASTXToolkit (Version 0.0.14), and reads less than 25 nt were discarded.
Reads were aligned to the reference genome K. pneumoniae ATCC 43816 (GenBank: NZ_CP009208.1) by BWA (Version: 0.7.17-r1198-dirty) with the default setting. Reads only unambiguously aligned to unique position were preserved to calculate reads number, CPM (counts per million) and RPKM (reads per kilobase and per million) for each gene.
Differential expression between the conditions was tested using DESeq2 in R packages. For each gene, significance p-value and FDR were obtained based on the model of negative binomial generalized linear model. Fold changes of gene expression were also estimated within the DESeq2 statistical package.
Assembly: NZ_CP009208.1
Supplementary files format and content: Tab-delimited text include counts of mapped reads
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| Submission date |
Mar 03, 2024 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Kejing Wu |
| E-mail(s) |
[email protected]
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| Organization name |
Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL33764 |
| Series (1) |
| GSE260738 |
RNA interactome profiling in hypervirulent Klebsiella pneumoniae reveals small RNA ArcZ as an inhibitor of mucoviscosity and virulence |
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| Relations |
| BioSample |
SAMN40239618 |
| SRA |
SRX23818568 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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