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| Status |
Public on Apr 09, 2021 |
| Title |
Kp180-3 |
| Sample type |
SRA |
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| Source name |
Bdellovibrio predated Klebsiella pneumoniae
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| Organism |
Bdellovibrio bacteriovorus HD100 |
| Characteristics |
group: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (180 min after predation)
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| Growth protocol |
The predatory bacterium Bdellovibrio bacteriovorus was maintained using Klebsiella pneumoniae clinical isolate as the prey in HEPES buffer with CaCl2 and MgCl2 salts added (3 mM and 2 mM, respectively) , as mentioned at previous report, 'Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth'
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| Extracted molecule |
total RNA |
| Extraction protocol |
Overnight cultures of B. bacteriovorus grown on Klebsiella pneumoniae clinical isolate were filtered (0.45 µM) to remove any residual prey or bdelloplasts. These cultures were mixed with Klebsiella pneumoniae clinical isolate (~3X10^9 cells/ml). The mixed culture was collected at 7 different time points (0, 15, 30, 60, 120, 180, 210 min), and they are centrifuged with 2,000xg, 2 min, 2,000xg, 1min, seqeuntially) and the total cellular RNA extracted using ChargeSwitch Total RNA Cell Kits (Invitrogen) and thier manual
After qualification of RNA samples, library was constructed via Hiseq 2500 (Illumina). Libraries for sequencing were made using the Truseq Standard mRNA sample preparation kit (Illumina, USA). The sequencing was done using single-end 50 bp sequencing on the Illumina Hiseq 2500 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Base-calling using the CLRNASeqTM program (ChunLab, South Korea)
The RNA sequencing reads in each sample were normalized using the RPKM method
Genome_build: NCBI Reference Sequence: NC_005363.1, Bioproject name : PRJNA224116
Supplementary_files_format_and_content: The excel file which include whole information of total reads, RPKM, RLE, TMM normalization. Actual publication would be conducted with RPKM version
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| Submission date |
Apr 09, 2018 |
| Last update date |
Apr 09, 2021 |
| Contact name |
Hansol Im |
| E-mail(s) |
[email protected]
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| Organization name |
Ulsan National Institute of Science and Technology
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| Street address |
UNIST gil 50st
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| City |
Ulsan |
| ZIP/Postal code |
689798 |
| Country |
South Korea |
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| Platform ID |
GPL21963 |
| Series (1) |
| GSE112863 |
Bdellovibrio RNA seqence (Klebsiella pneumoniae) |
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| Relations |
| BioSample |
SAMN08897477 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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