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| Status |
Public on Mar 24, 2022 |
| Title |
KlePneu, single, 3 |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organism |
Klebsiella pneumoniae |
| Characteristics |
strain id: ATCC 700603
culture: single culture
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| Growth protocol |
Cells were cultured statically for 24 hours at 37 °C in YPD medium. For mixed cultures, Aspergillus fumigatus spores were inoculated and allowed to germinate for 12 hours prior addition of Klebsiella pneumoniae.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Trizol reagent.
15μg of RNA was DNase-treated, cleaned up using the RNAeasy kit fron Qiagen and total RNA was subjected to rRNA depletion. Further library construction was done at the Next Generation Sequencing core facility (VBCF) at the Vienna BioCenter.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Data from Klebsiella pneumoniae single culture; replicate 3
Kle_AspKle_counts.xlsx
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| Data processing |
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to the concatenated genome of Aspergillus fumigatus (Af293, genome version s03-m05-r06) and Klebsiella pneumoniae (NCBI_Assembly GCF_001596075.2, sequence-region NZ_CP014696.2 1 5284734 ) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Reads mapping to rRNA loci were removed. Read counting was done using HTseq (Anders et al., 2014) in the union mode using the above mentioned annotations.
Assembly: Pairwise comparison of differential expression analysis of single cultures with co-cultures was performed using edgeR v3.8.6 (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts):
normalized (cpm; edgeR) read counts mapped to the indicated Aspergillus gene ID
normalized (cpm; edgeR) read counts mapped to the indicated Klebsiella gene ID
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| Submission date |
Mar 21, 2022 |
| Last update date |
Mar 24, 2022 |
| Contact name |
Sabrina Jenull |
| E-mail(s) |
sabrina.jenull@univie.ac.at
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| Organization name |
Max Perutz Labs
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| Lab |
Kuchler
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| Street address |
Dr. Bohrgasse 9/2
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL25164 |
| Series (1) |
| GSE199079 |
Integrated multi-omics reveals putative biomarkers of bacterial-fungal co-infections |
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| Relations |
| BioSample |
SAMN26867147 |
| SRA |
SRX14563908 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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