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| Status |
Public on Nov 19, 2019 |
| Title |
P3_25h_A |
| Sample type |
SRA |
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| Source name |
Culture cells
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| Organism |
Pseudomonas putida |
| Characteristics |
strain: KT2440
growth condition: Bioreactor with low glucose content
genotype: Wild-type
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| Growth protocol |
Bioreactor cultivations were carried out with a minimal medium containing (per liter) 13.14 g glucose, 1.00 g NaH2PO4·2H2O, 2.6 g K2HPO4, 9 g (NH4)2SO4, and trace element solution with the same composition as that used in the shaking flask minimal medium. One hundred and fifty milliliters of preculture was used as the inoculum. Cultivations were started with an initial volume of VSTR=1.5 L at a total pressure of 1.5 bar in a 3 L bioreactor at 37 °C (Bioengineering, Wald, Switzerland) with a six-blade Rushton type impeller (constant Power input of 5 W) and constant aeration rate (1.5 L min−1).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated following cell lysis and phenol:chloroform extraction as described in SOP (doi:10.15490/fairdomhub.1.sop.285.4)
Total RNA was sent to Stabvida for sequencing (Illumina, paired-end, 150bp, 20M reads). rRNA was depleted from the samples with the RiboZero kit and sequencing libraries were constructed with the TrueSeq kit for bacteria from Illumina.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
P3_25h_A
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| Data processing |
The quality of the RNA-Seq data was confirmed using fastQC program. Contaminant adapters and low quality reads were removed with cutadapt and the remaining reads were mapped against P. putida genome (NC_002947.4, downloaded from NCBI genome database) using Bowtie2 program. More than 90% of all reads were uniquely aligned. Samtools was used to sort the mapping files by genomic position.
Detection of novel putative sRNAs was performed with the sRNA-Detect program and the genome browser Artemis. Quantification of reads was accomplished with featureCounts and normalization of the expression levels was achieved with the Reads Per Kilobase Million (RPKM) method.
Genome_build: NC_002947.4
Supplementary_files_format_and_content: tab-delimited text file include novel predicted ncRNAs and RPKM values for each condition
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| Submission date |
Apr 17, 2019 |
| Last update date |
Nov 19, 2019 |
| Contact name |
Cecilia M. Arraiano |
| E-mail(s) |
cecilia@itqb.unl.pt
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| Phone |
+351214469547
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| Organization name |
Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa
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| Street address |
Av. Republica, Apt 127
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| City |
Oeiras |
| ZIP/Postal code |
2781-901 |
| Country |
Portugal |
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| Platform ID |
GPL26512 |
| Series (1) |
| GSE129947 |
Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor |
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| Relations |
| BioSample |
SAMN11455439 |
| SRA |
SRX5704150 |
| 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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