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| Status |
Public on Mar 04, 2021 |
| Title |
Sl_TK24-DG2-P41_Control_production_main_B |
| Sample type |
SRA |
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| Source name |
cell culture grown in pure SGG
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| Organism |
Streptomyces lividans |
| Characteristics |
strain: TK24-DG2-P41
treatment: control; untreated
time point: late production phase (48h after inoculation)
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| Treatment protocol |
The control culture was grown in pure SGG medium. For the experiment culture, talc microparticles (hydrous magnesium silicate, 3MgO∙4SiO2∙H2O, 10 µm, Sigma-Aldrich) were resuspended in 50 mM Na-acetate buffer (pH 6.5), autoclaved at 121°C for 20 min, and added to the sterile medium prior to inoculation. Samples were taken during growth phase (12h after inoculation) early production phase (24h after inoculation), and main production phase (48h after inoculation).
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| Growth protocol |
Liquid SGG medium was used for pre- and main cultures for bottromycin production and contained per liter: 10 g soluble starch (Sigma-Aldrich), 10 g glycerol, 2.5 g corn steep powder (Sigma-Aldrich), 5 g bacto peptone (Becton & Dickinson), 2 g yeast extract (Becton & Dickinson), 1 g sodium chloride, and 21 g MOPS. The pH of the medium was adjusted to 7.2, using 6 M NaOH. One loop of spores was scratched from a five-day old plate culture and used to inoculate a liquid pre-culture, which was grown overnight in a 500 mL baffled shake flask with 50 mL medium and 30 g soda-lime glass beads (5 mm, Sigma-Aldrich). When the pre-culture reached the late exponential phase, an appropriate amount of cells was collected (8500 x g, room temperature, 5 min), resuspended in 10 mL fresh medium, and used to inoculate the main-culture (50 mL medium in 500 mL baffled shake flasks). All cultivation experiments were conducted in triplicate on a rotary shaker (28 °C, 230 rpm, 75% relative humidity, 5 cm shaking diameter, Multitron, Infors AG, Bottmingen, Switzerland).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research, Freiburg, Germany). After DNase treatment, the obtained RNA was purified (RNA Clean & Concentrator-5 kit, Zymo Research) and quantified (DropSense 16, Trinean NV, Gent, Belgium).
To construct whole transcriptome cDNA libraries, 2.5 μg of total RNA each was depleted of rRNA (Ribo-Zero rRNA Removal Kit (Bacteria), Illumina, San Diego, CA, USA). Successful rRNA removal was validated (Agilent RNA Pico 6000 kit, Agilent 2100 Bioanalyzer, Agilent Technologies). The obtained mRNA was converted into a cDNA library according to the TruSeq Stranded mRNA Sample Preparation guide (Illumina). Appropriate cDNA quality and quantity was validated (Agilent High Sensitivity DNA kit, Agilent 2100 Bioanalyzer, Agilent Technologies). Sequencing was performed on an Illumina HiSeq 1500 instrument using 70 bases read length (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls were performed using RTA v 1.18.66.3
Sequenced reads were mapped to the CP071123.1 whole genome using bowtie2 v2.3.2 with parameters -X 600
Raw read counts per gene were calculated using featureCounts v2.0.0 with parameters -O -M -t gene -g locus_tag -s 1
Read cound normalization and data analysis were performed using DESeq2
Genome_build: CP071123
Supplementary_files_format_and_content: tab-delimited text files contain normalized read counts derived via DESeq2 for each gene
Supplementary_files_format_and_content: tab-delimited matrix table with raw read counts for every gene and every sample
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| Submission date |
Mar 02, 2021 |
| Last update date |
Mar 04, 2021 |
| Contact name |
Christian Ruckert-Reed |
| E-mail(s) |
[email protected]
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| Phone |
+49 521 106 86308
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| Organization name |
Bielefeld University
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| Department |
Medical School OWL
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| Lab |
CF Omics NGS
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| Street address |
Sequenz 1
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| City |
Bielefeld |
| ZIP/Postal code |
33615 |
| Country |
Germany |
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| Platform ID |
GPL29798 |
| Series (1) |
| GSE168044 |
Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development. |
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| Relations |
| BioSample |
SAMN18106515 |
| SRA |
SRX10206190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5124325_Control_production_main_B_NormalizedCounts.txt.gz |
52.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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