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| Status |
Public on Dec 12, 2024 |
| Title |
F. nucleatum Parent Strain Rep 1 |
| Sample type |
SRA |
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| Source name |
bacterial culture
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| Organism |
Fusobacterium nucleatum subsp. nucleatum ATCC 23726 |
| Characteristics |
strain: ATCC 23726
cell type: bacterial culture
genotype: {delta}galK
treatment: gene galK deleted
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| Extracted molecule |
total RNA |
| Extraction protocol |
F. nucleatum RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacture’s protocol. Fusobacterial cell pellets from 3 ml log-phase culture (OD600 ~ 0.6) were harvested and resuspended into 200 μl of chilled 10 mM RNA-free TE (10 mM Tris-HCl, pH 8; 1 mM EDTA). Each suspension was transferred to a fast-protein tube (Q BIOgene), which contained 700 μl RLT buffer (RNeasy Mini Kit, Qiagen) and 7 μL β-mercaptoethanol (BME) (ThermoFischer Scientific. Cells were lysed by using Ribolyser (Hybaid), and supernatants were obtained by centrifugation at 13000 x g for 5 min at 4°C. RNA was then purified from the supernatant accordingly, and purified RNA was treated with DNAse (Qiagen) and cleaned by using an RNeasy clean up kit (Qiagen). Quality of RNA samples was determined RNA Integrity Number (RIN) values greater than 8 using an Agilent 2100 Bioanalyzer (Agilent Technologies).
2 µg total RNA from F.nucleatum parent and mutant strains were used. Stable RNAs were depleted with the RiboZero Kit according to manufacturer's instructions (Epicentre). Afterwards the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality with the Bioanalyzer (Agilent). Fragmentation of mRNA, reverse transcription to cDNA, adenylation of 3' ends, adapter ligation and PCR amplification were performed according to TrueSeq Stranded mRNA library instructions (Illumina). Prior to paired-end sequencing of the whole transcriptome cDNA libraries on an Illumina MiSeq, the quality and concentration of the libraries were checked using the Bioanalyzer (Agilent).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
deltagalK_Iso1_ATCACG
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| Data processing |
Base calling with Illumina CASAVA
quality trimming with trimmomatic v0.36 from both ends with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
reverse complementing of R1 reads
mapping with bowtie2 2.2.7, --ff read orientation, default parameters
converting SAM to BAM with samtools 1.2
visualization and read counting with readXplorer 2.2.3
Analysis of differentially transcribed genes with DESeq2 in default parameters
Assembly: ASM17889v1
Supplementary files format and content: Supplementary Table S1.xlsx is a Excel file containing differential expression data for each gene including log2foldchange and adjusted p-values
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| Submission date |
Nov 02, 2024 |
| Last update date |
Dec 12, 2024 |
| Contact name |
Manuel Wittchen |
| Organization name |
Bielefeld University
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| Department |
Center for Biotechnology
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| Street address |
Universitaetsstr. 27
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| City |
Bielefeld |
| ZIP/Postal code |
33615 |
| Country |
Germany |
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| Platform ID |
GPL35071 |
| Series (1) |
| GSE280934 |
Ethanolamine-induced assembly of microcompartments is required for Fusobacterium nucleatum virulence |
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| Relations |
| BioSample |
SAMN44552251 |
| SRA |
SRX26584104 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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