|
| Status |
Public on Apr 01, 2013 |
| Title |
S. epi mcherry O-47 5 DPI, biol. repl. 3 |
| Sample type |
SRA |
| |
|
| Source name |
S. epi mcherry O-47 5 DPI
|
| Organism |
Danio rerio |
| Characteristics |
tissue: embryo
age: 5 days post fertilization
|
| Treatment protocol |
Zebrafish embryos were micro-injected into the yolk (2hpf) with 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. At 5 days post injection 100-200 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.
|
| Growth protocol |
Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Wildtype; injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 5 days post injection. Biological replica 3
|
| Data processing |
Base calling was done by the Illumina HCS version 1.15.1
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_63) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wouter Veneman |
| E-mail(s) |
w.j.veneman@biology.leidenuniv.nl
|
| Organization name |
Leiden University
|
| Department |
Institute Biology Leiden
|
| Lab |
Molecular Cell Biology
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE42846 |
Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (RNA-Seq) |
| GSE42847 |
Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos |
|
| Relations |
| SRA |
SRX209520 |
| BioSample |
SAMN01830790 |
