|
| Status |
Public on Aug 01, 2013 |
| Title |
zebrafish 5 days old larvae total RNA |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish 5 days old larvae total RNA
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 5 days post fertilisation embryos
agent: none (control)
|
| Treatment protocol |
Zebrafish embryos were either untreated or micro-injected into the yolk (2hpf) with 12 CFU (+/- 7) of Mycobacterium strain E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), At 5 days post fertilization embryos 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 zebrafish embryos untreated
|
| 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 mapped to ENSDARG genes
|
| |
|
| Submission date |
Feb 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Herman Pieter Spaink |
| E-mail(s) |
h.p.spaink@biology.leidenuniv.nl
|
| Phone |
31715275055
|
| Organization name |
Leiden University
|
| Department |
Institute of Biology
|
| Lab |
Molecular Cell Biology
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| ZIP/Postal code |
2333 CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE44351 |
Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq] |
| GSE44352 |
Gene expression profiling of zebrafish embryos at 5 days post fertilization |
|
| Relations |
| SRA |
SRX237619 |
| BioSample |
SAMN01921156 |
