|
| Status |
Public on Aug 01, 2010 |
| Title |
Embryo_Control morpholino.Injected_Not.Infected |
| Sample type |
SRA |
| |
|
| Source name |
D.rerio_embryo_traf6_mm_PBS_8hpi
|
| Organism |
Danio rerio |
| Characteristics |
agent/injection: Traf6 mismatch morpholino and PBS
development stage: embryos
strain: ABxTL
|
| Treatment protocol |
Embryos were injected with a 5bp mismatch morpholino (mm) directed against traf6 at the 1 cell stage. Subsequently these embryos were injected with PBS at 27 hours post fertilization and samples were collected at 8 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. For the duration of bacteria injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).
|
| 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 28,5-30°C in egg water (60µg/ml Instant Ocean sea salts).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAseq libraries were made from 4 µg of each sample, using the Illumina mRNA-Seq Sample Preparation Kit according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
The total RNA of three biological samples was pooled using equal amounts of RNA
|
| Data processing |
RNA-seq reads were mapped to the Ensembl 56 Zv8 'all cDNA' zebrafish transcript set using the CLC Genomics Workbench version 3.6.5 (www.clcbio.com).
Settings: maximum number of mismatches 2, no more than 5 matches for a read.
Reported values for a read are:
UGR (unique gene reads): number of reads mapping uniquely to the transcript.
TGR (total gene reads): if a read matches multiple (but no more than 5) transcripts, its count is allocated based on the UGR values of those transcripts. For example, if transcript A has an UGR of 20, and transcript B an UGR of 80, a single read mapping non-uniquely to both A and B contributes 0.2 to the TGR of transcript A, and 0.8 to the TGR of transcript B.
RPKM (reads per kilobase exon model per million mapped reads): the TGR value normalized for both reference length and total number of mapped reads (Mortazavi et al., 2008). In case of a cDNA reference, the 'kilobase exon model' simplifies to 'kilobase transcript'.
|
| |
|
| Submission date |
Mar 23, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Oliver Stockhammer |
| E-mail(s) |
o.w.stockhammer@amc.uva.nl
|
| Organization name |
AMC
|
| Department |
Medical Microbiology
|
| Street address |
Meibergdreef 15
|
| City |
Amsterdam |
| State/province |
NH |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE21024 |
Traf6 function in the innate immune response of zebrafish embryos |
|
| Relations |
| SRA |
SRX018171 |
| BioSample |
SAMN00010593 |
