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Sample GSM525242 Query DataSets for GSM525242
Status Public on Aug 01, 2010
Title Embryo_Morpholino.Injected_Infected
Sample type SRA
 
Source name D.rerio_embryo_traf6_mo_S.th._8hpi
Organism Danio rerio
Characteristics agent/injection: Traf6 morpholino and Salmonella typhimurium
development stage: embryos
strain: ABxTL
Treatment protocol Embryos were injected with a translation blocking morpholino directed against traf6 (traf6 mo) at the 1 cell stage. Subsequently these embryos were injected with Salmonella typhimurium strain SL1027 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 SRX018168
BioSample SAMN00010590

Supplementary file Size Download File type/resource
GSM525242.sam.gz 364.2 Mb (ftp)(http) SAM
GSM525242.txt.gz 997.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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