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Sample GSM1404382 Query DataSets for GSM1404382
Status Public on Aug 06, 2014
Title standard control_infected (rep1)
Sample type SRA
 
Source name zebrafish embryo injected with control morpholino, M. marinum infected, 4 dpi
Organism Danio rerio
Characteristics morpholino injection at 1-cell stage: control morpholino 0.2 mM
blood island injection at 28 hpf: M. marinum, Mma20 strain 200 cfu
developmental stage (rna isolation): 4 dpi
Treatment protocol Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 5 days post fertilization (4 days post infection) pools of 30 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using QIAZOL 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) containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich)
Extracted molecule total RNA
Extraction protocol Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample_2
Data processing Image analysis and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 was performed while the raw data from 3 sequencing runs (samples 2, 9 and 10) were combined to generate one fastq file and one tsv file each. The generated fastq files were used to calculate average insert sizes and standard deviations for paired end experiments.
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 (Danio_rerio.Zv9.67.dna.toplevel / Danio_rerio.Zv9.67.cdna.all.fa (http://www.ensembl.org/info/data/ftp/index.html)) 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
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jun 04, 2014
Last update date May 15, 2019
Contact name Annemarie H. Meijer
E-mail(s) a.h.meijer@biology.leidenuniv.nl
Organization name Institute of Biology, Leiden University
Department Animal Sciences and Health
Street address Einsteinweg 55
City Leiden
ZIP/Postal code 2333 CC
Country Netherlands
 
Platform ID GPL14875
Series (1)
GSE58230 Phagocytosis of mycobacteria by zebrafish macrophages is dependent on the scavenger receptor Marco, a key control factor of pro-inflammatory signalling
Relations
BioSample SAMN02839451
SRA SRX573021

Supplementary file Size Download File type/resource
GSM1404382_2.tsv.gz 399.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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