run_metadata: 37115

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
37115	SRR942771	SRX327594	SRS463966	SRP028229	PRJNA213244	Autophagy regulator DRAM1 functions downstream of MYD88 in defense against tuberculosis RNA seq	GSE49186	Transcriptome Analysis	MyD88 is an adaptor protein in Toll like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88 leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88 dependent genes. Overall design: This RNAseq analysis was used to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Myd88 mutant and wild type embryos were derived by incrossing homozygous myd88 mutant parents allele hu3568 van der Vaart et al. 2013 Disease models & mechanisms 6 841 854 or their wildtype siblings. RNA was isolated from pools of 20 embryos at 4 days post infection 4 dpi. The following treatment groups were used: homozygous mutants mock injected with PBS/2%PVP 4 dpi 2 wildtype siblings mock injected with PBS/2%PVP 4dpi 3 M. marinum infected homozygous mutants 4dpi 4 M. marinum infected wildtype siblings 4dpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hpf. Subsequently embryos were infected at 28 hpf by micro injecting 200 colony forming units CFU of Mycobacterium marinum Mma20 bacteria into the caudal vein or were mock injected with buffer PBS/2%PVP as a control. post injections embryos were transferred into fresh egg water and incubated for 4 days at 28°C. post the incubation period single embryos were snap frozen in liquid nitrogen and RNA was isolated for RNAseq analysis.	parent bioproject:PRJNA213243	pubmed:24922577;pubmed:25247677		myd88+/+ uninfected	GSM1195172		source name:wild type siblings myd88+/+ not infected\|sample type:wild type zebrafish embryos mock injected with PBS at xxx hpf; RNA isolated at 4 dpi\|treatment:PBS\|genotype:wild type\|tissue:embryo	myd88+/+ uninfected	Image analysis and base calling was done by the Illumina HCS version 1.15.1; raw data from 2 sample 20 and 3 sequencing runs samples 19 21 and 22 were combined to generate the tsv files and 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 Zv9 67 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: Danio rerio.Zv9.67.dna.toplevel / Danio rerio.Zv9.67.cdna.all.fa http://www.ensembl.org/info/data/ftp/index.html Supplementary files format and content: tab delimited text files include RPKM values for each Sample	wild type siblings myd88+/+ not infected	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 dpf 4 d post infection pools of 20 embryos per treatment group were snap frozen in liquid nitrogen and total RNA was isolated using TRIZOL reagent.	Pools of 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. 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.	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.	sample type:wild type zebrafish embryos mock injected with PBS at xxx hpf; RNA isolated at 4 dpi\|treatment:PBS\|genotype:wild type\|tissue:embryo	GSM1195172	GSM1195172: myd88+/+ uninfected; Danio rerio; RNA Seq	GSM1195172		1	Pools of 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. 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.	GEO Accession:GSM1195172	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP028229			21_CCGTCC_L008_R1_001_run3.fastq.gz 21_CCGTCC_L008_R2_001_run3.fastq.gz	fastq fastq	2245421166.0	22013933.0	GSM1195172 r3	0:51 1:51	A:604635890;C:525465932;G:510494585;T:603918129;N:906630	51	51			604635890	525465932	510494585	603918129	906630	SRX327594	SRS463966	SRA096049	GEO	Animal Sciences and Health, Institute of Biology, Leiden University	2	0.92278	0.91517	0.12499	0.12518	0.6734	0.67519	0.47029	0.47475	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Netherlands	2013-07-24	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures