run_metadata: 38029

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
38029	SRR1291416	SRX546374	SRS613404	SRP042084	PRJNA248106	Gene expression profiling of zebrafish embryos at 5 dpf	GSE57792	Transcriptome Analysis	We use the zebrafish embryo model to study the innate immune response against Mycobacterium marinum. Therefore we injected M. marinum into the yolk at the 64 cell stage and took samples at 5 days post injection. Overall design: This deep sequence study was designed to determine the gene expression profile by Mycobacterium marinum infection. RNA was isolated from embryos at 5 days post injection. Wildtypes zebrafish embryos were micro injected into the yolk 64 cell stage with 40 CFU of Mycobacterium marinum E11 mCherry bacteria suspended in PVP Polyvinylpyrrolidone or Non injected as a control. post injections embryos were transferred into fresh egg water and incubated at 28°C. At 5 days post injection 50 embryos per group were snap frozen in liquid nitrogen and total RNA was isolated using TRIZOL reagent.		pubmed:25503064		Non injected 5 DPI [IL 13 08 Anita 7 TAGCTT]	GSM1388560		tissue:embryo 5 dpf	Non injected 5 DPI [IL 13 08 Anita 7 TAGCTT]	GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel Supplementary files format and content: txt file containing read counts per gene	embryo 5 dpf	Zebrafish embryos were micro injected into the yolk 64 cell stage with M. marinum E11 mCherry bacteria suspended in PVP Polyvinylpyrrolidone or Non injected as a control. At 5 days post injection 50 embryos per treatment group were snap frozen in liquid nitrogen and total RNA was isolated using TRIZOL reagent.	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	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.	infection:control	GSM1388560	GSM1388560: Non injected 5 DPI [IL 13 08 Anita 7 TAGCTT]; Danio rerio; RNA Seq	GSM1388560		1	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	GEO Accession:GSM1388560	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP042084			IL-13-08_Anita_7_TAGCTT.fastq.gz	fastq	656797941.0	12878391.0	GSM1388560 r1	0:51	A:175051093;C:155466136;G:151481640;T:174025377;N:773695	51				175051093	155466136	151481640	174025377	773695	SRX546374	SRS613404	SRA165459	GEO	Molecular Cell Biology, Institute Biology Leiden, Leiden University	1	0.92338		0.10722		0.67014		0.47805		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Netherlands	2014-05-19	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures