run_metadata: 37909

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
37909	SRR1167763	SRX469456	SRS556743	SRP037583	PRJNA237966	Macrophage Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti Bacterial Function in Zebrafish	GSE54885	Transcriptome Analysis	Macrophage expressed gene 1 MPEG1 encodes an evolutionary conserved protein with a predicted Membrane Attack Complex/Perforin domain associated with host defence against invading pathogens. In vertebrates MPEG1 is an integral membrane protein of macrophages but how it contributes to the macrophage defence mechanisms remains unknown. Zebrafish have three copies of MPEG1 two of which mpeg1 and mpeg1.2 are expressed in macrophages whereas the third could be a pseudogene. The mpeg1 and mpeg1.2 genes show differential regulation during infection of zebrafish embryos with the bacterial pathogens Mycobacterium marinum and Salmonella typhimurium. While mpeg1 is down regulated during infection with both pathogens mpeg1.2 is infection inducible. Up regulation of mpeg1.2 is partially dependent on the presence of functional Mpeg1 and requires the Toll like receptor adaptor molecule MyD88 and transcription factor NF?B. Knockdown of mpeg1 alters the immune response to M. marinum infection and results in increased bacterial burden. In S. typhimurium infection both mpeg1 and mpeg1.2 knockdown increase bacterial burdens but mpeg1 morphants show an increased survival rate. The combined results of these two in vivo infection models support the anti bacterial function of the Mpeg1 family and indicate that the intricate cross regulation of the two mpeg1 copies aids the zebrafish host in combatting infection Overall design: Embryos were injected at the one cell stage with a morpholino targeting mpeg1 or with the standard control morpholino from GeneTools or with a morpholino targeting ptpn6 Kanwal et al. 2013 J. Immunol 190:1631 45 for comparison. Subsequently at 24 hpf the morphants and their controls were manually dechorionated at 24 hpf and at 28 hpf they were infected by injecting 200 colony forming units of M. marinum Mma20 into the caudal vein or mock injected with PBS/2%PVP. post injections embryos were transferred into fresh egg water containing 0.003% 1 phenyl 2 thiourea Sigma Aldrich to prevent melanisation and incubated for 4 days at 28°C. post the incubation period infected and uninfected morphants mutants and their controls were imaged and groups of 30 embryos were snap frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.		pubmed:25247677		ptpn6 morphant infected rep4	GSM1326129		tissue:zebrafish embryo injected with ptpn6 morpholino M. marinum infected 4 dpi\|morpholino injection at 1 cell stage:ptpn6 morpholino 0.06 mM\|blood island injection at 28 hpf:M. marinum Mma20 strain 200 cfu\|developmental stage rna isolation:4 dpi	ptpn6 morphant infected rep4	Image analysis and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 and 23 was performed while the raw data from 2 sequencing runs sample 25 and 3 sequencing runs samples 2 11 16 24 and 26 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 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	zebrafish embryo injected with ptpn6 morpholino M. marinum infected 4 dpi	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 days post infection pools of 30 embryos per treatment group were snap frozen in liquid nitrogen and total RNA was isolated using QIAZOL reagent.	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.	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	morpholino injection at 1 cell stage:ptpn6 morpholino 0.06 mM\|blood island injection at 28 hpf:M. marinum Mma20 strain 200 cfu\|developmental stage rna isolation:4 dpi	GSM1326129	GSM1326129: ptpn6 morphant infected rep4; Danio rerio; RNA Seq	GSM1326129		1	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.	GEO Accession:GSM1326129	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP037583			IL-12-05_26_ACTTGA_L005_R2_001.fastq.gz IL-12-05_26_ACTTGA_L005_R1_001.fastq.gz	fastq fastq	6319438560.0	61955280.0	GSM1326129 r1	0:51 1:51	A:1718210745;C:1460888565;G:1425603166;T:1712017305;N:2718779	51	51			1718210745	1460888565	1425603166	1712017305	2718779	SRX469456	SRS556743	SRA139243	GEO	Animal Sciences and Health, Institute of Biology, Leiden University	2	0.72599	0.74293	0.09205	0.09579	0.70074	0.7009	0.47487	0.47487	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Netherlands	2014-02-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures