run_metadata: 50648

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
50648	SRR8485410	SRX5021273	SRS4054038	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation. Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010 at 4 hours post amputation hpa. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer's instructions with a read length of 50 nucleotides.		pubmed:31072958		control amputated rep1	GSM3477130		tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep1	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477130	GSM3477130: control amputated rep1; Danio rerio; RNA Seq	GSM3477130		1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477130	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP169118					485992821.0	9529271.0	GSM3477130 r11	0:51	A:134082582;C:111125846;G:108604274;T:131898648;N:281471	51				134082582	111125846	108604274	131898648	281471	SRX5021273	SRS4054038	SRA811328	GEO	Leiden University	1	0.934		0.085		0.69246		0.46718		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system