run_metadata: 40490

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
40490	SRR3183438	SRX1597274	SRS1307300	SRP070686	PRJNA312899	Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction	GSE78194	Transcriptome Analysis	transcriptional profile of both macrophages and endothelial end cells between three different lesion stages uninjured control upon macrophage arrival and during macrophage traction. Overall design: Examination of gene expression different in 2 cell types.		pubmed:27156384		mac con1	GSM2069433		source name:mac con\|strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	mac con1	Raw data were filtered to obtain clean data using Perl scripts. Reference genome and annotations were downloaded from the ENSEMBL website http://www.ensembl.org/index.html. Reference genome library was built using the Bowtie2 v2.2.3 software and clean data was aligned to the library using the TopHat v2.0.12 software. Gene expression levels were calculated by the RPKM method using the HTSeq v0.6.0 software. Genes with P value<0.05 and \|log2 ratio\|≥1 were identified as differentially expressed genes using the DESeq v1.16.0 software. These data were then subject to GO gene ontology http://geneontology.org/ analyses and aligned to KEGG Kyoto Encyclopedia of Genes and Genomes http://www.kegg.jp/ database to build pathway maps. Genome build: zv9 Supplementary files format and content: [rpkm.txt] tab delimited text file includes RPKMs for each Sample Supplementary files format and content: [Table s1.xls] foldChange between lesion stages in each cell type	mac con		Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina		strain:ABGO\|fluorescence:Kaedared\|lesion stg:uninjured control\|tissue:brain\|cell type:Macrophage	GSM2069433	GSM2069433: mac con1; Danio rerio; RNA Seq	GSM2069433		1	Focused photoconversions of endothelial end cells or macrophages at three lesion stages uninjured control macrophage arrival and macrophage traction were achieved by irradiating Tgflk1:DenNTR; coro1a:eGFP or Tgcoro1a:Kaeda; flk1:eGFP transgenic larvae with a 405 nm laser equipped on an LSM780NLO confocal microscope for 30 seconds. About eighty cells repairing macrophages or endothelial end cells in twenty animals were photoconverted. post photoconversion zebrafish heads were dissected collected and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then the supernatant was removed and the cell pellet was resuspended in PBS followed by cell sorting by flow cytometry Moflo XDP Beckman. cDNA libraries were generated from these sorted cells using the Smart seq2 protocol. RNA sequencing was performed using the PE100 strategy HiSeq 2500 Illumina	GEO Accession:GSM2069433	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP070686			mac-con-2-26_2.fq.gz mac-con-2-26_1.fq.gz	fastq fastq	5593489486.0	27999140.0	GSM2069433 r1	0:99.89 1:99.89	A:1625139429;C:1195509047;G:1187687983;T:1585113551;N:39476	99	99			1625139429	1195509047	1187687983	1585113551	39476	SRX1597274	SRS1307300	SRA356990	GEO	SouthWest university Of China	2	0.91078	0.91073	0.29885	0.30068	0.83167	0.83244	0.62474	0.6305	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		China	2016-02-23	Larval	Larval	Brain	Nervous System