{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:27156384", null, "mac con1", "GSM2069433", null, "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|\u22651 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", null, "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 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C 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", null, "strain:ABGO|fluorescence:Kaedared|lesion stg:uninjured control|tissue:brain|cell type:Macrophage", "GSM2069433", "GSM2069433: mac con1; Danio rerio; RNA Seq", "GSM2069433", null, "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 \u00b0C. The homogenized cell suspension was centrifuged at 1000x g at 4 \u00b0C 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", null, "SRP070686", null, null, "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, null, null, 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", null, "China", "2016-02-23", "Larval", "Larval", "Brain", "Nervous System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["40490"], "units": {}, "query_ms": 11.294244000964682}