{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Undetermined\" and technology = \"marsseq\"", "rows": [[53255, "SRR9825000", "SRX6581675", "SRS5147373", "SRP216247", "PRJNA556201", "Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq", "GSE134706", "Other", "Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human  including ligands and receptors associated with interactions between glia and neurons. In most species  microglia show a single dominant transcriptional state  while humans express significant microglia heterogeneity. In addition  we observed notable differences in complement  phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders  including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6. The raw data for human subjects will be submitted through EGA for controlled access.", "parent bioproject:PRJNA556197", "pubmed:31835035", null, "MP 15 fish 3A.M", "GSM3963911", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 15 fish 3A.M", "Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5  with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: text files include mRNA molecule count values for each Sample", "Total brain", null, "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies  washed  and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. 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Science 2014  developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP216247", null, "loader:fastq load.py|options:  appendBCtoName", "MP_15_fish_3A.M.fastq.gz", "fastq", 438550950.0, 5847346.0, "GSM3963911 r1", "0:75", "A:133219954;C:87024588;G:96110755;T:122193517;N:2136", 75, null, null, null, 133219954, 87024588, 96110755, 122193517, 2136, "SRX6581675", "SRS5147373", "SRA926015", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.85665, null, 0.14851, null, 0.83855, null, 0.48702, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [53256, "SRR9824999", "SRX6581674", "SRS5147372", "SRP216247", "PRJNA556201", "Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq", "GSE134706", "Other", "Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. 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The raw data for human subjects will be submitted through EGA for controlled access.", "parent bioproject:PRJNA556197", "pubmed:31835035", null, "MP 14 fish 2A.M", "GSM3963910", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 14 fish 2A.M", "Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5  with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: text files include mRNA molecule count values for each Sample", "Total brain", null, "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies  washed  and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. 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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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"technology\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "marsseq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&technology=marsseq", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&technology=marsseq&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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