{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"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. 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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 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. 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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 13 fish 1A.M", "GSM3963909", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 13 fish 1A.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. 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In the  vascular system  endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify  to cater the different physiological demands of each organ . While LVs are known to originate from  multiple origins   lymphatic ECs LECs themselves are not known to generate other cell   types . Here  we  u s e recurrent imaging and lineage   tracing of ECs in zebrafish anal fins AF from early development  through maturity   to uncover an unexpected mechanism of specialized blood vessel formation  through transdifferentiation of LECs . Moreover  we demonstrate distinct functional implications for  deriving AF vessels from either LECs or blood ECs  uncovering a link between cell ontogeny and  functionality. We further use scRNA   seq to characterize the different cellular populations and transition  states involved in the transdifferentiation process . Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate3", "GSM5910460", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate3", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2  and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt  AB007.txt  AB008.txt: expression dataset  txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file  sheet1  pool barcode of plate1  sheet2  cell barcodes and coordinates  required for MARS seq pipeline Jaitin et al.  2014  sheet3  plate1 analyzed cell names. 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Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. 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Finally  we show that akin to its normal  development  the vasculature is re   derived from lymphatics during AF regeneration   demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs .  Overall  our work highlights a new innate mechanism of blood vess el formation through LEC  trans differentiation  and provides in vivo evidence for a link between cell ontogeny and functionality in  ECs Overall design: 80 anal fins from immature zebrafish were digested. 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