{"database": "metadata", "table": "run_metadata", "rows": [[62583, "SRR13238437", "SRX9670470", "SRS7869372", "SRP297552", "PRJNA684129", "Skeletal muscle injury responsive macrophage subsets in larval zebrafish", "GSE162979", "Transcriptome Analysis", "Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.", null, "pubmed:33568815", null, "PN3 2dpi mpeg1 mcherry R1", "GSM4969711", null, "tissue:mpeg1 expressing macrophages|development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2", "PN3 2dpi mpeg1 mcherry R1", "Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3\u2019 UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI\u2019s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.", "mpeg1 expressing macrophages", "4dpf larvae were anaesthetized in 0.01% tricaine in Ringer\u2019s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.", "Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 \u03bcl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80\u00b0C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.", "All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer\u2019s solution at 28.5\u00b0C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.", "development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2", "GSM4969711", "GSM4969711: PN3 2dpi mpeg1 mcherry R1; Danio rerio; RNA Seq", "GSM4969711", null, "1", "Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 \u03bcl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80\u00b0C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.", "GEO Accession:GSM4969711", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP297552", null, null, "PN3_L004_R1_001.fastq.gz PN3_L004_R2_001.fastq.gz", "fastq fastq", 2947338266.0, 19527523.0, "GSM4969711 r4", "0:75.46 1:75.47", "A:826921712;C:453009451;G:543071709;T:1124092188;N:243206", 75, 75, null, null, 826921712, 453009451, 543071709, 1124092188, 243206, "SRX9670470", "SRS7869372", "SRA1169931", "GEO", "The University of Melbourne", 2, 0.23443, 0.71193, 0.13859, 0.24106, 0.98202, 0.85202, 0.44751, 0.55877, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "celseq", null, "Australia", "2020-12-10", "Larval", "Larval", "Blood", "Hematopoietic 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": ["62583"], "units": {}, "query_ms": 9.748031996423379}