{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation = \"Multi-tissue\"", "rows": [[10186, "ERR6212423", "ERX5847531", "ERS7094943", "ERP130388", "PRJEB46176", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "E-MTAB-10379_3", "Transcriptome Analysis", "To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", null, "Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Naive", "SAMEA9361876", "University Of Edinburgh", "ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10379 3:Naive p", "Naive p", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP130388", "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", "Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz", "fastq fastq fastq", 60168324125.0, 481346593.0, "E MTAB 10379 3:Naive", "0:8 1:27 2:90", "A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241", 8, 27, 90, null, 12424400694, 9366563781, 10029312355, 11497237299, 3679241, "ERX5847531", 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"Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Lesi1d", "SAMEA9361875", "University Of Edinburgh", "ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord", "E MTAB 10379 3:Lesioned p", "Lesioned p", "scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines", "Experimental Factor: injury:spinal cord lesion", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP130388", "Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord", "ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08", "Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz", "fastq fastq fastq", 61701873000.0, 493614984.0, "E MTAB 10379 3:Lesioned", "0:8 1:27 2:90", "A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277", 8, 27, 90, null, 12952533019, 9222397450, 9920185920, 12326470894, 3761277, "ERX5847530", "ERS7094942", "ERA5186263", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 1, 0.93082, null, 0.10862, null, 0.80302, null, 0.54924, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-07-08", "Larval", "Larval", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 2, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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], 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