{"database": "metadata", "table": "run_metadata", "rows": [[8123, "ERR2724010", "ERX2737779", "ERS2635230", "ERP110227", "PRJEB28062", "Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish", "E-MTAB-7117", "Transcriptome Analysis", "Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tgcd4 1:mCherry  Tglck:EGFP  Tgmhc2dab:GFP  cd45:dsRed  AB.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 08 03", null, "Protocols: Kidneys  guts  spleens  gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney  gut  gills  spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys  guts  spleens  gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney  gut  gills  spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation  we used the Illumina Nextera XT DNA kit  incubating the mixture for 5 min at 55 \u00b0C. post stripping the transposase enzyme  adaptor ligation was carried out using the Nextera PCR master mix and index primers  cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check  the libraries were pooled and diluted to the concentration required for sequencing.", "CD4 thymus G5", "SAMEA4815332", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:28Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815332|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:28Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 thymus G5|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:thymus|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 thymus G5|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish", "E MTAB 7117:CD4 thymus G5 p", "CD4 thymus G5 p", "Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish", "Kidneys  guts  spleens  gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney  gut  gills  spleen and thymus from non transgenic zebrafish line were used for gating. Kidneys  guts  spleens  gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. For Smart seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney  gut  gills  spleen and thymus from non transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation  we used the Illumina Nextera XT DNA kit  incubating the mixture for 5\u2009min at 55\u2009\u00b0C. post stripping the transposase enzyme  adaptor ligation was carried out using the Nextera PCR master mix and index primers  cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check  the libraries were pooled and diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tgcd4 1:mCherry|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:CD4 thymus G5", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110227", "Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16", "SLX-12119.i721_i510.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i721_i510.HKCTNBBXX.s_1.r_2.fq.gz", "fastq fastq", 346846800.0, 1156156.0, "E MTAB 7117:SLX 12119.i721 i510.HKCTNBBXX.s 1.r ", "0:150 1:150", "A:95363866;C:78024771;G:75165091;T:98285320;N:7752", 150, 150, null, null, 95363866, 78024771, 75165091, 98285320, 7752, "ERX2737779", "ERS2635230", "ERA1555808", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 2, 0.93335, 0.93318, 0.60406, 0.61164, 0.99001, 0.99078, 0.49673, 0.49258, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2018-08-03", "Adult", "Adult", "Multi-tissue", "Multi-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": ["8123"], "units": {}, "query_ms": 13.514795999981288}