{"database": "metadata", "table": "run_metadata", "rows": [[4239, "ERR1620516", "ERX1690881", "ERS1343569", "ERP015799", "PRJEB14175", "Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish", "E-MTAB-4617", "Transcriptome Analysis", "Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining", "ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617", null, "Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40\u03bcm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.", "LCK 9#21", "SAMEA4432120", "Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics", "ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432120|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:10|Submitter Id:E MTAB 46171473686057:LCK 9#21|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:29223|genotype:heterozygous Tglck:EGFP|gfp fluorescence:820|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#21|side scatter:46|single cell well quality:good quality|well:B9|well information:single cell", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish", "E MTAB 46171473686057:LCK 9#21 p", "LCK 9#21 p", "Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish", "Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40\u03bcm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.", "Experimental Factor: spleen:organism part|Experimental Factor: 29223:forward scatter|Experimental Factor: 46:side scatter|Experimental Factor: 820:GFP fluorescence", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</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>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP015799", "Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish", "ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16", "LCK_9_21_1.fq.gz LCK_9_21_2.fq.gz", "fastq fastq", 1486186750.0, 5944747.0, "E MTAB 46171473686057:LCK 9 21 ", "0:125 1:125", "A:463125146;C:294854645;G:259484614;T:466566596;N:2155749", 125, 125, null, null, 463125146, 294854645, 259484614, 466566596, 2155749, "ERX1690881", "ERS1343569", "ERA701304", "Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive", "Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive", 2, 0.81356, 0.81367, 0.37507, 0.37673, 0.98561, 0.98543, 0.40477, 0.56369, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Switzerland", "2016-05-26", "Adult", "Adult", "Spleen", "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": ["4239"], "units": {}, "query_ms": 7.760910986689851}