run_metadata: 5911
This data as json
| 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 |
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| 5911 | ERR1889852 | ERX1950350 | ERS1612616 | ERP022169 | PRJEB20058 | Single cell RNA Seq data of zebrafish blood cells | E-MTAB-5530 | Transcriptome Analysis | Transcriptome data from zebrafish single and bulk cells from blood and testes. Blood cells were collected from adult Tgcd4:mCherry Tgcd41:EGFP Tggata1a:GFP Tglyz:DsRed2 Tgmfap4:tdTomato Tgmpx:EGFP Tgrunx1:mCherry Tgtal1:EGFP and Tubingen Long Fin wild type fish. | ENA FIRST PUBLIC:2017 11 17|ENA LAST UPDATE:2017 03 20|ArrayExpress:E MTAB 5530 | Protocols: A single kidney from heterozygous transgenic or wild type fish was dissected and placed in ice cold PBS/5% fetal bovine serum. At the same time testes were dissected from the same fish. Single cell suspensions were generated by first passing through a 40 um strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 um strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 for mCherry/dsRed2 or propidium iodide PI Sigma cat no P4864 for GFP/EGFP. Individual cells were index sorted into wells of a 96 well plate using a BD Influx Index Sorter. Kidney from a non transgenic line was used as a control for gating. cDNA and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture dilution 1:10^7 according to manufacturer's instructions | WT P5 F5 | SAMEA103923448 | Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK | ENA FIRST PUBLIC:2017 11 17T17:02:11Z|ENA LAST UPDATE:2017 03 20T08:41:51Z|External Id:SAMEA103923448|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge UK Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute Cambridge CB2 1QR UK|INSDC first public:2017 11 17T17:02:11Z|INSDC last update:2017 03 20T08:41:51Z|INSDC status:public|Submitter Id:E MTAB 5530:WT P5 F5|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|forward scatter:58433|genotype:wild type genotype|organism part:kidney|reporter fluorescence:NaN|sample name:E MTAB 5530:WT P5 F5|scientific name:Danio rerio|side scatter:120|single cell well quality:OK|strain:Tubingen Long Fin|well information:1 cell | Illumina HiSeq 4000 paired end sequencing; Single cell RNA Seq data of zebrafish blood cells | E MTAB 5530:WT P5 F5 p | WT P5 F5 p | Single cell RNA Seq data of zebrafish blood cells | A single kidney from heterozygous transgenic or wild type fish was dissected and placed in ice cold PBS/5% fetal bovine serum. At the same time testes were dissected from the same fish. Single cell suspensions were generated by first passing through a 40 um strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 um strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 for mCherry/dsRed2 or propidium iodide PI Sigma cat no P4864 for GFP/EGFP. Individual cells were index sorted into wells of a 96 well plate using a BD Influx Index Sorter. Kidney from a non transgenic line was used as a control for gating. cDNA and library preparation was performed using the Smart seq2 protocol 27 28 with ERCC spike in controls added at the same time as the oligo dT and dNTP mixture dilution 1:10^7 according to manufacturer's instructions | Experimental Factor: wild type genotype:genotype|Experimental Factor: kidney:organism part|Experimental Factor: NaN:reporter fluorescence | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | <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> | ERP022169 | Illumina HiSeq 4000 paired end sequencing; Single cell RNA Seq data of zebrafish blood cells | ENA FIRST PUBLIC:2017 11 17|ENA LAST UPDATE:2018 11 16 | SLX-10882.N721_S520.C9FTNANXX.s_7.r_1.fq.gz SLX-10882.N721_S520.C9FTNANXX.s_7.r_2.fq.gz | fastq fastq | 139092250.0 | 556369.0 | E MTAB 5530:SLX 10882.N721 S520.C9FTNANXX.s 7.r | 0:125 1:125 | A:36633152;C:33585349;G:31666956;T:37205060;N:1733 | 125 | 125 | 36633152 | 33585349 | 31666956 | 37205060 | 1733 | ERX1950350 | ERS1612616 | ERA851041 | Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK|European Nucleotide Archive | Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 1QR, UK|European Nucleotide Archive | 2 | 0.90509 | 0.9025 | 0.10644 | 0.11841 | 0.95479 | 0.95603 | 0.53339 | 0.54004 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_plate | smartseq | United Kingdom | 2017-03-20 | Adult | Adult | Multi-tissue | Multi-system |