run_metadata: 2424
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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| 2424 | ERR1125009 | ERX1204208 | ERS959219 | ERP013160 | PRJEB11748 | Analysis of single CD41 cell transcriptomes from Zebrafish | E-MTAB-3947 | Transcriptome Analysis | Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter. | ArrayExpress:E MTAB 3947 | Protocols: A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 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. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification 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. | HIGH 2 B11 | SAMEA3652070 | EMBL-EBI | ENA FIRST PUBLIC:2016 01 08T17:01:53Z|ENA LAST UPDATE:2018 03 09T09:24:38Z|External Id:SAMEA3652070|INSDC center name:EMBL EBI|INSDC first public:2016 01 08T17:01:53Z|INSDC last update:2018 03 09T09:24:38Z|INSDC status:public|Submitter Id:E MTAB 3947:HIGH 2 B11|broker name:ArrayExpress|cells:1.0|common name:zebrafish|condition:EGFP high|egfp fluorescence:2080.0|experiment:Original|fsc:30888.0|location:Kidney|plate:HIGH 2|sample name:E MTAB 3947:HIGH 2 B11|scientific name:Danio rerio|ssc:121.0|well:B11 | Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish | E MTAB 3947:HIGH 2 B11 | HIGH 2 B11 | Analysis of single CD41 cell transcriptomes from Zebrafish | A single kidney from heterozygous Tgcd41:EGFP or wild type fish was dissected and carefully passed through a strainer using the plunger of a 1 mL syringe. In the follow up experiment circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide PI staining. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers 26 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. At the same time information about cell size and granularity as well as the level of the fluorescence were recorded. Whole transcriptome amplification 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. | Experimental Factor: Kidney:location|Experimental Factor: EGFP high:condition|Experimental Factor: 2080.0:egfp fluorescence|Experimental Factor: 30888.0:fsc|Experimental Factor: 121.0:ssc | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | <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> | ERP013160 | Illumina HiSeq 2500 paired end sequencing; Analysis of single CD41 cell transcriptomes from Zebrafish | ENA FIRST PUBLIC:2016 01 08|ENA LAST UPDATE:2018 11 16 | HIGH_2_B11_1.fq.gz HIGH_2_B11_2.fq.gz | fastq fastq | 686882000.0 | 2747528.0 | E MTAB 3947:HIGH 2 B11 | 0:125 1:125 | A:193878282;C:158790264;G:145680246;T:188450276;N:82932 | 125 | 125 | 193878282 | 158790264 | 145680246 | 188450276 | 82932 | ERX1204208 | ERS959219 | ERA533479 | EMBL-EBI|European Nucleotide Archive | EMBL-EBI|European Nucleotide Archive | 2 | 0.73609 | 0.62279 | 0.39912 | 0.33433 | 0.95937 | 0.9623 | 0.53785 | 0.50022 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | unknown | sc | single_cell_plate | smartseq | United Kingdom | 2016-01-08 | Undetermined | Undetermined | Multi-tissue | Multi-system |