run_metadata: 8186
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8186 | ERR2723947 | ERX2737716 | ERS2635167 | 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 | 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 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm 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 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm 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 °C. 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. | Rag1 kidney F11 | SAMEA4815269 | 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 03T10:54:26Z|External Id:SAMEA4815269|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 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney F11|age:4|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 / |individual:4|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:Rag1 kidney F11|scientific name:Danio rerio|sex:female|single cell well quality:OK|strain:AB|well information:single cell | Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish | E MTAB 7117:Rag1 kidney F11 p | Rag1 kidney F11 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 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm 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 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm 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 °C. 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:Tglck:EGFP; Rag1 / |Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:Rag1 kidney F11 | 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-12114.i728_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i520.HKKG2BBXX.s_1.r_2.fq.gz | fastq fastq | 116534400.0 | 388448.0 | E MTAB 7117:SLX 12114.i728 i520.HKKG2BBXX.s 1.r | 0:150 1:150 | A:31755909;C:26396912;G:25437290;T:32942906;N:1383 | 150 | 150 | 31755909 | 26396912 | 25437290 | 32942906 | 1383 | ERX2737716 | ERS2635167 | ERA1555808 | 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|European Nucleotide Archive | 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|European Nucleotide Archive | 2 | 0.87538 | 0.88378 | 0.36008 | 0.36315 | 0.97784 | 0.97885 | 0.54811 | 0.55909 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | nextera | sc | single_cell_plate | smartseq | United Kingdom | 2018-08-03 | Adult | Adult | Multi-tissue | Multi-system |