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
312,ERR977399,ERX1054382,ERS805483,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R3,SAMEA3498334,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498334|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:3|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:3|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 3,unspecified,1,nextera XT,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B703_nkx2_TCCTGAGC_L003_R1_001.fastq.gz NGS14-B703_nkx2_TCCTGAGC_L003_R2_001.fastq.gz,fastq fastq,14253683247.0,70913847.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 3,0:101 1:100,A:3767730088;C:2759135663;G:2772107550;T:3905748607;N:1048961339,101,100,,,3767730088,2759135663,2772107550,3905748607,1048961339,ERX1054382,ERS805483,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.74612,0.7459,0.10937,0.11122,0.81704,0.81913,0.54841,0.53764,101,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
313,ERR977398,ERX1054381,ERS805482,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R2,SAMEA3498333,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498333|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:2|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:2|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 2,unspecified,1,Truseq nano DNAsample,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R2_001.fastq.gz NGS14-B424_NKX6-1_3000C_CTTGTA_L005_R1_001.fastq.gz,fastq fastq,17434323262.0,86308531.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 2,0:101 1:101,A:5014046305;C:3245710338;G:3382410145;T:5701198546;N:90957928,101,101,,,5014046305,3245710338,3382410145,5701198546,90957928,ERX1054381,ERS805482,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.87938,0.83068,0.30659,0.31351,0.80162,0.8438,0.50285,0.47987,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
314,ERR977397,ERX1054380,ERS805481,ERP011343,PRJEB10137,RNAseq from mature ductal cells from nkx6.1:GFP zebrafish lines,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-09:45:38:475-48",Other,Background: In contrast to mammals  the zebrafish has the remarkable capacity to regenerate very efficiently its pancreatic beta cells. Understanding the mechanisms of regeneration in zebrafish and the differences with mammals will be fundamental to discovering molecules able to stimulate the regeneration process in mammals. To identify the pancreatic cells able to give rise to new beta cells in zebrafish  we generated new transgenic lines allowing the tracing of multipotent pancreatic progenitors and endocrine precursors. Results: Using novel bacterial artificial chromosome transgenic nkx6.1 and ascl1b reporter lines  we established that nkx6.1 positive cells give rise to all the pancreatic cell types and ascl1b positive cells give rise to all the endocrine cell types in the zebrafish embryo. These two genes are initially co expressed in the pancreatic primordium and their domains segregate  not as a result of mutual repression  but through the opposite effects of Notch signaling  maintaining nkx6.1 expression while repressing ascl1b in progenitors. In adult zebrafish  nkx6.1 expression persists exclusively in the ductal tree at the tip of which its expression coincides with Notch active signaling in centroacinar/terminal end duct cells. Tracing these cells reveals that they are able to differentiate into other ductal cells and into Insulin expressing cells in normal – non diabetic – animals. This capacity of ductal cells to generate endocrine cells is supported by the detection of ascl1b in the nkx6.1:GFP ductal cell transcriptome. This transcriptome also reveals  besides actors of the Notch and Wnt pathways  several novel markers such as id2a. Finally  we show that beta cell ablation in adult zebrafish triggers proliferation of ductal cells and their differentiation into Insulin  expressing cells. Conclusions: We have shown that  in the zebrafish embryo  nkx6.1+ cells are bona fide multipotent pancreatic progenitors  while ascl1b+ cells represent committed endocrine precursors. In contrast to mouse  pancreatic progenitor markers nkx6.1 and pdx1 continue to be expressed in adult ductal cells  a subset of which we show are still able to proliferate and undergo ductal and endocrine differentiation  providing the first robust evidence of the existence of pancreatic progenitor/stem cells in adult zebrafish. Our findings support the hypothesis that nkx6.1+ pancreatic progenitors contribute to beta cell regeneration. Further characterization of these cells will open up new perspectives for anti diabetic therapies.,,,,Ductal cells R1,SAMEA3498332,"GIGA-R, University of Liege",ENA first public:2015 08 17|ENA last update:2015 08 05|External Id:SAMEA3498332|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2015 08 17T17:01:08Z|INSDC last update:2015 08 05T10:19:01Z|INSDC status:public|Submitter Id:1|cell type:Pancreatic Ductal cells|collected by:Isabelle Manfroid and David Bergeman|common name:zebrafish|dev stage:Adult|isolate:Tgnkx6.1:GPF|lab host:ZDDM|sample name:1|strain:Tgnkx6.1:GPF,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 10:18:44:269 1,unspecified,1,Truseq nano DNA sample,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011343,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2015 08 17|ENA LAST UPDATE:2018 11 16,NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R1_001.fastq.gz NGS14-B423_NKX6-1_1000C_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,8147922500.0,40336250.0,ena RUN GIGA R  University of Liege 05 08 2015 10:18:44:269 1,0:101 1:101,A:2422471356;C:1435392327;G:1491979725;T:2755195660;N:42883432,101,101,,,2422471356,1435392327,1491979725,2755195660,42883432,ERX1054380,ERS805481,ERA463457,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.85302,0.79849,0.41437,0.41711,0.83871,0.87012,0.48354,0.50046,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
315,ERR1675931,ERX1745976,ERS805781,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R2 1,SAMEA3498632,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498632|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:37|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:37,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 06 10 2016 15:53:35:325 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A028_tefa_acinar_GTCCGC_L006_R1_001.fastq.gz A028_tefa_acinar_GTCCGC_L006_R2_001.fastq.gz,fastq fastq,10323596830.0,51106915.0,ena RUN GIGA R  University of Liege 06 10 2016 15:53:35:325 1,0:101 1:101,A:2531431314;C:2448656972;G:2434247998;T:2833404838;N:75855708,101,101,,,2531431314,2448656972,2434247998,2833404838,75855708,ERX1745976,ERS805781,ERA727496,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.86878,0.78451,0.03164,0.02157,0.95077,0.96161,0.52068,0.26664,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
316,ERR977594,ERX1054577,ERS805784,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R4,SAMEA3498635,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498635|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:40|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:40,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 19,Acinar R4,1,Truseq nano DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B702_Acinar4_GTGAAA_L008_R1_001.fastq.gz NGS14-B702_Acinar4_GTGAAA_L008_R2_001.fastq.gz,fastq fastq,16935208936.0,83837668.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 19,0:101 1:101,A:4069193994;C:3974803883;G:4029409265;T:4779969672;N:81832122,101,101,,,4069193994,3974803883,4029409265,4779969672,81832122,ERX1054577,ERS805784,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.93976,0.89939,0.01468,0.01416,0.93801,0.94795,0.50718,0.50041,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
317,ERR977593,ERX1054576,ERS805783,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R3,SAMEA3498634,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498634|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:39|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:39,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 18,Acinar R3,1,Truseq nano DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B701_Acinar3_ACAGTG_L008_R1_001.fastq.gz NGS14-B701_Acinar3_ACAGTG_L008_R2_001.fastq.gz,fastq fastq,15710260534.0,77773567.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 18,0:101 1:101,A:3788172647;C:3700546898;G:3749520213;T:4395516227;N:76504549,101,101,,,3788172647,3700546898,3749520213,4395516227,76504549,ERX1054576,ERS805783,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.95517,0.92587,0.0153,0.01529,0.91504,0.92553,0.49096,0.48449,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
318,ERR977592,ERX1054575,ERS805782,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R2 2,SAMEA3498633,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498633|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:38|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:38,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 17,Acinar R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Acinar_A028_GTCCGC_L003_R1_001.fastq.gz Acinar_A028_GTCCGC_L003_R2_001.fastq.gz,fastq fastq,3461595220.0,17136610.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 17,0:101 1:101,A:847745846;C:824702298;G:830498571;T:958264119;N:384386,101,101,,,847745846,824702298,830498571,958264119,384386,ERX1054575,ERS805782,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.86246,0.7781,0.03038,0.02178,0.95357,0.96327,0.56719,0.35588,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
319,ERR977591,ERX1054574,ERS805780,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R1 2,SAMEA3498631,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498631|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:36|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:36,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:490 16,Acinar R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Exocrine_GTGAAA_L005_R1_001.fastq.gz Exocrine_GTGAAA_L005_R2_001.fastq.gz,fastq fastq,9528535334.0,47170967.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:490 16,0:101 1:101,A:2522050794;C:2076658898;G:2097686086;T:2672752253;N:159387303,101,101,,,2522050794,2076658898,2097686086,2672752253,159387303,ERX1054574,ERS805780,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.48352,0.37495,0.01258,0.01002,0.94194,0.95345,0.51746,0.51938,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
320,ERR977590,ERX1054573,ERS805779,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Acinar cells from adults purified by FACS,Acinar cells R1 1,SAMEA3498630,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498630|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:35|cell type:Pancreatic Acinar cells|collected by:Isabelle Manfroid|common name:zebrafish|dev stage:Adult|isolate:Tgptf1a:GFP|lab host:ZDDM|sample name:35,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 15,Acinar R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Exocrine_30000_GTGAAA_L008_R1_001.fastq.gz Exocrine_30000_GTGAAA_L008_R2_001.fastq.gz,fastq fastq,2352127188.0,11644194.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 15,0:101 1:101,A:575791638;C:562486325;G:570096367;T:643677230;N:75628,101,101,,,575791638,562486325,570096367,643677230,75628,ERX1054573,ERS805779,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.96358,0.92791,0.02614,0.02577,0.91534,0.92786,0.51791,0.51855,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
321,ERR977589,ERX1054572,ERS805778,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Delta cells R3,SAMEA3498629,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498629|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:34|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:34,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 14,Delta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B176_SSTcells-03122013_CAGATC_L001_R1_001.fastq.gz NGS14-B176_SSTcells-03122013_CAGATC_L001_R2_001.fastq.gz,fastq fastq,17691597128.0,87582164.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 14,0:101 1:101,A:4843643109;C:3683816237;G:3736882877;T:5332210638;N:95044267,101,101,,,4843643109,3683816237,3736882877,5332210638,95044267,ERX1054572,ERS805778,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.92685,0.84146,0.10249,0.11723,0.76532,0.78309,0.39721,0.43714,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
322,ERR977588,ERX1054571,ERS805777,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R2,SAMEA3498628,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498628|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:33|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:33,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 13,Delta R2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,STS2_cDNA_A085_CAGATC_L003_R1_001.fastq.gz STS2_cDNA_A085_CAGATC_L003_R2_001.fastq.gz,fastq fastq,9070241774.0,44902187.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 13,0:101 1:101,A:2535637917;C:1854694115;G:1908489704;T:2770396981;N:1023057,101,101,,,2535637917,1854694115,1908489704,2770396981,1023057,ERX1054571,ERS805777,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.94245,0.86716,0.11229,0.13234,0.76114,0.78171,0.38511,0.43811,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
323,ERR977587,ERX1054570,ERS805776,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R1 2,SAMEA3498627,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498627|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:32|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:32,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:489 12,Delta R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,SST1_A027_CCGTCC_L004_R1_001.fastq.gz SST1_A027_CCGTCC_L004_R2_001.fastq.gz,fastq fastq,7937290636.0,39293518.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 12,0:101 1:101,A:2179525147;C:1634082904;G:1676353742;T:2446333583;N:995260,101,101,,,2179525147,1634082904,1676353742,2446333583,995260,ERX1054570,ERS805776,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.81928,0.64028,0.09426,0.0961,0.80626,0.83763,0.33992,0.39097,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
324,ERR977586,ERX1054569,ERS805775,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Delta cells from adults purified by FACS,Delta cells R1 1,SAMEA3498626,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498626|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:31|cell type:Pancreatic Delta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgsst2:GFP|lab host:ZDDM|sample name:31,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 11,Delta R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,SST_CCGTCC_L005_R1_001.fastq.gz SST_CCGTCC_L005_R2_001.fastq.gz,fastq fastq,2808424382.0,13903091.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:489 11,0:101 1:101,A:745970072;C:575317830;G:590596279;T:849527061;N:47013140,101,101,,,745970072,575317830,590596279,849527061,47013140,ERX1054569,ERS805775,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.80308,0.60403,0.09111,0.08841,0.80582,0.84035,0.34177,0.38788,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
325,ERR977585,ERX1054568,ERS805774,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R3,SAMEA3498625,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498625|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:30|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:30,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 10,Alpha R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R1_001.fastq.gz NGS14-B175_AlphaCells-12122013_CTTGTA_L002_R2_001.fastq.gz,fastq fastq,18205394430.0,90125715.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 10,0:101 1:101,A:5028541426;C:3813667922;G:3871329588;T:5386457109;N:105398385,101,101,,,5028541426,3813667922,3871329588,5386457109,105398385,ERX1054568,ERS805774,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.84473,0.83714,0.12924,0.13497,0.76581,0.77928,0.43397,0.42534,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
326,ERR977584,ERX1054567,ERS805773,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R2 2,SAMEA3498624,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498624|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:29|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:29,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 9,Alpha R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A084_Alpha2cDNA_GCCAAT_L006_R1_001.fastq.gz A084_Alpha2cDNA_GCCAAT_L006_R2_001.fastq.gz,fastq fastq,8621351314.0,42679957.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 9,0:101 1:101,A:2420008540;C:1748459249;G:1778002039;T:2610255006;N:64626480,101,101,,,2420008540,1748459249,1778002039,2610255006,64626480,ERX1054567,ERS805773,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.8123,0.7894,0.13948,0.14682,0.76609,0.78624,0.43594,0.4281,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
327,ERR977583,ERX1054566,ERS805772,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R2 1,SAMEA3498623,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498623|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:28|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:28,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 8,Alpha R2 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Alpha_2_cDNA_A084_GCCAAT_L003_R1_001.fastq.gz Alpha_2_cDNA_A084_GCCAAT_L003_R2_001.fastq.gz,fastq fastq,7447261462.0,36867631.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 8,0:101 1:101,A:2085646680;C:1521470549;G:1568678066;T:2270630726;N:835441,101,101,,,2085646680,1521470549,1568678066,2270630726,835441,ERX1054566,ERS805772,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.81689,0.79405,0.13796,0.14503,0.76583,0.78535,0.40729,0.42815,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
328,ERR977582,ERX1054565,ERS805771,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R1 2,SAMEA3498622,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498622|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:27|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:27,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:488 7,Alpha R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,A083_Alpha1cDNA_ACAGTG_L006_R1_001.fastq.gz A083_Alpha1cDNA_ACAGTG_L006_R2_001.fastq.gz,fastq fastq,8598483904.0,42566752.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:488 7,0:101 1:101,A:2424152802;C:1756999772;G:1780718036;T:2571949581;N:64663713,101,101,,,2424152802,1756999772,1780718036,2571949581,64663713,ERX1054565,ERS805771,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.80654,0.78693,0.13676,0.14263,0.76475,0.78173,0.4476,0.44884,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
329,ERR977581,ERX1054564,ERS805770,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Alpha cells from adults purified by FACS,Alpha cells R1 1,SAMEA3498621,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498621|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:26|cell type:Pancreatic Alpha cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tggcga:GFP;Tgins:NTR mCherry|lab host:ZDDM|sample name:26|strain:Tggcga:GFP; Tgins:NTR mCherry,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 6,Alpha R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,Alpha1_cDNA_A083_ACAGTG_L003_R2_001.fastq.gz Alpha1_cDNA_A083_ACAGTG_L003_R1_001.fastq.gz,fastq fastq,7584054852.0,37544826.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 6,0:101 1:101,A:2134120600;C:1561394450;G:1604139016;T:2283553056;N:847730,101,101,,,2134120600,1561394450,1604139016,2283553056,847730,ERX1054564,ERS805770,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.8102,0.79183,0.13509,0.1414,0.76459,0.77958,0.44897,0.42232,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Undetermined,Undetermined
330,ERR977580,ERX1054563,ERS805769,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R3,SAMEA3498620,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498620|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:25|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:25,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 5,Beta R3,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,NGS14-B174_Betacells-03122013_GCCAAT_L002_R1_001.fastq.gz NGS14-B174_Betacells-03122013_GCCAAT_L002_R2_001.fastq.gz,fastq fastq,17625660086.0,87255743.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 5,0:101 1:101,A:4840276660;C:3724973884;G:3755195525;T:5214977933;N:90236084,101,101,,,4840276660,3724973884,3755195525,5214977933,90236084,ERX1054563,ERS805769,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90631,0.8718,0.11791,0.11942,0.76203,0.77638,0.53654,0.49457,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
331,ERR977579,ERX1054562,ERS805768,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 2,SAMEA3498619,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498619|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:24|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:24,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 4,Beta R2 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell2_A026_ATGTCA_L004_R1_001.fastq.gz BetaCell2_A026_ATGTCA_L004_R2_001.fastq.gz,fastq fastq,8532015198.0,42237699.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 4,0:101 1:101,A:2314776471;C:1823939144;G:1839244845;T:2552984556;N:1070182,101,101,,,2314776471,1823939144,1839244845,2552984556,1070182,ERX1054562,ERS805768,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.69844,0.57999,0.09124,0.07501,0.80876,0.82964,0.56023,0.5159,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
332,ERR977578,ERX1054561,ERS805767,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R2 1,SAMEA3498618,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498618|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:23|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:23,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 3,Beta R2 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell_ATGTCA_L005_R1_001.fastq.gz BetaCell_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3250611068.0,16092134.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 3,0:101 1:101,A:854826460;C:691024995;G:695294721;T:954934438;N:54530454,101,101,,,854826460,691024995,695294721,954934438,54530454,ERX1054561,ERS805767,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.67496,0.53873,0.08771,0.06606,0.80969,0.83433,0.56231,0.51717,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
333,ERR977577,ERX1054560,ERS805766,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 2,SAMEA3498617,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498617|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:22|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:22,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:487 2,Beta R1 2,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCell1_A003_GTCCGC_L004_R1_001.fastq.gz BetaCell1_A003_GTCCGC_L004_R2_001.fastq.gz,fastq fastq,3765102038.0,18639119.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:487 2,0:101 1:101,A:1050226787;C:789381360;G:801049952;T:1123973291;N:470648,101,101,,,1050226787,789381360,801049952,1123973291,470648,ERX1054560,ERS805766,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90456,0.86125,0.12934,0.13194,0.77721,0.79109,0.56708,0.53213,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
334,ERR977576,ERX1054559,ERS805765,ERP011346,PRJEB10140,RNAseq from the pancreatic acinar  alpha  beta and delta cells from zebrafish,"ena-STUDY-GIGA-R, University of Liege-05-08-2015-10:47:24:447-55",Other,We took advantage of zebrafish transgenic tools to isolate by FACS the major pancreatic cell types and obtain pure preparations of endocrine a   ß  and d cells as well as exocrine acinar and ductal cells.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 01 31,,Beta cells from adults purified by FACS,Beta cells R1 1,SAMEA3498616,"GIGA-R, University of Liege",ENA first public:2017 01 31|ENA last update:2015 08 05|External Id:SAMEA3498616|INSDC center alias:GIGA R  University of Liege|INSDC center name:GIGA R  University of Liege|INSDC first public:2017 01 31T17:01:11Z|INSDC last update:2015 08 05T16:56:59Z|INSDC status:public|Submitter Id:21|cell type:Pancreatic Beta cells|collected by:Estefania Tarifeño Saldivia|common name:zebrafish|dev stage:Adult|isolate:Tgins:GFP|lab host:ZDDM|sample name:21,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT GIGA R  University of Liege 05 08 2015 16:56:42:486 1,Beta R1 1,1,Truseq DNA Sample prep,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP011346,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2018 11 16,BetaCells_30000_GTCCGC_L008_R1_001.fastq.gz BetaCells_30000_GTCCGC_L008_R2_001.fastq.gz,fastq fastq,10597717092.0,52463946.0,ena RUN GIGA R  University of Liege 05 08 2015 16:56:42:486 1,0:101 1:101,A:2951812422;C:2213949786;G:2252957090;T:3178649938;N:347856,101,101,,,2951812422,2213949786,2252957090,3178649938,347856,ERX1054559,ERS805765,ERA463595,"GIGA-R, University of Liege|European Nucleotide Archive","GIGA-R, University of Liege",2,0.90302,0.84857,0.12843,0.12749,0.77745,0.79157,0.56129,0.52011,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2015-08-05,Adult,Adult,Pancreas,Endocrine System
3759,ERR1294279,ERX1365625,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,vbu13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu13_GCCAAT_L008_R1_001.fastq.gz,fastq,2376143675.0,23526175.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9,0:101,A:655940769;C:534990399;G:527934646;T:655773043;N:1504818,101,,,,655940769,534990399,527934646,655773043,1504818,ERX1365625,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95443,,0.10666,,0.73176,,0.50978,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3760,ERR1294278,ERX1365624,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,vbu12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu12_GTGAAA_L008_R1_001.fastq.gz,fastq,1449181835.0,14348335.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8,0:101,A:399518584;C:327615685;G:323868050;T:397240465;N:939051,101,,,,399518584,327615685,323868050,397240465,939051,ERX1365624,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95893,,0.09315,,0.73464,,0.48744,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3761,ERR1294277,ERX1365623,ERS1067820,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVBU1/tVBU1 skin transcriptome,SAMEA3880686,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,vbu11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,vbu11_GTCCGC_L008_R1_001.fastq.gz,fastq,1455235169.0,14408269.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7,0:101,A:392100064;C:337980617;G:331091626;T:393178582;N:884280,101,,,,392100064,337980617,331091626,393178582,884280,ERX1365623,ERS1067820,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95485,,0.08016,,0.72845,,0.47549,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3762,ERR1294276,ERX1365622,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,ve13,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve13_CCGTCC_L008_R1_001.fastq.gz,fastq,1029294030.0,10191030.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6,0:101,A:284612731;C:231451012;G:228443320;T:284135536;N:651431,101,,,,284612731,231451012,228443320,284135536,651431,ERX1365622,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93287,,0.10726,,0.72585,,0.4913,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3763,ERR1294275,ERX1365621,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,ve12,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve12_ATGTCA_L008_R1_001.fastq.gz,fastq,1446322222.0,14320022.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5,0:101,A:400821160;C:324210104;G:320286425;T:400078485;N:926048,101,,,,400821160,324210104,320286425,400078485,926048,ERX1365621,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.92778,,0.09489,,0.73093,,0.48493,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3764,ERR1294274,ERX1365620,ERS1067819,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,Mau tVE1/tVE1 skin transcriptome,SAMEA3880685,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,ve11,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,ve11_AGTTCC_L008_R1_001.fastq.gz,fastq,2117238861.0,20962761.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4,0:101,A:591654664;C:469803769;G:462550117;T:591863795;N:1366516,101,,,,591654664,469803769,462550117,591863795,1366516,ERX1365620,ERS1067819,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.93146,,0.09666,,0.73501,,0.48749,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3765,ERR1294273,ERX1365619,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,wt3,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt3_AGTCAA_L008_R1_001.fastq.gz,fastq,2631687411.0,26056311.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3,0:101,A:734843629;C:584316000;G:577487406;T:733356850;N:1683526,101,,,,734843629,584316000,577487406,733356850,1683526,ERX1365619,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.95114,,0.1036,,0.72474,,0.48261,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3766,ERR1294272,ERX1365618,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,wt2,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt2_CTTGTA_L008_R1_001.fastq.gz,fastq,2093443463.0,20727163.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2,0:101,A:607582034;C:442802229;G:437957089;T:603752294;N:1349817,101,,,,607582034,442802229,437957089,603752294,1349817,ERX1365618,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94792,,0.10892,,0.73277,,0.51067,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
3767,ERR1294271,ERX1365617,ERS1067818,ERP014370,PRJEB12848,Danio rerio Mau mutants skin Transcriptome,ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265,Other,Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects  we analyze skin transcriptome of adult wild type TU fish and two mau alleles.,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25,,,WT skin transcriptome,SAMEA3880684,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin,,,,,,,,,Illumina HiSeq 2000 sequencing,ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,wt1,1,Illumina TruSeq RNA,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina HiSeq 2000,,ERP014370,Illumina HiSeq 2000 sequencing,ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16,wt1_CAGATC_L008_R1_001.fastq.gz,fastq,1701561241.0,16847141.0,ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1,0:101,A:505358711;C:348893979;G:343445186;T:502880170;N:983195,101,,,,505358711,348893979,343445186,502880170,983195,ERX1365617,ERS1067818,ERA567249,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive,MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY,1,0.94565,,0.13032,,0.73669,,0.50473,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2016-02-25,Adult,Adult,Skin,Surface Structure
8110,ERR2724023,ERX2737792,ERS2635243,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 F1,SAMEA4815345,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815345|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney F1|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 F1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 kidney F1 p,Rag1 kidney F1 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 F1,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.i716_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i520.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,37287900.0,124293.0,E MTAB 7117:SLX 12114.i716 i520.HKKG2BBXX.s 1.r ,0:150 1:150,A:9752914;C:9040023;G:8665437;T:9829107;N:419,150,150,,,9752914,9040023,8665437,9829107,419,ERX2737792,ERS2635243,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",2,0.84559,0.84961,0.25366,0.2614,0.87371,0.88172,0.59878,0.59883,150,150,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
8111,ERR2724022,ERX2737791,ERS2635242,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 E1,SAMEA4815344,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815344|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney E1|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 E1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 kidney E1 p,Rag1 kidney E1 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 E1,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.i716_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i518.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,11274000.0,37580.0,E MTAB 7117:SLX 12114.i716 i518.HKKG2BBXX.s 1.r ,0:150 1:150,A:2926114;C:2747598;G:2634051;T:2966113;N:124,150,150,,,2926114,2747598,2634051,2966113,124,ERX2737791,ERS2635242,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",2,0.8296,0.8425,0.26896,0.27904,0.92364,0.93077,0.6102,0.61311,150,150,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
8112,ERR2724021,ERX2737790,ERS2635241,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 D1,SAMEA4815343,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815343|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney D1|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 D1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 kidney D1 p,Rag1 kidney D1 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 D1,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.i716_i517.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i517.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,12474900.0,41583.0,E MTAB 7117:SLX 12114.i716 i517.HKKG2BBXX.s 1.r ,0:150 1:150,A:3257834;C:3043701;G:2896026;T:3277216;N:123,150,150,,,3257834,3043701,2896026,3277216,123,ERX2737790,ERS2635241,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",2,0.83651,0.85178,0.24924,0.26112,0.90914,0.91942,0.55363,0.56789,150,150,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
8113,ERR2724020,ERX2737789,ERS2635240,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 gut F1,SAMEA4815342,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815342|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 gut F1|age:4|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1  / |individual:4|organism part:gut|phenotype:EGFP positive cell|sample name:E MTAB 7117:Rag1 gut F1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 gut F1 p,Rag1 gut F1 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:gut|Experimental Factor: single cell identifier:Rag1 gut F1,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.i701_i508.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i508.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,12988500.0,43295.0,E MTAB 7117:SLX 12114.i701 i508.HKKG2BBXX.s 1.r ,0:150 1:150,A:3461959;C:3059299;G:2933330;T:3533768;N:144,150,150,,,3461959,3059299,2933330,3533768,144,ERX2737789,ERS2635240,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",2,0.85611,0.86366,0.20961,0.21567,0.90782,0.91557,0.60043,0.54265,150,150,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
8114,ERR2724019,ERX2737788,ERS2635239,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 gut E1,SAMEA4815341,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815341|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 gut E1|age:4|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1  / |individual:4|organism part:gut|phenotype:EGFP positive cell|sample name:E MTAB 7117:Rag1 gut E1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 gut E1 p,Rag1 gut E1 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:gut|Experimental Factor: single cell identifier:Rag1 gut E1,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.i701_i507.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i507.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,16703700.0,55679.0,E MTAB 7117:SLX 12114.i701 i507.HKKG2BBXX.s 1.r ,0:150 1:150,A:4474340;C:3934992;G:3734743;T:4559406;N:219,150,150,,,4474340,3934992,3734743,4559406,219,ERX2737788,ERS2635239,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",2,0.86009,0.86698,0.21869,0.21703,0.9009,0.90863,0.61396,0.62254,150,150,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
8115,ERR2724018,ERX2737787,ERS2635238,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 gut D1,SAMEA4815340,"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:SAMEA4815340|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:Rag1 gut D1|age:4|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1  / |individual:4|organism part:gut|phenotype:EGFP positive cell|sample name:E MTAB 7117:Rag1 gut D1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:Rag1 gut D1 p,Rag1 gut D1 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:gut|Experimental Factor: single cell identifier:Rag1 gut D1,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.i701_i506.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i506.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,20109900.0,67033.0,E MTAB 7117:SLX 12114.i701 i506.HKKG2BBXX.s 1.r ,0:150 1:150,A:5462955;C:4667929;G:4478326;T:5500442;N:248,150,150,,,5462955,4667929,4478326,5500442,248,ERX2737787,ERS2635238,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",2,0.87317,0.88395,0.22588,0.22941,0.88836,0.89635,0.59254,0.59398,150,150,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
8116,ERR2724017,ERX2737786,ERS2635237,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.,mhc2dab kidney pl2 G2,SAMEA4815339,"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:SAMEA4815339|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:mhc2dab kidney pl2 G2|age:10|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:GFP and dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl2 G2|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl2 G2 p,mhc2dab kidney pl2 G2 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl2 G2,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.i702_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i702_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,165358800.0,551196.0,E MTAB 7117:SLX 12114.i702 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:42147164;C:40764409;G:38853267;T:43591839;N:2121,150,150,,,42147164,40764409,38853267,43591839,2121,ERX2737786,ERS2635237,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",2,0.51525,0.50872,0.27056,0.26811,0.98817,0.98863,0.57694,0.57913,150,150,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
8117,ERR2724016,ERX2737785,ERS2635236,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.,mhc2dab kidney pl2 G1,SAMEA4815338,"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:SAMEA4815338|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:mhc2dab kidney pl2 G1|age:10|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:GFP and dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl2 G1|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl2 G1 p,mhc2dab kidney pl2 G1 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl2 G1,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.i701_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i701_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,148696500.0,495655.0,E MTAB 7117:SLX 12114.i701 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:37512136;C:36958044;G:35224815;T:38999534;N:1971,150,150,,,37512136,36958044,35224815,38999534,1971,ERX2737785,ERS2635236,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",2,0.43607,0.42817,0.31231,0.30716,0.98837,0.98926,0.63049,0.62338,150,150,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
8118,ERR2724015,ERX2737784,ERS2635235,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.,mhc2dab kidney pl2 E2,SAMEA4815337,"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:SAMEA4815337|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:mhc2dab kidney pl2 E2|age:10|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:GFP and dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl2 E2|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl2 E2 p,mhc2dab kidney pl2 E2 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl2 E2,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.i702_i518.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i702_i518.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,187041000.0,623470.0,E MTAB 7117:SLX 12114.i702 i518.HKKG2BBXX.s 1.r ,0:150 1:150,A:49389638;C:44123341;G:42141034;T:51384635;N:2352,150,150,,,49389638,44123341,42141034,51384635,2352,ERX2737784,ERS2635235,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",2,0.64392,0.64634,0.3608,0.36339,0.98859,0.989,0.5416,0.54533,150,150,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
8119,ERR2724014,ERX2737783,ERS2635234,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.,mhc2dab kidney pl1 H10,SAMEA4815336,"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:SAMEA4815336|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:mhc2dab kidney pl1 H10|age:10|broker name:ArrayExpress|cell type:blood cell|cluster:2|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl1 H10|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl1 H10 p,mhc2dab kidney pl1 H10 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl1 H10,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.i727_i511.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i511.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,220240200.0,734134.0,E MTAB 7117:SLX 12114.i727 i511.HKKG2BBXX.s 1.r ,0:150 1:150,A:54938529;C:55870591;G:53804950;T:55623473;N:2657,150,150,,,54938529,55870591,53804950,55623473,2657,ERX2737783,ERS2635234,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",2,0.65146,0.63182,0.21753,0.21931,0.97555,0.97676,0.64203,0.61402,150,150,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
8120,ERR2724013,ERX2737782,ERS2635233,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.,mhc2dab kidney pl1 F9,SAMEA4815335,"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:SAMEA4815335|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:mhc2dab kidney pl1 F9|age:10|broker name:ArrayExpress|cell type:blood cell|cluster:2|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl1 F9|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl1 F9 p,mhc2dab kidney pl1 F9 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl1 F9,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.i726_i508.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i508.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,177822900.0,592743.0,E MTAB 7117:SLX 12114.i726 i508.HKKG2BBXX.s 1.r ,0:150 1:150,A:45477562;C:43694070;G:42010119;T:46638998;N:2151,150,150,,,45477562,43694070,42010119,46638998,2151,ERX2737782,ERS2635233,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",2,0.61993,0.60069,0.1457,0.14507,0.96039,0.96157,0.58852,0.59377,150,150,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
8121,ERR2724012,ERX2737781,ERS2635232,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.,mhc2dab kidney pl1 E8,SAMEA4815334,"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:SAMEA4815334|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:mhc2dab kidney pl1 E8|age:10|broker name:ArrayExpress|cell type:blood cell|cluster:2|common name:zebrafish|developmental stage:adult|genotype:Tgmhc2dab:GFP  cd45:dsRed|individual:3|organism part:kidney|phenotype:dsRed positive cell|sample name:E MTAB 7117:mhc2dab kidney pl1 E8|scientific name:Danio rerio|sex:female|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:mhc2dab kidney pl1 E8 p,mhc2dab kidney pl1 E8 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:Tgmhc2dab:GFP  cd45:dsRed|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:mhc2dab kidney pl1 E8,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.i724_i507.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i507.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,53810700.0,179369.0,E MTAB 7117:SLX 12114.i724 i507.HKKG2BBXX.s 1.r ,0:150 1:150,A:13871534;C:13212554;G:12616252;T:14109780;N:580,150,150,,,13871534,13212554,12616252,14109780,580,ERX2737781,ERS2635232,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",2,0.89611,0.90099,0.08881,0.0909,0.90262,0.90611,0.52812,0.52726,150,150,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
8122,ERR2724011,ERX2737780,ERS2635231,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.,CD4 thymus H1,SAMEA4815333,"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:SAMEA4815333|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 H1|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 H1|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 thymus H1 p,CD4 thymus H1 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:Tgcd4 1:mCherry|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:CD4 thymus H1,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.i716_i511.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i716_i511.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,65942400.0,219808.0,E MTAB 7117:SLX 12119.i716 i511.HKCTNBBXX.s 1.r ,0:150 1:150,A:15633170;C:17548955;G:17103880;T:15654910;N:1485,150,150,,,15633170,17548955,17103880,15654910,1485,ERX2737780,ERS2635231,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",2,0.30317,0.2954,0.19698,0.19711,0.98599,0.98808,0.58605,0.57143,150,150,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
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,,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.,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,,,,,,,,,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 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: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,,,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 – 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",2,0.93335,0.93318,0.60406,0.61164,0.99001,0.99078,0.49673,0.49258,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2018-08-03,Adult,Adult,Multi-tissue,Multi-system
8124,ERR2724009,ERX2737778,ERS2635229,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.,CD4 thymus G4,SAMEA4815331,"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:SAMEA4815331|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 G4|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 G4|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 thymus G4 p,CD4 thymus G4 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:Tgcd4 1:mCherry|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:CD4 thymus G4,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.i720_i510.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i720_i510.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,461552100.0,1538507.0,E MTAB 7117:SLX 12119.i720 i510.HKCTNBBXX.s 1.r ,0:150 1:150,A:126164428;C:105641045;G:101502649;T:128233257;N:10721,150,150,,,126164428,105641045,101502649,128233257,10721,ERX2737778,ERS2635229,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",2,0.93958,0.93555,0.41416,0.42894,0.99194,0.99247,0.51712,0.52812,150,150,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
8125,ERR2724008,ERX2737777,ERS2635228,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.,CD4 kidney D3,SAMEA4815330,"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:SAMEA4815330|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 kidney D3|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney D3|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney D3 p,CD4 kidney D3 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney D3,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N703_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N703_S506.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,566790750.0,2267163.0,E MTAB 7117:SLX 10874.N703 S506.C9FTNANXX.s 4.r ,0:125 1:125,A:171738679;C:113474320;G:105652185;T:175917546;N:8020,125,125,,,171738679,113474320,105652185,175917546,8020,ERX2737777,ERS2635228,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",2,0.90273,0.90184,0.55846,0.5605,0.99904,0.9991,0.99722,0.82975,125,125,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
8126,ERR2724007,ERX2737776,ERS2635227,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.,CD4 kidney D2,SAMEA4815329,"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:SAMEA4815329|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 kidney D2|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney D2|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney D2 p,CD4 kidney D2 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney D2,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N702_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N702_S506.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,277111250.0,1108445.0,E MTAB 7117:SLX 10874.N702 S506.C9FTNANXX.s 4.r ,0:125 1:125,A:82435920;C:57203613;G:52019151;T:85448114;N:4452,125,125,,,82435920,57203613,52019151,85448114,4452,ERX2737776,ERS2635227,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",2,0.82299,0.82476,0.57143,0.57476,0.98415,0.98449,0.58875,0.58969,125,125,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
8127,ERR2724006,ERX2737775,ERS2635226,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.,CD4 kidney D12,SAMEA4815328,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815328|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 kidney D12|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney D12|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney D12 p,CD4 kidney D12 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney D12,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N715_S506.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N715_S506.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,120347500.0,481390.0,E MTAB 7117:SLX 10874.N715 S506.C9FTNANXX.s 4.r ,0:125 1:125,A:34833149;C:25858968;G:23765495;T:35888156;N:1732,125,125,,,34833149,25858968,23765495,35888156,1732,ERX2737775,ERS2635226,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",2,0.74258,0.74099,0.4164,0.42068,0.99086,0.99109,0.69164,0.68237,125,125,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
8128,ERR2724005,ERX2737774,ERS2635225,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.,CD4 gill C11,SAMEA4815327,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815327|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 gill C11|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:gill|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 gill C11|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 gill C11 p,CD4 gill C11 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:Tgcd4 1:mCherry|Experimental Factor: organism part:gill|Experimental Factor: single cell identifier:CD4 gill C11,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N714_S516.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N714_S516.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,165997000.0,663988.0,E MTAB 7117:SLX 10875.N714 S516.C9FTNANXX.s 5.r ,0:125 1:125,A:49371380;C:34732413;G:31052964;T:50839053;N:1190,125,125,,,49371380,34732413,31052964,50839053,1190,ERX2737774,ERS2635225,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",2,0.82287,0.82566,0.53775,0.54259,0.98798,0.9881,0.63953,0.62734,125,125,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
8129,ERR2724004,ERX2737773,ERS2635224,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.,CD4 gill B10,SAMEA4815326,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815326|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 gill B10|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:gill|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 gill B10|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 gill B10 p,CD4 gill B10 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:Tgcd4 1:mCherry|Experimental Factor: organism part:gill|Experimental Factor: single cell identifier:CD4 gill B10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N712_S515.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N712_S515.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,383976500.0,1535906.0,E MTAB 7117:SLX 10875.N712 S515.C9FTNANXX.s 5.r ,0:125 1:125,A:118831629;C:76296476;G:69785982;T:119059622;N:2791,125,125,,,118831629,76296476,69785982,119059622,2791,ERX2737773,ERS2635224,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",2,0.85658,0.85722,0.65298,0.65529,0.98973,0.98995,0.57674,0.54701,125,125,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
8130,ERR2724003,ERX2737772,ERS2635223,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.,CD4 spleen G7,SAMEA4815325,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815325|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 spleen G7|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:3|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:spleen|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 spleen G7|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 spleen G7 p,CD4 spleen G7 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:Tgcd4 1:mCherry|Experimental Factor: organism part:spleen|Experimental Factor: single cell identifier:CD4 spleen G7,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N723_S510.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N723_S510.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,177573500.0,710294.0,E MTAB 7117:SLX 10875.N723 S510.C9FTNANXX.s 5.r ,0:125 1:125,A:48445252;C:41183835;G:38570754;T:49372448;N:1211,125,125,,,48445252,41183835,38570754,49372448,1211,ERX2737772,ERS2635223,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",2,0.76107,0.76087,0.2578,0.2632,0.96331,0.96404,0.59545,0.60013,125,125,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
8131,ERR2724002,ERX2737771,ERS2635222,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.,CD4 spleen E8,SAMEA4815324,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815324|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 spleen E8|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:3|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:spleen|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 spleen E8|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 spleen E8 p,CD4 spleen E8 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:Tgcd4 1:mCherry|Experimental Factor: organism part:spleen|Experimental Factor: single cell identifier:CD4 spleen E8,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N724_S507.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N724_S507.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,257265750.0,1029063.0,E MTAB 7117:SLX 10875.N724 S507.C9FTNANXX.s 5.r ,0:125 1:125,A:72268420;C:57460553;G:53691082;T:73843922;N:1773,125,125,,,72268420,57460553,53691082,73843922,1773,ERX2737771,ERS2635222,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",2,0.78515,0.78466,0.29915,0.30955,0.97047,0.97112,0.53525,0.53581,125,125,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
8132,ERR2724001,ERX2737770,ERS2635221,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.,CD4 gill A11,SAMEA4815323,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815323|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 gill A11|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:3|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:gill|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 gill A11|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 gill A11 p,CD4 gill A11 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:Tgcd4 1:mCherry|Experimental Factor: organism part:gill|Experimental Factor: single cell identifier:CD4 gill A11,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N714_S513.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N714_S513.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,124536000.0,498144.0,E MTAB 7117:SLX 10875.N714 S513.C9FTNANXX.s 5.r ,0:125 1:125,A:33962304;C:28877389;G:27029516;T:34665844;N:947,125,125,,,33962304,28877389,27029516,34665844,947,ERX2737770,ERS2635221,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",2,0.78979,0.79005,0.2588,0.26313,0.97981,0.98044,0.57157,0.56676,125,125,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
8133,ERR2724000,ERX2737769,ERS2635220,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.,CD4 kidney F7,SAMEA4815322,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815322|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 kidney F7|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:2|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney F7|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney F7 p,CD4 kidney F7 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney F7,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N707_S508.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N707_S508.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,113655500.0,454622.0,E MTAB 7117:SLX 10874.N707 S508.C9FTNANXX.s 4.r ,0:125 1:125,A:33870000;C:23611974;G:21194053;T:34977343;N:2130,125,125,,,33870000,23611974,21194053,34977343,2130,ERX2737769,ERS2635220,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",2,0.85267,0.85506,0.25904,0.26014,0.943,0.94383,0.59233,0.60505,125,125,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
8134,ERR2723999,ERX2737768,ERS2635219,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.,CD4 kidney B12,SAMEA4815321,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815321|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 kidney B12|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:2|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney B12|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney B12 p,CD4 kidney B12 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney B12,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N715_S503.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N715_S503.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,41609000.0,166436.0,E MTAB 7117:SLX 10874.N715 S503.C9FTNANXX.s 4.r ,0:125 1:125,A:11753969;C:9216161;G:8702127;T:11935923;N:820,125,125,,,11753969,9216161,8702127,11935923,820,ERX2737768,ERS2635219,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",2,0.82459,0.82764,0.17061,0.17378,0.93854,0.93878,0.54477,0.55123,125,125,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
8135,ERR2723998,ERX2737767,ERS2635218,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.,CD4 spleen A12,SAMEA4815320,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815320|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 spleen A12|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:spleen|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 spleen A12|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 spleen A12 p,CD4 spleen A12 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:Tgcd4 1:mCherry|Experimental Factor: organism part:spleen|Experimental Factor: single cell identifier:CD4 spleen A12,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N729_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N729_S502.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,236353500.0,945414.0,E MTAB 7117:SLX 10875.N729 S502.C9FTNANXX.s 5.r ,0:125 1:125,A:64839700;C:54488967;G:51265476;T:65757276;N:2081,125,125,,,64839700,54488967,51265476,65757276,2081,ERX2737767,ERS2635218,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",2,0.69382,0.69224,0.33275,0.33643,0.9833,0.98346,0.54137,0.53281,125,125,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
8136,ERR2723997,ERX2737766,ERS2635217,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.,CD4 spleen A11,SAMEA4815319,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815319|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 spleen A11|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:spleen|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 spleen A11|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 spleen A11 p,CD4 spleen A11 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:Tgcd4 1:mCherry|Experimental Factor: organism part:spleen|Experimental Factor: single cell identifier:CD4 spleen A11,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N728_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N728_S502.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,308428500.0,1233714.0,E MTAB 7117:SLX 10875.N728 S502.C9FTNANXX.s 5.r ,0:125 1:125,A:83665727;C:71720130;G:68234442;T:84805861;N:2340,125,125,,,83665727,71720130,68234442,84805861,2340,ERX2737766,ERS2635217,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",2,0.70583,0.70452,0.29793,0.30065,0.97885,0.97906,0.62417,0.61241,125,125,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
8137,ERR2723996,ERX2737765,ERS2635216,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.,CD4 spleen A10,SAMEA4815318,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815318|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 spleen A10|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:spleen|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 spleen A10|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 spleen A10 p,CD4 spleen A10 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:Tgcd4 1:mCherry|Experimental Factor: organism part:spleen|Experimental Factor: single cell identifier:CD4 spleen A10,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10875.N727_S502.C9FTNANXX.s_5.r_1.fq.gz SLX-10875.N727_S502.C9FTNANXX.s_5.r_2.fq.gz,fastq fastq,328761500.0,1315046.0,E MTAB 7117:SLX 10875.N727 S502.C9FTNANXX.s 5.r ,0:125 1:125,A:89742953;C:76043831;G:72070914;T:90901345;N:2457,125,125,,,89742953,76043831,72070914,90901345,2457,ERX2737765,ERS2635216,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",2,0.7281,0.72679,0.30613,0.30863,0.98137,0.98184,0.61337,0.61341,125,125,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
8138,ERR2723995,ERX2737764,ERS2635215,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.,CD4 kidney H11,SAMEA4815317,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815317|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 kidney H11|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney H11|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney H11 p,CD4 kidney H11 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney H11,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N714_S511.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N714_S511.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,38522250.0,154089.0,E MTAB 7117:SLX 10874.N714 S511.C9FTNANXX.s 4.r ,0:125 1:125,A:10506506;C:8914382;G:8393250;T:10707317;N:795,125,125,,,10506506,8914382,8393250,10707317,795,ERX2737764,ERS2635215,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",2,0.67795,0.67789,0.33735,0.34027,0.98478,0.98512,0.5973,0.58484,125,125,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
8139,ERR2723994,ERX2737763,ERS2635214,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.,CD4 kidney G9,SAMEA4815316,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815316|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:CD4 kidney G9|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tgcd4 1:mCherry|individual:2|organism part:kidney|phenotype:mCherry positive cell|sample name:E MTAB 7117:CD4 kidney G9|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:CD4 kidney G9 p,CD4 kidney G9 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:Tgcd4 1:mCherry|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:CD4 kidney G9,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,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>,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-10874.N711_S510.C9FTNANXX.s_4.r_1.fq.gz SLX-10874.N711_S510.C9FTNANXX.s_4.r_2.fq.gz,fastq fastq,221927750.0,887711.0,E MTAB 7117:SLX 10874.N711 S510.C9FTNANXX.s 4.r ,0:125 1:125,A:67713095;C:44853314;G:41236151;T:68121004;N:4186,125,125,,,67713095,44853314,41236151,68121004,4186,ERX2737763,ERS2635214,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",2,0.86217,0.86277,0.36625,0.36915,0.97137,0.97155,0.61749,0.61418,125,125,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
8140,ERR2723993,ERX2737762,ERS2635213,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.,LCK thymus C1,SAMEA4815315,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815315|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK thymus C1|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:thymus|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK thymus C1|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK thymus C1 p,LCK thymus C1 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|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:LCK thymus C1,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.i701_i505.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i701_i505.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,214753500.0,715845.0,E MTAB 7117:SLX 12119.i701 i505.HKCTNBBXX.s 1.r ,0:150 1:150,A:58043697;C:49133850;G:47539293;T:60032128;N:4532,150,150,,,58043697,49133850,47539293,60032128,4532,ERX2737762,ERS2635213,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",2,0.90796,0.9075,0.47549,0.49027,0.98733,0.98784,0.44635,0.44113,150,150,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
8141,ERR2723992,ERX2737761,ERS2635212,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.,LCK thymus B8,SAMEA4815314,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815314|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK thymus B8|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:thymus|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK thymus B8|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK thymus B8 p,LCK thymus B8 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|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:LCK thymus B8,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.i710_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i710_i503.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,301541400.0,1005138.0,E MTAB 7117:SLX 12119.i710 i503.HKCTNBBXX.s 1.r ,0:150 1:150,A:80889588;C:70114577;G:68676561;T:81854043;N:6631,150,150,,,80889588,70114577,68676561,81854043,6631,ERX2737761,ERS2635212,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",2,0.90679,0.90475,0.5614,0.56522,0.99291,0.99302,0.45816,0.45886,150,150,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
8142,ERR2723991,ERX2737760,ERS2635211,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.,LCK thymus B6,SAMEA4815313,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815313|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK thymus B6|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:thymus|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK thymus B6|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK thymus B6 p,LCK thymus B6 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|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:LCK thymus B6,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.i706_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i706_i503.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,184856100.0,616187.0,E MTAB 7117:SLX 12119.i706 i503.HKCTNBBXX.s 1.r ,0:150 1:150,A:49138791;C:43366279;G:42353773;T:49993540;N:3717,150,150,,,49138791,43366279,42353773,49993540,3717,ERX2737760,ERS2635211,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",2,0.88928,0.88981,0.53378,0.54911,0.98802,0.98912,0.53874,0.51283,150,150,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
8143,ERR2723990,ERX2737759,ERS2635210,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.,LCK thymus B2,SAMEA4815312,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815312|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK thymus B2|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:thymus|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK thymus B2|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK thymus B2 p,LCK thymus B2 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|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:LCK thymus B2,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.i702_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i702_i503.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,505800.0,1686.0,E MTAB 7117:SLX 12119.i702 i503.HKCTNBBXX.s 1.r ,0:150 1:150,A:130422;C:126765;G:117769;T:130837;N:7,150,150,,,130422,126765,117769,130837,7,ERX2737759,ERS2635210,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",2,0.59969,0.58629,0.2609,0.2583,0.99354,0.99527,0.53571,0.55405,150,150,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
8144,ERR2723989,ERX2737758,ERS2635209,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.,LCK thymus B10,SAMEA4815311,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815311|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK thymus B10|age:6|broker name:ArrayExpress|cell type:blood cell|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:thymus|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK thymus B10|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK thymus B10 p,LCK thymus B10 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|Experimental Factor: organism part:thymus|Experimental Factor: single cell identifier:LCK thymus B10,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.i712_i503.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i712_i503.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,247476300.0,824921.0,E MTAB 7117:SLX 12119.i712 i503.HKCTNBBXX.s 1.r ,0:150 1:150,A:68013465;C:55551292;G:54322136;T:69583621;N:5786,150,150,,,68013465,55551292,54322136,69583621,5786,ERX2737758,ERS2635209,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",2,0.9046,0.90455,0.49135,0.50578,0.98677,0.98739,0.4365,0.39972,150,150,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
8145,ERR2723988,ERX2737757,ERS2635208,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.,LCK kidney E7,SAMEA4815310,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815310|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney E7|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney E7|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney E7 p,LCK kidney E7 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney E7,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.i723_i518.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i723_i518.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,232390500.0,774635.0,E MTAB 7117:SLX 12119.i723 i518.HKCTNBBXX.s 1.r ,0:150 1:150,A:61370741;C:54657214;G:52783802;T:63573865;N:4878,150,150,,,61370741,54657214,52783802,63573865,4878,ERX2737757,ERS2635208,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",2,0.88735,0.89152,0.31373,0.32461,0.97319,0.97465,0.52638,0.53463,150,150,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
8146,ERR2723987,ERX2737756,ERS2635207,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.,LCK kidney E10,SAMEA4815309,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815309|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney E10|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney E10|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney E10 p,LCK kidney E10 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney E10,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.i727_i518.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i727_i518.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,364697700.0,1215659.0,E MTAB 7117:SLX 12119.i727 i518.HKCTNBBXX.s 1.r ,0:150 1:150,A:95675868;C:86934996;G:84117263;T:97961987;N:7586,150,150,,,95675868,86934996,84117263,97961987,7586,ERX2737756,ERS2635207,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",2,0.88034,0.88626,0.39506,0.4105,0.98443,0.98516,0.52064,0.52752,150,150,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
8147,ERR2723986,ERX2737755,ERS2635206,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.,LCK kidney D3,SAMEA4815308,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815308|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney D3|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney D3|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney D3 p,LCK kidney D3 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney D3,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.i719_i517.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i719_i517.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,189068100.0,630227.0,E MTAB 7117:SLX 12119.i719 i517.HKCTNBBXX.s 1.r ,0:150 1:150,A:49359046;C:45298627;G:43481326;T:50925211;N:3890,150,150,,,49359046,45298627,43481326,50925211,3890,ERX2737755,ERS2635206,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",2,0.90143,0.89821,0.27981,0.29122,0.97741,0.97847,0.52388,0.52707,150,150,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
8148,ERR2723985,ERX2737754,ERS2635205,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.,LCK kidney A9,SAMEA4815307,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815307|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney A9|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney A9|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney A9 p,LCK kidney A9 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney A9,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.i726_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i726_i513.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,337984500.0,1126615.0,E MTAB 7117:SLX 12119.i726 i513.HKCTNBBXX.s 1.r ,0:150 1:150,A:92362762;C:76764558;G:73890731;T:94958687;N:7762,150,150,,,92362762,76764558,73890731,94958687,7762,ERX2737754,ERS2635205,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",2,0.92075,0.9174,0.36307,0.37491,0.98301,0.98348,0.50947,0.52782,150,150,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
8149,ERR2723984,ERX2737753,ERS2635204,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.,LCK kidney A8,SAMEA4815306,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815306|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney A8|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney A8|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney A8 p,LCK kidney A8 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney A8,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.i724_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i724_i513.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,256610100.0,855367.0,E MTAB 7117:SLX 12119.i724 i513.HKCTNBBXX.s 1.r ,0:150 1:150,A:68825150;C:59610677;G:57682582;T:70486458;N:5233,150,150,,,68825150,59610677,57682582,70486458,5233,ERX2737753,ERS2635204,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",2,0.90086,0.89794,0.35242,0.36169,0.98088,0.98147,0.48826,0.50311,150,150,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
8150,ERR2723983,ERX2737752,ERS2635203,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.,LCK kidney A7,SAMEA4815305,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:27Z|External Id:SAMEA4815305|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:27Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney A7|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney A7|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney A7 p,LCK kidney A7 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney A7,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.i723_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i723_i513.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,277473600.0,924912.0,E MTAB 7117:SLX 12119.i723 i513.HKCTNBBXX.s 1.r ,0:150 1:150,A:74081873;C:64503157;G:62299967;T:76582517;N:6086,150,150,,,74081873,64503157,62299967,76582517,6086,ERX2737752,ERS2635203,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",2,0.90225,0.90246,0.35509,0.36408,0.98027,0.98098,0.54551,0.53005,150,150,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
8151,ERR2723982,ERX2737751,ERS2635202,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.,LCK kidney A6,SAMEA4815304,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815304|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney A6|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney A6|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney A6 p,LCK kidney A6 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney A6,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.i722_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i722_i513.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,199380300.0,664601.0,E MTAB 7117:SLX 12119.i722 i513.HKCTNBBXX.s 1.r ,0:150 1:150,A:53339247;C:46384000;G:44842527;T:54810170;N:4356,150,150,,,53339247,46384000,44842527,54810170,4356,ERX2737751,ERS2635202,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",2,0.90656,0.90507,0.28527,0.29363,0.9727,0.97384,0.50665,0.52084,150,150,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
8152,ERR2723981,ERX2737750,ERS2635201,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.,LCK kidney A5,SAMEA4815303,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815303|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:LCK kidney A5|age:6|broker name:ArrayExpress|cell type:blood cell|cluster:1|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:1|organism part:kidney|phenotype:EGFP positive cell|sample name:E MTAB 7117:LCK kidney A5|scientific name:Danio rerio|sex:male|single cell well quality:not OK|strain:AB|well information:50 cells,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; Single cell transcriptional analysis reveals innate lymphoid cell ILC like cells in zebrafish,E MTAB 7117:LCK kidney A5 p,LCK kidney A5 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|Experimental Factor: organism part:kidney|Experimental Factor: single cell identifier:LCK kidney A5,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_i513.HKCTNBBXX.s_1.r_1.fq.gz SLX-12119.i721_i513.HKCTNBBXX.s_1.r_2.fq.gz,fastq fastq,228681900.0,762273.0,E MTAB 7117:SLX 12119.i721 i513.HKCTNBBXX.s 1.r ,0:150 1:150,A:62064639;C:52192654;G:50570771;T:63849396;N:4440,150,150,,,62064639,52192654,50570771,63849396,4440,ERX2737750,ERS2635201,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",2,0.91143,0.9113,0.38029,0.38612,0.97812,0.97938,0.5556,0.55549,150,150,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
8153,ERR2723980,ERX2737749,ERS2635200,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 H9,SAMEA4815302,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815302|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H9|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 H9|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 H9 p,Rag1 kidney H9 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 H9,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.i726_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,266967000.0,889890.0,E MTAB 7117:SLX 12114.i726 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:72936497;C:61564543;G:58506328;T:73956365;N:3267,150,150,,,72936497,61564543,58506328,73956365,3267,ERX2737749,ERS2635200,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",2,0.89229,0.89466,0.28452,0.29065,0.98593,0.98618,0.49404,0.48931,150,150,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
8154,ERR2723979,ERX2737748,ERS2635199,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 H8,SAMEA4815301,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815301|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H8|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 H8|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 H8 p,Rag1 kidney H8 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 H8,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.i724_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,142694100.0,475647.0,E MTAB 7117:SLX 12114.i724 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:38465370;C:33223562;G:32019646;T:38983841;N:1681,150,150,,,38465370,33223562,32019646,38983841,1681,ERX2737748,ERS2635199,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",2,0.88313,0.88606,0.24707,0.25454,0.97153,0.9726,0.49136,0.50097,150,150,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
8155,ERR2723978,ERX2737747,ERS2635198,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 H7,SAMEA4815300,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815300|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H7|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 H7|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 H7 p,Rag1 kidney H7 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 H7,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.i723_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,74628600.0,248762.0,E MTAB 7117:SLX 12114.i723 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:16733962;C:20859916;G:20170167;T:16863672;N:883,150,150,,,16733962,20859916,20170167,16863672,883,ERX2737747,ERS2635198,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",2,0.5047,0.52498,0.16597,0.17713,0.9726,0.97352,0.60194,0.62146,150,150,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
8156,ERR2723977,ERX2737746,ERS2635197,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 H6,SAMEA4815299,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815299|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H6|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 H6|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 H6 p,Rag1 kidney H6 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 H6,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.i722_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,122152500.0,407175.0,E MTAB 7117:SLX 12114.i722 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:32764089;C:28490846;G:27469008;T:33427148;N:1409,150,150,,,32764089,28490846,27469008,33427148,1409,ERX2737746,ERS2635197,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",2,0.79287,0.80107,0.30929,0.32026,0.97206,0.97313,0.55781,0.55838,150,150,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
8157,ERR2723976,ERX2737745,ERS2635196,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 H5,SAMEA4815298,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815298|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H5|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 H5|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 H5 p,Rag1 kidney H5 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 H5,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.i721_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,129788100.0,432627.0,E MTAB 7117:SLX 12114.i721 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:35236161;C:30081249;G:29009363;T:35459913;N:1414,150,150,,,35236161,30081249,29009363,35459913,1414,ERX2737745,ERS2635196,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",2,0.89451,0.89576,0.19999,0.20491,0.96625,0.96743,0.50804,0.49439,150,150,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
8158,ERR2723975,ERX2737744,ERS2635195,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 H4,SAMEA4815297,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815297|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H4|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 H4|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 H4 p,Rag1 kidney H4 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 H4,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.i720_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,119907300.0,399691.0,E MTAB 7117:SLX 12114.i720 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:32516536;C:27737809;G:26669245;T:32982313;N:1397,150,150,,,32516536,27737809,26669245,32982313,1397,ERX2737744,ERS2635195,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",2,0.85448,0.85693,0.28483,0.29668,0.96861,0.9699,0.51867,0.51004,150,150,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
8159,ERR2723974,ERX2737743,ERS2635194,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 H3,SAMEA4815296,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815296|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H3|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 H3|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 H3 p,Rag1 kidney H3 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 H3,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.i719_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,717900.0,2393.0,E MTAB 7117:SLX 12114.i719 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:184605;C:180972;G:168309;T:184011;N:3,150,150,,,184605,180972,168309,184011,3,ERX2737743,ERS2635194,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",2,0.5248,0.47818,0.18826,0.19849,0.99151,0.99411,0.60743,0.56575,150,150,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
8160,ERR2723973,ERX2737742,ERS2635193,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 H2,SAMEA4815295,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815295|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H2|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 H2|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 H2 p,Rag1 kidney H2 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 H2,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.i718_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,251043900.0,836813.0,E MTAB 7117:SLX 12114.i718 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:68320114;C:58141192;G:55866806;T:68712922;N:2866,150,150,,,68320114,58141192,55866806,68712922,2866,ERX2737742,ERS2635193,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",2,0.85705,0.86239,0.26656,0.27442,0.97273,0.97354,0.54258,0.53766,150,150,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
8161,ERR2723972,ERX2737741,ERS2635192,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 H12,SAMEA4815294,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815294|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H12|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 H12|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 H12 p,Rag1 kidney H12 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 H12,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.i729_i522.HKKG2BBXX.s_1.r_2.fq.gz SLX-12114.i729_i522.HKKG2BBXX.s_1.r_1.fq.gz,fastq fastq,205536300.0,685121.0,E MTAB 7117:SLX 12114.i729 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:54575803;C:48923788;G:46554826;T:55479471;N:2412,150,150,,,54575803,48923788,46554826,55479471,2412,ERX2737741,ERS2635192,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",2,0.88176,0.88607,0.44943,0.45367,0.98346,0.98332,0.59478,0.58035,150,150,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
8162,ERR2723971,ERX2737740,ERS2635191,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 H11,SAMEA4815293,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815293|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H11|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 H11|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 H11 p,Rag1 kidney H11 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 H11,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_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,218551200.0,728504.0,E MTAB 7117:SLX 12114.i728 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:59914721;C:49712610;G:47874165;T:61047094;N:2610,150,150,,,59914721,49712610,47874165,61047094,2610,ERX2737740,ERS2635191,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",2,0.89681,0.89967,0.31764,0.32917,0.97924,0.97973,0.51522,0.51708,150,150,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
8163,ERR2723970,ERX2737739,ERS2635190,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 H10,SAMEA4815292,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815292|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H10|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 H10|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 H10 p,Rag1 kidney H10 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 H10,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.i727_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,148134600.0,493782.0,E MTAB 7117:SLX 12114.i727 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:40215105;C:34309220;G:32968610;T:40639940;N:1725,150,150,,,40215105,34309220,32968610,40639940,1725,ERX2737739,ERS2635190,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",2,0.85472,0.86027,0.3246,0.33485,0.9735,0.97494,0.53066,0.50715,150,150,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
8164,ERR2723969,ERX2737738,ERS2635189,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 H1,SAMEA4815291,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815291|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney H1|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 H1|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 H1 p,Rag1 kidney H1 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 H1,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.i716_i522.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i522.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,210196800.0,700656.0,E MTAB 7117:SLX 12114.i716 i522.HKKG2BBXX.s 1.r ,0:150 1:150,A:52816299;C:53122529;G:51064568;T:53191053;N:2351,150,150,,,52816299,53122529,51064568,53191053,2351,ERX2737738,ERS2635189,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",2,0.82744,0.84153,0.16889,0.17748,0.9542,0.95493,0.55348,0.55212,150,150,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
8165,ERR2723968,ERX2737737,ERS2635188,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 G9,SAMEA4815290,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815290|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G9|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 G9|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 G9 p,Rag1 kidney G9 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 G9,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.i726_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,205987500.0,686625.0,E MTAB 7117:SLX 12114.i726 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:57262398;C:46388763;G:43950404;T:58383283;N:2652,150,150,,,57262398,46388763,43950404,58383283,2652,ERX2737737,ERS2635188,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",2,0.8772,0.87939,0.37456,0.37809,0.97871,0.97934,0.56985,0.58161,150,150,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
8166,ERR2723967,ERX2737736,ERS2635187,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 G8,SAMEA4815289,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815289|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G8|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 G8|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 G8 p,Rag1 kidney G8 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 G8,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.i724_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i724_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,138236700.0,460789.0,E MTAB 7117:SLX 12114.i724 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:38231050;C:31102804;G:30059891;T:38841286;N:1669,150,150,,,38231050,31102804,30059891,38841286,1669,ERX2737736,ERS2635187,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",2,0.89024,0.8918,0.32094,0.32933,0.97437,0.97536,0.51993,0.52818,150,150,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
8167,ERR2723966,ERX2737735,ERS2635186,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 G7,SAMEA4815288,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815288|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G7|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 G7|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 G7 p,Rag1 kidney G7 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 G7,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.i723_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i723_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,77073300.0,256911.0,E MTAB 7117:SLX 12114.i723 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:18220192;C:20562829;G:19856183;T:18433242;N:854,150,150,,,18220192,20562829,19856183,18433242,854,ERX2737735,ERS2635186,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",2,0.48981,0.57084,0.17877,0.21647,0.9684,0.96852,0.63691,0.64125,150,150,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
8168,ERR2723965,ERX2737734,ERS2635185,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 G6,SAMEA4815287,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815287|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G6|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 G6|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 G6 p,Rag1 kidney G6 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 G6,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.i722_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i722_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,66912000.0,223040.0,E MTAB 7117:SLX 12114.i722 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:16469009;C:17213266;G:16620613;T:16608292;N:820,150,150,,,16469009,17213266,16620613,16608292,820,ERX2737734,ERS2635185,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",2,0.54771,0.63559,0.19195,0.23078,0.96534,0.96512,0.57228,0.5806,150,150,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
8169,ERR2723964,ERX2737733,ERS2635184,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 G5,SAMEA4815286,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815286|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G5|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 G5|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 G5 p,Rag1 kidney 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 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 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-12114.i721_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i721_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,127597200.0,425324.0,E MTAB 7117:SLX 12114.i721 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:34778626;C:29213451;G:28164730;T:35438856;N:1537,150,150,,,34778626,29213451,28164730,35438856,1537,ERX2737733,ERS2635184,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",2,0.86881,0.87329,0.35885,0.36707,0.96962,0.97183,0.50972,0.50832,150,150,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
8170,ERR2723963,ERX2737732,ERS2635183,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 G4,SAMEA4815285,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815285|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G4|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 G4|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 G4 p,Rag1 kidney G4 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 G4,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.i720_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i720_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,208706100.0,695687.0,E MTAB 7117:SLX 12114.i720 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:49506811;C:55639927;G:53649832;T:49906916;N:2614,150,150,,,49506811,55639927,53649832,49906916,2614,ERX2737732,ERS2635183,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",2,0.59828,0.62274,0.23345,0.24511,0.98837,0.9891,0.52332,0.54143,150,150,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
8171,ERR2723962,ERX2737731,ERS2635182,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 G3,SAMEA4815284,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815284|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G3|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 G3|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 G3 p,Rag1 kidney G3 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 G3,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.i719_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i719_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,78470100.0,261567.0,E MTAB 7117:SLX 12114.i719 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:20861944;C:18531657;G:17910833;T:21164717;N:949,150,150,,,20861944,18531657,17910833,21164717,949,ERX2737731,ERS2635182,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",2,0.84211,0.84705,0.21181,0.21987,0.96197,0.9639,0.52563,0.53396,150,150,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
8172,ERR2723961,ERX2737730,ERS2635181,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 G2,SAMEA4815283,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815283|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G2|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 G2|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 G2 p,Rag1 kidney G2 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 G2,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.i718_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i718_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,170317500.0,567725.0,E MTAB 7117:SLX 12114.i718 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:46279278;C:39388939;G:38119248;T:46528005;N:2030,150,150,,,46279278,39388939,38119248,46528005,2030,ERX2737730,ERS2635181,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",2,0.86893,0.87291,0.26507,0.27212,0.97007,0.97163,0.53986,0.51551,150,150,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
8173,ERR2723960,ERX2737729,ERS2635180,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 G12,SAMEA4815282,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815282|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G12|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 G12|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 G12 p,Rag1 kidney G12 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 G12,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.i729_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i729_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,184555800.0,615186.0,E MTAB 7117:SLX 12114.i729 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:49685531;C:42960556;G:41166991;T:50740527;N:2195,150,150,,,49685531,42960556,41166991,50740527,2195,ERX2737729,ERS2635180,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",2,0.87399,0.878,0.32312,0.33071,0.97423,0.97433,0.47728,0.47512,150,150,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
8174,ERR2723959,ERX2737728,ERS2635179,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 G11,SAMEA4815281,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815281|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G11|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 G11|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 G11 p,Rag1 kidney G11 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 G11,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_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i728_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,174227700.0,580759.0,E MTAB 7117:SLX 12114.i728 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:47124445;C:40338390;G:38827876;T:47934892;N:2097,150,150,,,47124445,40338390,38827876,47934892,2097,ERX2737728,ERS2635179,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",2,0.87068,0.87397,0.32244,0.33114,0.97924,0.98037,0.5677,0.58727,150,150,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
8175,ERR2723958,ERX2737727,ERS2635178,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 G10,SAMEA4815280,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815280|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G10|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 G10|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 G10 p,Rag1 kidney G10 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 G10,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.i727_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i727_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,119128800.0,397096.0,E MTAB 7117:SLX 12114.i727 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:32538117;C:27143637;G:26209284;T:33236228;N:1534,150,150,,,32538117,27143637,26209284,33236228,1534,ERX2737727,ERS2635178,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",2,0.88413,0.88973,0.34973,0.35892,0.97321,0.97415,0.53322,0.55266,150,150,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
8176,ERR2723957,ERX2737726,ERS2635177,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 G1,SAMEA4815279,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815279|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney G1|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 G1|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 G1 p,Rag1 kidney G1 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 G1,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.i716_i521.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i716_i521.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,192269700.0,640899.0,E MTAB 7117:SLX 12114.i716 i521.HKKG2BBXX.s 1.r ,0:150 1:150,A:52209157;C:44619638;G:42999231;T:52439338;N:2336,150,150,,,52209157,44619638,42999231,52439338,2336,ERX2737726,ERS2635177,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",2,0.903,0.90329,0.2165,0.22388,0.96956,0.97055,0.51313,0.49792,150,150,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
8177,ERR2723956,ERX2737725,ERS2635176,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 F9,SAMEA4815278,"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 16T17:03:29Z|ENA LAST UPDATE:2018 08 03T10:54:26Z|External Id:SAMEA4815278|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 16T17:03:29Z|INSDC last update:2018 08 03T10:54:26Z|INSDC status:public|Submitter Id:E MTAB 7117:Rag1 kidney F9|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 F9|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 F9 p,Rag1 kidney F9 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 F9,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.i726_i520.HKKG2BBXX.s_1.r_1.fq.gz SLX-12114.i726_i520.HKKG2BBXX.s_1.r_2.fq.gz,fastq fastq,156714600.0,522382.0,E MTAB 7117:SLX 12114.i726 i520.HKKG2BBXX.s 1.r ,0:150 1:150,A:43302587;C:35378974;G:33959883;T:44071238;N:1918,150,150,,,43302587,35378974,33959883,44071238,1918,ERX2737725,ERS2635176,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",2,0.88305,0.88608,0.27135,0.28056,0.96895,0.96997,0.5322,0.54601,150,150,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