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2,789 rows where experiment.library_layout = "PAIRED" and experiment.library_selection = "Oligo-dT"

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tissue_curation >10

devstage_curation >10

devstage_curation_coarse 6

technology 5

experiment.library_strategy 4

experiment.platform 2

experiment.library_source 2

experiment.library_selection 1

  • Oligo-dT · 2,789 ✖

experiment.library_layout 1

  • PAIRED · 2,789 ✖
Link 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
280 280 DRR161311 DRX151936 DRS095335 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of female Danio rerio liver SAMD00153247   sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153247 DRX151936 f 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><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_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153247       2338564937.0 15498367.0 DRR161311 0:75.45 1:75.44 A:613899755;C:541756858;G:548366901;T:633083422;N:1458001 75 75     613899755 541756858 548366901 633083422 1458001 DRX151936 DRS095335 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.95814 0.96362 0.05394 0.04517 0.77932 0.7834 0.37385 0.37264 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
281 281 DRR161310 DRX151935 DRS095334 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of male Danio rerio liver SAMD00153246   sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153246 DRX151935 m 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><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_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153246       2506978527.0 16611154.0 DRR161310 0:75.48 1:75.44 A:672321355;C:568289588;G:569411670;T:695545626;N:1410288 75 75     672321355 568289588 569411670 695545626 1410288 DRX151935 DRS095334 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.94746 0.95115 0.07899 0.06363 0.80837 0.8115 0.52008 0.58743 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
312 312 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…       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
313 313 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…       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
314 314 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…       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
315 315 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
316 316 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
317 317 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
318 318 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
319 319 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
320 320 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
321 321 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
322 322 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
323 323 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
324 324 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
325 325 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
326 326 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
327 327 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
328 328 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
329 329 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
330 330 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
331 331 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
332 332 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
333 333 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
334 334 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
7953 7953 ERR2146982 ERX2203515 ERS1952873 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control6 SAMEA104327895 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327895|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:23Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP negative|sample name:E MTAB 6077:XY control6|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control6 p XY control6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP negative|Experimental Factor: single cell identifier:XY control6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control6_R2.fastq.gz XY_control6_R1.fastq.gz fastq fastq 4549556088.0 18053794.0 E MTAB 6077:XY control6 R 0:126 1:126 A:1249771585;C:1032539820;G:1013780979;T:1253138208;N:325496 126 126     1249771585 1032539820 1013780979 1253138208 325496 ERX2203515 ERS1952873 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.93704 0.93646 0.09456 0.0963 0.77989 0.78277 0.49027 0.49534 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7954 7954 ERR2146981 ERX2203514 ERS1952872 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control5 SAMEA104327894 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327894|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|sample name:E MTAB 6077:XY control5|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control5 p XY control5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY control5|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control5_R1.fastq.gz XY_control5_R2.fastq.gz fastq fastq 4716306756.0 18715503.0 E MTAB 6077:XY control5 R 0:126 1:126 A:1270474643;C:1095125173;G:1073972754;T:1276395367;N:338819 126 126     1270474643 1095125173 1073972754 1276395367 338819 ERX2203514 ERS1952872 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.93411 0.93498 0.08638 0.08804 0.77893 0.78094 0.48544 0.49009 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7955 7955 ERR2146980 ERX2203513 ERS1952871 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control4 SAMEA104327893 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327893|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP negative|sample name:E MTAB 6077:XY control4|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control4 p XY control4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP negative|Experimental Factor: single cell identifier:XY control4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control4_R1.fastq.gz XY_control4_R2.fastq.gz fastq fastq 5945132844.0 23591797.0 E MTAB 6077:XY control4 R 0:126 1:126 A:1626789290;C:1357026290;G:1322234145;T:1638578806;N:504313 126 126     1626789290 1357026290 1322234145 1638578806 504313 ERX2203513 ERS1952871 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.92339 0.92233 0.10762 0.11113 0.77218 0.77833 0.48434 0.47741 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7956 7956 ERR2146979 ERX2203512 ERS1952870 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control3 SAMEA104327892 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327892|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|sample name:E MTAB 6077:XY control3|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control3 p XY control3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY control3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control3_R1.fastq.gz XY_control3_R2.fastq.gz fastq fastq 5535067608.0 21964554.0 E MTAB 6077:XY control3 R 0:126 1:126 A:1514179525;C:1264413791;G:1243494617;T:1512516950;N:462725 126 126     1514179525 1264413791 1243494617 1512516950 462725 ERX2203512 ERS1952870 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.91933 0.9182 0.10843 0.11009 0.77662 0.77839 0.48196 0.48344 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7957 7957 ERR2146978 ERX2203511 ERS1952869 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control2 SAMEA104327891 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327891|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP negative|sample name:E MTAB 6077:XY control2|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control2 p XY control2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP negative|Experimental Factor: single cell identifier:XY control2|Experimental Factor: block:batch 1 2015 03 25 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control2_R1.fastq.gz XY_control2_R2.fastq.gz fastq fastq 5765575536.0 22879268.0 E MTAB 6077:XY control2 R 0:126 1:126 A:1577072713;C:1319503344;G:1284653366;T:1583881864;N:464249 126 126     1577072713 1319503344 1284653366 1583881864 464249 ERX2203511 ERS1952869 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.90176 0.90134 0.09386 0.09519 0.78654 0.7875 0.48786 0.48901 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7958 7958 ERR2146977 ERX2203510 ERS1952868 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY control1 SAMEA104327890 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327890|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY control1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|sample name:E MTAB 6077:XY control1|well information:4000 cells tube control                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY control1 p XY control1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY control1|Experimental Factor: block:batch 1 2015 03 25 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_control1_R1.fastq.gz XY_control1_R2.fastq.gz fastq fastq 5364104256.0 21286128.0 E MTAB 6077:XY control1 R 0:126 1:126 A:1451397579;C:1239771441;G:1215928457;T:1456576239;N:430540 126 126     1451397579 1239771441 1215928457 1456576239 430540 ERX2203510 ERS1952868 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87836 0.87758 0.09375 0.09537 0.79101 0.79385 0.48123 0.48531 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7959 7959 ERR2146976 ERX2203509 ERS1952867 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H8 SAMEA104327889 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327889|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H8 p XY H8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H8_R1.fastq.gz XY_H8_R2.fastq.gz fastq fastq 864210816.0 3429408.0 E MTAB 6077:XY H8 R 0:126 1:126 A:249771934;C:187002108;G:178230223;T:249134097;N:72454 126 126     249771934 187002108 178230223 249134097 72454 ERX2203509 ERS1952867 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81405 0.81553 0.21726 0.2187 0.94909 0.94913 0.762 0.75712 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7960 7960 ERR2146975 ERX2203508 ERS1952866 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H7 SAMEA104327888 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327888|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H7 p XY H7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H7_R1.fastq.gz XY_H7_R2.fastq.gz fastq fastq 756021672.0 3000086.0 E MTAB 6077:XY H7 R 0:126 1:126 A:218450821;C:163414581;G:153421674;T:220674025;N:60571 126 126     218450821 163414581 153421674 220674025 60571 ERX2203508 ERS1952866 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.86606 0.86563 0.20652 0.20672 0.90678 0.90684 0.52647 0.52546 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7961 7961 ERR2146974 ERX2203507 ERS1952865 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H6 SAMEA104327887 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327887|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H6 p XY H6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H6_R1.fastq.gz XY_H6_R2.fastq.gz fastq fastq 1074550176.0 4264088.0 E MTAB 6077:XY H6 R 0:126 1:126 A:308254957;C:234011984;G:222627836;T:309568320;N:87079 126 126     308254957 234011984 222627836 309568320 87079 ERX2203507 ERS1952865 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.83064 0.8297 0.17609 0.17705 0.94706 0.94688 0.70976 0.71858 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7962 7962 ERR2146973 ERX2203506 ERS1952864 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G7 SAMEA104327886 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327886|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G7 p XY G7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G7_R1.fastq.gz XY_G7_R2.fastq.gz fastq fastq 888876576.0 3527288.0 E MTAB 6077:XY G7 R 0:126 1:126 A:254439819;C:194980753;G:181687161;T:257695391;N:73452 126 126     254439819 194980753 181687161 257695391 73452 ERX2203506 ERS1952864 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.90072 0.89984 0.2275 0.22842 0.91116 0.91165 0.56832 0.5707 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7963 7963 ERR2146972 ERX2203505 ERS1952863 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G6 SAMEA104327885 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327885|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G6 p XY G6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G6_R1.fastq.gz XY_G6_R2.fastq.gz fastq fastq 996116436.0 3952843.0 E MTAB 6077:XY G6 R 0:126 1:126 A:275654881;C:226382568;G:215845958;T:278153726;N:79303 126 126     275654881 226382568 215845958 278153726 79303 ERX2203505 ERS1952863 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.91202 0.91213 0.07492 0.07611 0.93454 0.93446 0.48374 0.48865 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7964 7964 ERR2146971 ERX2203504 ERS1952862 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F8 SAMEA104327884 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327884|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F8 p XY F8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F8_R1.fastq.gz XY_F8_R2.fastq.gz fastq fastq 877436028.0 3481889.0 E MTAB 6077:XY F8 R 0:126 1:126 A:241235862;C:201062056;G:193297643;T:241769388;N:71079 126 126     241235862 201062056 193297643 241769388 71079 ERX2203504 ERS1952862 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80726 0.80669 0.05191 0.05278 0.9447 0.94481 0.4442 0.44721 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7965 7965 ERR2146970 ERX2203503 ERS1952861 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F7 SAMEA104327883 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327883|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F7 p XY F7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F7_R1.fastq.gz XY_F7_R2.fastq.gz fastq fastq 958632192.0 3804096.0 E MTAB 6077:XY F7 R 0:126 1:126 A:273424334;C:210648698;G:198846984;T:275634740;N:77436 126 126     273424334 210648698 198846984 275634740 77436 ERX2203503 ERS1952861 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.90705 0.90578 0.17689 0.17782 0.90224 0.90258 0.52906 0.52965 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7966 7966 ERR2146969 ERX2203502 ERS1952860 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F6 SAMEA104327882 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327882|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F6 p XY F6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F6_R1.fastq.gz XY_F6_R2.fastq.gz fastq fastq 819905940.0 3253595.0 E MTAB 6077:XY F6 R 0:126 1:126 A:235169787;C:178657976;G:168253811;T:237755989;N:68377 126 126     235169787 178657976 168253811 237755989 68377 ERX2203502 ERS1952860 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.8318 0.83391 0.25866 0.26072 0.93363 0.93413 0.64306 0.64461 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7967 7967 ERR2146968 ERX2203501 ERS1952859 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E8 SAMEA104327881 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327881|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E8 p XY E8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E8_R1.fastq.gz XY_E8_R2.fastq.gz fastq fastq 842724540.0 3344145.0 E MTAB 6077:XY E8 R 0:126 1:126 A:242981289;C:183320053;G:172749908;T:243603429;N:69861 126 126     242981289 183320053 172749908 243603429 69861 ERX2203501 ERS1952859 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81153 0.81108 0.25264 0.25373 0.95215 0.95243 0.7481 0.748 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7968 7968 ERR2146967 ERX2203500 ERS1952858 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E7 SAMEA104327880 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327880|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E7 p XY E7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E7_R1.fastq.gz XY_E7_R2.fastq.gz fastq fastq 776402424.0 3080962.0 E MTAB 6077:XY E7 R 0:126 1:126 A:219057494;C:173933939;G:161687576;T:221658032;N:65383 126 126     219057494 173933939 161687576 221658032 65383 ERX2203500 ERS1952858 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81289 0.8127 0.17319 0.17455 0.93941 0.94002 0.61509 0.61689 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7969 7969 ERR2146966 ERX2203499 ERS1952857 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E6 SAMEA104327879 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327879|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E6 p XY E6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E6_R1.fastq.gz XY_E6_R2.fastq.gz fastq fastq 857047464.0 3400982.0 E MTAB 6077:XY E6 R 0:126 1:126 A:241359294;C:190499276;G:181314236;T:243803691;N:70967 126 126     241359294 190499276 181314236 243803691 70967 ERX2203499 ERS1952857 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87204 0.87145 0.14714 0.1482 0.92618 0.92654 0.51966 0.40678 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7970 7970 ERR2146965 ERX2203498 ERS1952856 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D8 SAMEA104327878 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327878|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D8 p XY D8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D8_R1.fastq.gz XY_D8_R2.fastq.gz fastq fastq 843642324.0 3347787.0 E MTAB 6077:XY D8 R 0:126 1:126 A:242903477;C:184375610;G:173102506;T:243189515;N:71216 126 126     242903477 184375610 173102506 243189515 71216 ERX2203498 ERS1952856 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80439 0.80704 0.25569 0.25887 0.95485 0.9554 0.77117 0.77377 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7971 7971 ERR2146964 ERX2203497 ERS1952855 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D7 SAMEA104327877 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327877|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D7 p XY D7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D7_R1.fastq.gz XY_D7_R2.fastq.gz fastq fastq 984207168.0 3905584.0 E MTAB 6077:XY D7 R 0:126 1:126 A:283251031;C:217529580;G:197592673;T:285746776;N:87108 126 126     283251031 217529580 197592673 285746776 87108 ERX2203497 ERS1952855 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85387 0.85464 0.19987 0.20244 0.94343 0.94416 0.76877 0.76643 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7972 7972 ERR2146963 ERX2203496 ERS1952854 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D6 SAMEA104327876 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327876|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D6 p XY D6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D6_R1.fastq.gz XY_D6_R2.fastq.gz fastq fastq 822279780.0 3263015.0 E MTAB 6077:XY D6 R 0:126 1:126 A:235190518;C:179206449;G:169869879;T:237947879;N:65055 126 126     235190518 179206449 169869879 237947879 65055 ERX2203496 ERS1952854 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87845 0.88077 0.13151 0.13349 0.91488 0.915 0.58175 0.58204 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7973 7973 ERR2146962 ERX2203495 ERS1952853 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C8 SAMEA104327875 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327875|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C8 p XY C8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C8_R1.fastq.gz XY_C8_R2.fastq.gz fastq fastq 1013469408.0 4021704.0 E MTAB 6077:XY C8 R 0:126 1:126 A:292880928;C:221164286;G:209883396;T:289460688;N:80110 126 126     292880928 221164286 209883396 289460688 80110 ERX2203495 ERS1952853 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.83814 0.8391 0.24905 0.24961 0.93736 0.93667 0.61348 0.61766 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7974 7974 ERR2146961 ERX2203494 ERS1952852 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C7 SAMEA104327874 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327874|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C7 p XY C7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C7_R1.fastq.gz XY_C7_R2.fastq.gz fastq fastq 1006828704.0 3995352.0 E MTAB 6077:XY C7 R 0:126 1:126 A:287564865;C:223387104;G:208613518;T:287183841;N:79376 126 126     287564865 223387104 208613518 287183841 79376 ERX2203494 ERS1952852 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87244 0.87249 0.16434 0.16605 0.91597 0.91687 0.55002 0.54756 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7975 7975 ERR2146960 ERX2203493 ERS1952851 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C6 SAMEA104327873 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327873|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C6 p XY C6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C6_R1.fastq.gz XY_C6_R2.fastq.gz fastq fastq 961789500.0 3816625.0 E MTAB 6077:XY C6 R 0:126 1:126 A:278781495;C:205421491;G:197677532;T:279831229;N:77753 126 126     278781495 205421491 197677532 279831229 77753 ERX2203493 ERS1952851 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.90742 0.90809 0.18725 0.18852 0.9068 0.90642 0.54244 0.46695 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7976 7976 ERR2146959 ERX2203492 ERS1952850 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B8 SAMEA104327872 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327872|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B8 p XY B8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B8_R1.fastq.gz XY_B8_R2.fastq.gz fastq fastq 919461816.0 3648658.0 E MTAB 6077:XY B8 R 0:126 1:126 A:269811899;C:193898193;G:185943309;T:269733141;N:75274 126 126     269811899 193898193 185943309 269733141 75274 ERX2203492 ERS1952850 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85046 0.8503 0.27069 0.27204 0.91944 0.92046 0.54761 0.54669 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7977 7977 ERR2146958 ERX2203491 ERS1952849 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B7 SAMEA104327871 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327871|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B7 p XY B7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B7_R1.fastq.gz XY_B7_R2.fastq.gz fastq fastq 1105211268.0 4385759.0 E MTAB 6077:XY B7 R 0:126 1:126 A:319612550;C:237937703;G:225942677;T:321629855;N:88483 126 126     319612550 237937703 225942677 321629855 88483 ERX2203491 ERS1952849 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.89722 0.89732 0.2253 0.22622 0.9223 0.92214 0.46651 0.47996 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7978 7978 ERR2146957 ERX2203490 ERS1952848 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B6 SAMEA104327870 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327870|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B6 p XY B6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B6|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B6_R1.fastq.gz XY_B6_R2.fastq.gz fastq fastq 888803496.0 3526998.0 E MTAB 6077:XY B6 R 0:126 1:126 A:259157968;C:187867811;G:181734930;T:259972893;N:69894 126 126     259157968 187867811 181734930 259972893 69894 ERX2203490 ERS1952848 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.905 0.90517 0.14694 0.14784 0.90173 0.90205 0.5606 0.53635 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7979 7979 ERR2146956 ERX2203489 ERS1952847 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A9 SAMEA104327869 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327869|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A9|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A9|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A9 p XY A9 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A9|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A9_R1.fastq.gz XY_A9_R2.fastq.gz fastq fastq 852383952.0 3382476.0 E MTAB 6077:XY A9 R 0:126 1:126 A:243063922;C:186833267;G:175428225;T:246986620;N:71918 126 126     243063922 186833267 175428225 246986620 71918 ERX2203489 ERS1952847 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.791 0.79236 0.26001 0.26219 0.95495 0.95515 0.67722 0.67292 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7980 7980 ERR2146955 ERX2203488 ERS1952846 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A8 SAMEA104327868 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327868|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A8|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A8|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A8 p XY A8 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A8|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A8_R1.fastq.gz XY_A8_R2.fastq.gz fastq fastq 930505212.0 3692481.0 E MTAB 6077:XY A8 R 0:126 1:126 A:265557007;C:204874994;G:193354741;T:266645204;N:73266 126 126     265557007 204874994 193354741 266645204 73266 ERX2203488 ERS1952846 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80883 0.81059 0.25464 0.25659 0.95024 0.95051 0.75494 0.76047 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7981 7981 ERR2146954 ERX2203487 ERS1952845 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A7 SAMEA104327867 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327867|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A7|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A7|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A7 p XY A7 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A7|Experimental Factor: block:batch 3 2015 04 15 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A7_R1.fastq.gz XY_A7_R2.fastq.gz fastq fastq 947373588.0 3759419.0 E MTAB 6077:XY A7 R 0:126 1:126 A:269034866;C:210414489;G:195690143;T:272157870;N:76220 126 126     269034866 210414489 195690143 272157870 76220 ERX2203487 ERS1952845 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.90451 0.90515 0.17025 0.17226 0.90774 0.90776 0.59799 0.60776 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7982 7982 ERR2146953 ERX2203486 ERS1952844 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H5 SAMEA104327866 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327866|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H5 p XY H5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H5_R1.fastq.gz XY_H5_R2.fastq.gz fastq fastq 661968468.0 2626859.0 E MTAB 6077:XY H5 R 0:126 1:126 A:182197480;C:151742936;G:143603852;T:184373864;N:50336 126 126     182197480 151742936 143603852 184373864 50336 ERX2203486 ERS1952844 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.43701 0.45028 0.1003 0.10327 0.94828 0.94809 0.66076 0.66111 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7983 7983 ERR2146952 ERX2203485 ERS1952843 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H4 SAMEA104327865 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327865|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H4 p XY H4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H4_R1.fastq.gz XY_H4_R2.fastq.gz fastq fastq 763960932.0 3031591.0 E MTAB 6077:XY H4 R 0:126 1:126 A:210454823;C:173613405;G:168163464;T:211676418;N:52822 126 126     210454823 173613405 168163464 211676418 52822 ERX2203485 ERS1952843 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88746 0.88783 0.1341 0.13524 0.89613 0.8966 0.41929 0.50102 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7984 7984 ERR2146951 ERX2203484 ERS1952842 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H3 SAMEA104327864 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327864|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H3 p XY H3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H3_R1.fastq.gz XY_H3_R2.fastq.gz fastq fastq 659294244.0 2616247.0 E MTAB 6077:XY H3 R 0:126 1:126 A:188850616;C:143711118;G:137850770;T:188835454;N:46286 126 126     188850616 143711118 137850770 188835454 46286 ERX2203484 ERS1952842 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80539 0.80566 0.23678 0.23789 0.92013 0.92086 0.63014 0.63224 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7985 7985 ERR2146950 ERX2203483 ERS1952841 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H2 SAMEA104327863 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327863|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H2 p XY H2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H2_R1.fastq.gz XY_H2_R2.fastq.gz fastq fastq 800579556.0 3176903.0 E MTAB 6077:XY H2 R 0:126 1:126 A:223283547;C:180576112;G:171695116;T:224965999;N:58782 126 126     223283547 180576112 171695116 224965999 58782 ERX2203483 ERS1952841 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.49111 0.50915 0.12273 0.12834 0.93322 0.93324 0.63392 0.63061 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7986 7986 ERR2146949 ERX2203482 ERS1952840 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H12 SAMEA104327862 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327862|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:22Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H12|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H12|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H12 p XY H12 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H12|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H12_R1.fastq.gz XY_H12_R2.fastq.gz fastq fastq 1012529952.0 4017976.0 E MTAB 6077:XY H12 R 0:126 1:126 A:296329041;C:212818812;G:204681970;T:298612968;N:87161 126 126     296329041 212818812 204681970 298612968 87161 ERX2203482 ERS1952840 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85208 0.85109 0.2762 0.2772 0.90857 0.9096 0.5945 0.59648 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7987 7987 ERR2146948 ERX2203481 ERS1952839 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H1 SAMEA104327861 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327861|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H1 p XY H1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H1_R1.fastq.gz XY_H1_R2.fastq.gz fastq fastq 1013476716.0 4021733.0 E MTAB 6077:XY H1 R 0:126 1:126 A:285093595;C:224698069;G:216782708;T:286832156;N:70188 126 126     285093595 224698069 216782708 286832156 70188 ERX2203481 ERS1952839 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85277 0.85221 0.20343 0.20573 0.91727 0.91735 0.5053 0.51218 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7988 7988 ERR2146947 ERX2203480 ERS1952838 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G5 SAMEA104327860 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327860|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G5 p XY G5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G5_R1.fastq.gz XY_G5_R2.fastq.gz fastq fastq 573735204.0 2276727.0 E MTAB 6077:XY G5 R 0:126 1:126 A:160393081;C:130403439;G:120151582;T:162737783;N:49319 126 126     160393081 130403439 120151582 162737783 49319 ERX2203480 ERS1952838 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.67173 0.67076 0.21171 0.21167 0.94113 0.94111 0.70844 0.70511 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7989 7989 ERR2146946 ERX2203479 ERS1952837 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G4 SAMEA104327859 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327859|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G4 p XY G4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G4_R1.fastq.gz XY_G4_R2.fastq.gz fastq fastq 545927004.0 2166377.0 E MTAB 6077:XY G4 R 0:126 1:126 A:155307335;C:120841181;G:111873434;T:157868534;N:36520 126 126     155307335 120841181 111873434 157868534 36520 ERX2203479 ERS1952837 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.74895 0.75073 0.23536 0.23798 0.93166 0.93129 0.62288 0.63112 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7990 7990 ERR2146945 ERX2203478 ERS1952836 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G3 SAMEA104327858 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327858|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G3 p XY G3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G3_R1.fastq.gz XY_G3_R2.fastq.gz fastq fastq 865575396.0 3434823.0 E MTAB 6077:XY G3 R 0:126 1:126 A:247249274;C:189448794;G:180244568;T:248572085;N:60675 126 126     247249274 189448794 180244568 248572085 60675 ERX2203478 ERS1952836 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85277 0.85221 0.24206 0.24438 0.9025 0.90327 0.54937 0.54992 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7991 7991 ERR2146944 ERX2203477 ERS1952835 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G2 SAMEA104327857 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327857|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G2 p XY G2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G2_R1.fastq.gz XY_G2_R2.fastq.gz fastq fastq 896890428.0 3559089.0 E MTAB 6077:XY G2 R 0:126 1:126 A:253308278;C:199243055;G:188714589;T:255563791;N:60715 126 126     253308278 199243055 188714589 255563791 60715 ERX2203477 ERS1952835 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87194 0.87088 0.16803 0.17014 0.90358 0.90402 0.51979 0.52116 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7992 7992 ERR2146943 ERX2203476 ERS1952834 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G12 SAMEA104327856 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327856|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G12|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G12|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G12 p XY G12 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G12|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G12_R1.fastq.gz XY_G12_R2.fastq.gz fastq fastq 1125374040.0 4465770.0 E MTAB 6077:XY G12 R 0:126 1:126 A:327288208;C:244109991;G:225102810;T:328783539;N:89492 126 126     327288208 244109991 225102810 328783539 89492 ERX2203476 ERS1952834 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81746 0.81706 0.23392 0.23534 0.90504 0.90542 0.57236 0.5639 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7993 7993 ERR2146942 ERX2203475 ERS1952833 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY G1 SAMEA104327855 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327855|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY G1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY G1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY G1 p XY G1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY G1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_G1_R1.fastq.gz XY_G1_R2.fastq.gz fastq fastq 1044608796.0 4145273.0 E MTAB 6077:XY G1 R 0:126 1:126 A:286857143;C:240643381;G:229200315;T:287832267;N:75690 126 126     286857143 240643381 229200315 287832267 75690 ERX2203475 ERS1952833 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80886 0.80723 0.05734 0.05871 0.95225 0.95195 0.45793 0.45613 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7994 7994 ERR2146941 ERX2203474 ERS1952832 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F5 SAMEA104327854 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327854|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F5 p XY F5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F5_R1.fastq.gz XY_F5_R2.fastq.gz fastq fastq 711136440.0 2821970.0 E MTAB 6077:XY F5 R 0:126 1:126 A:204645320;C:153976075;G:145232961;T:207224102;N:57982 126 126     204645320 153976075 145232961 207224102 57982 ERX2203474 ERS1952832 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81603 0.81552 0.21691 0.21789 0.90546 0.90638 0.5987 0.59269 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7995 7995 ERR2146940 ERX2203473 ERS1952831 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F4 SAMEA104327853 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327853|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F4 p XY F4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F4_R1.fastq.gz XY_F4_R2.fastq.gz fastq fastq 536057172.0 2127211.0 E MTAB 6077:XY F4 R 0:126 1:126 A:150969583;C:119522056;G:112226958;T:153300653;N:37922 126 126     150969583 119522056 112226958 153300653 37922 ERX2203473 ERS1952831 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.73615 0.73496 0.20708 0.20786 0.92772 0.92847 0.63249 0.63336 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7996 7996 ERR2146939 ERX2203472 ERS1952830 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F3 SAMEA104327852 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327852|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F3 p XY F3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F3_R1.fastq.gz XY_F3_R2.fastq.gz fastq fastq 1011342024.0 4013262.0 E MTAB 6077:XY F3 R 0:126 1:126 A:290499568;C:219169313;G:209796959;T:291802472;N:73712 126 126     290499568 219169313 209796959 291802472 73712 ERX2203472 ERS1952830 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87586 0.87628 0.25771 0.25973 0.89895 0.89927 0.50683 0.49896 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7997 7997 ERR2146938 ERX2203471 ERS1952829 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F2 SAMEA104327851 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327851|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F2 p XY F2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F2_R1.fastq.gz XY_F2_R2.fastq.gz fastq fastq 655849908.0 2602579.0 E MTAB 6077:XY F2 R 0:126 1:126 A:185384632;C:145678225;G:137663286;T:187075170;N:48595 126 126     185384632 145678225 137663286 187075170 48595 ERX2203471 ERS1952829 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.74833 0.74693 0.18103 0.18218 0.91977 0.92013 0.59183 0.58697 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7998 7998 ERR2146937 ERX2203470 ERS1952828 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F12 SAMEA104327850 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327850|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F12|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F12|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F12 p XY F12 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F12|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F12_R1.fastq.gz XY_F12_R2.fastq.gz fastq fastq 600785892.0 2384071.0 E MTAB 6077:XY F12 R 0:126 1:126 A:168276037;C:142094582;G:130010572;T:160355651;N:49050 126 126     168276037 142094582 130010572 160355651 49050 ERX2203470 ERS1952828 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.73023 0.72607 0.13773 0.13694 0.92251 0.92194 0.61985 0.64885 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
7999 7999 ERR2146936 ERX2203469 ERS1952827 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY F1 SAMEA104327849 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327849|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY F1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY F1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY F1 p XY F1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY F1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_F1_R1.fastq.gz XY_F1_R2.fastq.gz fastq fastq 997460100.0 3958175.0 E MTAB 6077:XY F1 R 0:126 1:126 A:281570675;C:220590738;G:211855088;T:283372566;N:71033 126 126     281570675 220590738 211855088 283372566 71033 ERX2203469 ERS1952827 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88181 0.88086 0.18012 0.182 0.90408 0.90392 0.46631 0.47014 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8000 8000 ERR2146935 ERX2203468 ERS1952826 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E5 SAMEA104327848 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327848|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E5 p XY E5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E5_R1.fastq.gz XY_E5_R2.fastq.gz fastq fastq 432076680.0 1714590.0 E MTAB 6077:XY E5 R 0:126 1:126 A:121965441;C:95536720;G:89987057;T:124553150;N:34312 126 126     121965441 95536720 89987057 124553150 34312 ERX2203468 ERS1952826 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.76796 0.76857 0.18379 0.18457 0.92285 0.92273 0.67279 0.67103 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8001 8001 ERR2146934 ERX2203467 ERS1952825 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E4 SAMEA104327847 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327847|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E4 p XY E4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E4_R1.fastq.gz XY_E4_R2.fastq.gz fastq fastq 936553212.0 3716481.0 E MTAB 6077:XY E4 R 0:126 1:126 A:263117120;C:208551987;G:198259840;T:266556826;N:67439 126 126     263117120 208551987 198259840 266556826 67439 ERX2203467 ERS1952825 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.86272 0.86395 0.18092 0.18393 0.91963 0.92009 0.48049 0.47567 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8002 8002 ERR2146933 ERX2203466 ERS1952824 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E3 SAMEA104327846 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327846|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E3 p XY E3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E3_R1.fastq.gz XY_E3_R2.fastq.gz fastq fastq 722298276.0 2866263.0 E MTAB 6077:XY E3 R 0:126 1:126 A:205661883;C:158846036;G:151046574;T:206691454;N:52329 126 126     205661883 158846036 151046574 206691454 52329 ERX2203466 ERS1952824 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.8281 0.82888 0.227 0.22808 0.91151 0.91224 0.57671 0.56941 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8003 8003 ERR2146932 ERX2203465 ERS1952823 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E2 SAMEA104327845 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327845|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E2 p XY E2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E2_R1.fastq.gz XY_E2_R2.fastq.gz fastq fastq 898576812.0 3565781.0 E MTAB 6077:XY E2 R 0:126 1:126 A:253404969;C:199204646;G:190410032;T:255492244;N:64921 126 126     253404969 199204646 190410032 255492244 64921 ERX2203465 ERS1952823 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88647 0.88521 0.17368 0.17572 0.90567 0.9066 0.43691 0.51405 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8004 8004 ERR2146931 ERX2203464 ERS1952822 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E12 SAMEA104327844 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327844|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E12|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E12|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E12 p XY E12 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E12|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E12_R1.fastq.gz XY_E12_R2.fastq.gz fastq fastq 1097535852.0 4355301.0 E MTAB 6077:XY E12 R 0:126 1:126 A:300243354;C:263382681;G:238183855;T:295635494;N:90468 126 126     300243354 263382681 238183855 295635494 90468 ERX2203464 ERS1952822 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.61006 0.606 0.14083 0.13917 0.92001 0.92078 0.6148 0.61556 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8005 8005 ERR2146930 ERX2203463 ERS1952821 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY E1 SAMEA104327843 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327843|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY E1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY E1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY E1 p XY E1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY E1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_E1_R1.fastq.gz XY_E1_R2.fastq.gz fastq fastq 746685072.0 2963036.0 E MTAB 6077:XY E1 R 0:126 1:126 A:211710079;C:165593782;G:155759006;T:213566590;N:55615 126 126     211710079 165593782 155759006 213566590 55615 ERX2203463 ERS1952821 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.75556 0.75733 0.19795 0.20011 0.91632 0.91672 0.60899 0.60441 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8006 8006 ERR2146929 ERX2203462 ERS1952820 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D5 SAMEA104327842 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327842|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D5 p XY D5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D5_R1.fastq.gz XY_D5_R2.fastq.gz fastq fastq 660547188.0 2621219.0 E MTAB 6077:XY D5 R 0:126 1:126 A:188043609;C:145685742;G:136282398;T:190482268;N:53171 126 126     188043609 145685742 136282398 190482268 53171 ERX2203462 ERS1952820 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81152 0.81307 0.24567 0.24771 0.9152 0.9162 0.62955 0.42909 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8007 8007 ERR2146928 ERX2203461 ERS1952819 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D4 SAMEA104327841 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327841|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D4 p XY D4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D4_R1.fastq.gz XY_D4_R2.fastq.gz fastq fastq 837525276.0 3323513.0 E MTAB 6077:XY D4 R 0:126 1:126 A:236023482;C:186075815;G:177194660;T:238169798;N:61521 126 126     236023482 186075815 177194660 238169798 61521 ERX2203461 ERS1952819 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.89213 0.89192 0.12147 0.12558 0.9083 0.91062 0.51202 0.51681 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8008 8008 ERR2146927 ERX2203460 ERS1952818 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D3 SAMEA104327840 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327840|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D3 p XY D3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D3_R1.fastq.gz XY_D3_R2.fastq.gz fastq fastq 929369952.0 3687976.0 E MTAB 6077:XY D3 R 0:126 1:126 A:268574709;C:200604190;G:190405734;T:269719266;N:66053 126 126     268574709 200604190 190405734 269719266 66053 ERX2203460 ERS1952818 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85669 0.85766 0.26039 0.26737 0.91948 0.92113 0.52044 0.51927 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8009 8009 ERR2146926 ERX2203459 ERS1952817 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D2 SAMEA104327839 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327839|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D2 p XY D2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D2_R1.fastq.gz XY_D2_R2.fastq.gz fastq fastq 689447808.0 2735904.0 E MTAB 6077:XY D2 R 0:126 1:126 A:196263920;C:152901761;G:142462888;T:197767203;N:52036 126 126     196263920 152901761 142462888 197767203 52036 ERX2203459 ERS1952817 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.81038 0.81259 0.1659 0.16893 0.91587 0.91758 0.6298 0.6291 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8010 8010 ERR2146925 ERX2203458 ERS1952816 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY D1 SAMEA104327838 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327838|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY D1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY D1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY D1 p XY D1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY D1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_D1_R1.fastq.gz XY_D1_R2.fastq.gz fastq fastq 1074802428.0 4265089.0 E MTAB 6077:XY D1 R 0:126 1:126 A:295122432;C:249510143;G:233653745;T:296436723;N:79385 126 126     295122432 249510143 233653745 296436723 79385 ERX2203458 ERS1952816 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88767 0.88989 0.14758 0.15226 0.90096 0.90254 0.50951 0.50804 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8011 8011 ERR2146924 ERX2203457 ERS1952815 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C5 SAMEA104327837 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327837|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C5 p XY C5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C5_R1.fastq.gz XY_C5_R2.fastq.gz fastq fastq 763663068.0 3030409.0 E MTAB 6077:XY C5 R 0:126 1:126 A:218783973;C:168189496;G:157662131;T:218961836;N:65632 126 126     218783973 168189496 157662131 218961836 65632 ERX2203457 ERS1952815 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.78078 0.78189 0.22088 0.22216 0.92429 0.92476 0.6094 0.60799 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8012 8012 ERR2146923 ERX2203456 ERS1952814 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C4 SAMEA104327836 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327836|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C4 p XY C4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C4_R1.fastq.gz XY_C4_R2.fastq.gz fastq fastq 628535880.0 2494190.0 E MTAB 6077:XY C4 R 0:126 1:126 A:178148646;C:141113691;G:131448439;T:177778949;N:46155 126 126     178148646 141113691 131448439 177778949 46155 ERX2203456 ERS1952814 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.73091 0.73106 0.16098 0.16176 0.9303 0.93048 0.75666 0.75542 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8013 8013 ERR2146922 ERX2203455 ERS1952813 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C3 SAMEA104327835 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327835|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C3 p XY C3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C3_R2.fastq.gz XY_C3_R1.fastq.gz fastq fastq 1143928548.0 4539399.0 E MTAB 6077:XY C3 R 0:126 1:126 A:333818058;C:244426168;G:233177976;T:332420812;N:85534 126 126     333818058 244426168 233177976 332420812 85534 ERX2203455 ERS1952813 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85792 0.85722 0.28359 0.28517 0.91725 0.91703 0.49423 0.49677 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8014 8014 ERR2146921 ERX2203454 ERS1952812 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C2 SAMEA104327834 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327834|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C2 p XY C2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C2_R1.fastq.gz XY_C2_R2.fastq.gz fastq fastq 1109822868.0 4404059.0 E MTAB 6077:XY C2 R 0:126 1:126 A:315349917;C:244964515;G:234207255;T:315223120;N:78061 126 126     315349917 244964515 234207255 315223120 78061 ERX2203454 ERS1952812 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.89018 0.88918 0.18419 0.18554 0.90617 0.90698 0.51664 0.5151 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8015 8015 ERR2146920 ERX2203453 ERS1952811 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY C1 SAMEA104327833 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327833|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY C1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY C1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY C1 p XY C1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY C1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_C1_R1.fastq.gz XY_C1_R2.fastq.gz fastq fastq 1023038100.0 4059675.0 E MTAB 6077:XY C1 R 0:126 1:126 A:289423372;C:226901377;G:218604509;T:288035093;N:73749 126 126     289423372 226901377 218604509 288035093 73749 ERX2203453 ERS1952811 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.8847 0.88446 0.09904 0.10044 0.91187 0.91273 0.50218 0.50146 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8016 8016 ERR2146919 ERX2203452 ERS1952810 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B5 SAMEA104327832 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327832|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B5 p XY B5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B5_R1.fastq.gz XY_B5_R2.fastq.gz fastq fastq 1157792580.0 4594415.0 E MTAB 6077:XY B5 R 0:126 1:126 A:332377265;C:250239737;G:240957301;T:334125637;N:92640 126 126     332377265 250239737 240957301 334125637 92640 ERX2203452 ERS1952810 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88876 0.88961 0.2351 0.23604 0.89509 0.89485 0.43495 0.50926 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8017 8017 ERR2146918 ERX2203451 ERS1952809 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B4 SAMEA104327831 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327831|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B4 p XY B4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B4_R1.fastq.gz XY_B4_R2.fastq.gz fastq fastq 1210007988.0 4801619.0 E MTAB 6077:XY B4 R 0:126 1:126 A:347394878;C:262886787;G:250224660;T:349411084;N:90579 126 126     347394878 262886787 250224660 349411084 90579 ERX2203451 ERS1952809 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.88955 0.88989 0.24237 0.24323 0.90794 0.90735 0.49869 0.49848 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8018 8018 ERR2146917 ERX2203450 ERS1952808 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B3 SAMEA104327830 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327830|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B3 p XY B3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B3_R1.fastq.gz XY_B3_R2.fastq.gz fastq fastq 1176133896.0 4667198.0 E MTAB 6077:XY B3 R 0:126 1:126 A:335919936;C:258107071;G:247773671;T:334248508;N:84710 126 126     335919936 258107071 247773671 334248508 84710 ERX2203450 ERS1952808 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.84653 0.84743 0.19732 0.19994 0.92178 0.92186 0.51636 0.48599 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8019 8019 ERR2146916 ERX2203449 ERS1952807 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B2 SAMEA104327829 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327829|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B2 p XY B2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B2_R1.fastq.gz XY_B2_R2.fastq.gz fastq fastq 690569208.0 2740354.0 E MTAB 6077:XY B2 R 0:126 1:126 A:198979532;C:149863253;G:142526360;T:199148360;N:51703 126 126     198979532 149863253 142526360 199148360 51703 ERX2203449 ERS1952807 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80432 0.80459 0.18079 0.18089 0.92368 0.92395 0.66657 0.66039 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8020 8020 ERR2146915 ERX2203448 ERS1952806 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY B1 SAMEA104327828 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327828|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY B1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY B1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY B1 p XY B1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY B1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_B1_R1.fastq.gz XY_B1_R2.fastq.gz fastq fastq 1099919772.0 4364761.0 E MTAB 6077:XY B1 R 0:126 1:126 A:320782014;C:232447890;G:224643364;T:321968049;N:78455 126 126     320782014 232447890 224643364 321968049 78455 ERX2203448 ERS1952806 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.86247 0.863 0.30591 0.30783 0.90155 0.90199 0.52033 0.52673 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8021 8021 ERR2146914 ERX2203447 ERS1952805 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A6 SAMEA104327827 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327827|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:21Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A6|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A6|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A6 p XY A6 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A6|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A6_R1.fastq.gz XY_A6_R2.fastq.gz fastq fastq 512695008.0 2034504.0 E MTAB 6077:XY A6 R 0:126 1:126 A:142817402;C:116839066;G:108882918;T:144112206;N:43416 126 126     142817402 116839066 108882918 144112206 43416 ERX2203447 ERS1952805 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.68622 0.68692 0.14751 0.14781 0.93825 0.93906 0.74578 0.74484 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8022 8022 ERR2146913 ERX2203446 ERS1952804 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A5 SAMEA104327826 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327826|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A5|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A5|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A5 p XY A5 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A5|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A5_R1.fastq.gz XY_A5_R2.fastq.gz fastq fastq 781978176.0 3103088.0 E MTAB 6077:XY A5 R 0:126 1:126 A:213601286;C:183203675;G:166424027;T:218688044;N:61144 126 126     213601286 183203675 166424027 218688044 61144 ERX2203446 ERS1952804 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.70128 0.70185 0.23891 0.24003 0.92316 0.92305 0.5932 0.58961 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8023 8023 ERR2146912 ERX2203445 ERS1952803 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A4 SAMEA104327825 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327825|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A4|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A4|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A4 p XY A4 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A4|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A4_R1.fastq.gz XY_A4_R2.fastq.gz fastq fastq 963604152.0 3823826.0 E MTAB 6077:XY A4 R 0:126 1:126 A:274833754;C:210148026;G:199842855;T:278711035;N:68482 126 126     274833754 210148026 199842855 278711035 68482 ERX2203445 ERS1952803 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.85087 0.85235 0.23408 0.23608 0.90278 0.90423 0.52332 0.51671 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8024 8024 ERR2146911 ERX2203444 ERS1952802 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A3 SAMEA104327824 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327824|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A3|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A3 p XY A3 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A3|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A3_R1.fastq.gz XY_A3_R2.fastq.gz fastq fastq 659648052.0 2617651.0 E MTAB 6077:XY A3 R 0:126 1:126 A:189357994;C:143277472;G:136135683;T:190829498;N:47405 126 126     189357994 143277472 136135683 190829498 47405 ERX2203444 ERS1952802 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.79506 0.79671 0.18692 0.18896 0.92529 0.92644 0.60886 0.60533 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8025 8025 ERR2146910 ERX2203443 ERS1952801 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A2 SAMEA104327823 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327823|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A2|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A2|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A2 p XY A2 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A2|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A2_R1.fastq.gz XY_A2_R2.fastq.gz fastq fastq 1128768228.0 4479239.0 E MTAB 6077:XY A2 R 0:126 1:126 A:308213498;C:261633998;G:246008259;T:312829796;N:82677 126 126     308213498 261633998 246008259 312829796 82677 ERX2203443 ERS1952801 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.87413 0.87359 0.16944 0.17295 0.89631 0.89741 0.5001 0.49423 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8026 8026 ERR2146909 ERX2203442 ERS1952800 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY A1 SAMEA104327822 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327822|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY A1|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY A1|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY A1 p XY A1 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY A1|Experimental Factor: block:batch 2 2015 04 08 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_A1_R1.fastq.gz XY_A1_R2.fastq.gz fastq fastq 788118660.0 3127455.0 E MTAB 6077:XY A1 R 0:126 1:126 A:224956393;C:172218956;G:163283909;T:227604645;N:54757 126 126     224956393 172218956 163283909 227604645 54757 ERX2203442 ERS1952800 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.80149 0.80336 0.21497 0.21728 0.91088 0.91161 0.5548 0.55294 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures
8027 8027 ERR2146908 ERX2203441 ERS1952799 ERP104575 PRJEB22861 Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E-MTAB-6077 Transcriptome Analysis Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer 10.7554/eLife.03848. Specifically the 2.7 kb Mouse Smarcd3 F6 sequence chr5: 24113559 24116342 from mm9 assembly was sub cloned from a gateway entry vector into the Zebrafish Enhancer Detection ZED. Tol2 mediated transgenesis was performed and stable lines were created. The Smarcd3 F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3 F6:EGFPhsc70 embryos were dissociated at 10 hpf for fluorescent activated cell sorting FACS to collect GFP+ cells. Single cell cDNA libraries were prepared using Fluidgim C1 system Fluidgim PN 100 7168 Rev. B1. 96 single cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells number of genes detected > 2000 were kept for clustering analysis. For the tube control experiments we performed mRNA seq on 4000 cells from the same embryo batches as the scRNA seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP comparison. Libraries were made following the Fluidgim C1 mRNA seq tube control protocol Fluidgim PN 100 7168 Rev. B1. Polyadenylated mRNA was captured by Oligo dT primers and PCR amplified post reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair end sequenced on the Illumina HiSeq 2500 platform. ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2017 10 03   Protocols: Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Si… XY H9 SAMEA104327821 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto ENA first public:2018 08 20|ENA last update:2017 10 03|External Id:SAMEA104327821|INSDC center alias:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC center name:Genetics and Genome Biology Program Hospital for Sick Children Toronto Canada; Department of Molecular Genetics University of Toronto|INSDC first public:2018 08 20T17:01:55Z|INSDC last update:2017 10 03T09:08:20Z|INSDC status:public|Submitter Id:E MTAB 6077:XY H9|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:gastrula bud|genotype:Smarcd3 F6:EGFPhsc70|organism part:whole organism|phenotype:GFP postitive|post analysis well quantity:pass|sample name:E MTAB 6077:XY H9|well information:single cell                 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf E MTAB 6077:XY H9 p XY H9 p Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf Around 100 TgSmarcd3 F6: EGFP embryos were dechorionated with pronase Sigma Cat# 11459643001 and transferred to a 1.5mL Eppendorf tube when they reached bud stage. post incubated in 200ul calcium free Ringer solution 116 mM NaCl 2.6mM KCl 5mM HEPE pH 7.0 for 5 min embryos were transferred into a 24 well plate filled with 500 ul TrypLE solution GIBOCO TrypLE Express Enzyme cat #: 12604 013 for dissociation at room temperature. Embryos were gently homogenized every 5min with P1000 tips. Dissociation was monitored under a dissection scope until most cells were in single cell suspension. The cell suspension was transferred into 200ul ice cold FBS to stop the reaction. Cells were centrifuged at 300g for 3min at 4 degree and washed with 500 ul ice cold DMEM with 10% FBS before resuspended in 500 ul ice cold DMEM with 1% FBS. Right before the FACS cells were filtered through a 40um strainer and DAPI was added at a concentration of 5 ug/ml to exclude dead cells. FACS was performed on Beckman Coulter Mo Flo XDP or Mo Flo Astrios sorter with a 100um nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Cell doublets and dead cells were excluded based on forward scatter side scatter and DAPI channel. GFP+ and GFP cells were sorted into 100% FBS and subjected to RNA seq or procedures immediately once sorting finished. 30 000 50 000 GFP+ cells and 100 000 GFP cells were usually collected in one sort. Single cell cDNA libraries were prepared using Fluidgim C1 system. post FACS GFP positive cells were washed twice in DMEM with 3%FBS and filtered through a 40um cell strainer. Cells were adjusted to a concentration of 400 500 cells/ul before mixed with C1 suspension solution at a 5.2:4.8 ratio. Then 10ul final cell mixture was loaded into a C1 medium or small Chip. Cell capture was examined under a microscope and only wells with a single cell captured were included in library construction. Reverse transcription PCR amplification and cDNA harvesting were performed as per manufactures instruction. Since the o… Experimental Factor: phenotype:GFP postitive|Experimental Factor: single cell identifier:XY H9|Experimental Factor: block:batch 1 2015 03 25 RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>252</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>127</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP104575 Illumina HiSeq 2500 paired end sequencing; Determining single cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hpf ENA FIRST PUBLIC:2018 08 20|ENA LAST UPDATE:2018 11 16 XY_H9_R1.fastq.gz XY_H9_R2.fastq.gz fastq fastq 807594228.0 3204739.0 E MTAB 6077:XY H9 R 0:126 1:126 A:218595449;C:187636861;G:181518262;T:219784313;N:59343 126 126     218595449 187636861 181518262 219784313 59343 ERX2203441 ERS1952799 ERA1108167 Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto|European Nucleotide Archive 2 0.78544 0.78636 0.05597 0.05666 0.93269 0.93221 0.43413 0.42718 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a nextera sc_generic single_cell_generic generic-scrnaseq-only   Canada 2017-10-03 Gastrula Embryo Whole Organism All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;