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
4162,ERR1620593,ERX1690958,ERS1343646,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#95,SAMEA4432197,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432197|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:17|Submitter Id:E MTAB 46171473686057:LCK 9#95|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31714|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1238|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#95|side scatter:36|single cell well quality:good quality|well:H11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#95 p,LCK 9#95 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31714:forward scatter|Experimental Factor: 36:side scatter|Experimental Factor: 1238:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_95_1.fq.gz LCK_9_95_2.fq.gz,fastq fastq,474750.0,1899.0,E MTAB 46171473686057:LCK 9 95 ,0:125 1:125,A:136505;C:125919;G:96114;T:115865;N:347,125,125,,,136505,125919,96114,115865,347,ERX1690958,ERS1343646,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.64665,0.58253,0.06713,0.17475,0.99697,0.99918,0.62883,0.60975,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4163,ERR1620592,ERX1690957,ERS1343645,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#94,SAMEA4432196,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432196|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:9|Submitter Id:E MTAB 46171473686057:LCK 9#94|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:25724|genotype:heterozygous Tglck:EGFP|gfp fluorescence:725|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#94|side scatter:35|single cell well quality:good quality|well:H10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#94 p,LCK 9#94 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 25724:forward scatter|Experimental Factor: 35:side scatter|Experimental Factor: 725:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_94_1.fq.gz LCK_9_94_2.fq.gz,fastq fastq,532198750.0,2128795.0,E MTAB 46171473686057:LCK 9 94 ,0:125 1:125,A:157501334;C:111259905;G:101266460;T:161502762;N:668289,125,125,,,157501334,111259905,101266460,161502762,668289,ERX1690957,ERS1343645,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.75986,0.75328,0.2661,0.26681,0.98614,0.98658,0.57082,0.58891,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4164,ERR1620591,ERX1690956,ERS1343644,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#93,SAMEA4432195,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432195|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:8|Submitter Id:E MTAB 46171473686057:LCK 9#93|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36702|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1420|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#93|side scatter:60|single cell well quality:good quality|well:H9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#93 p,LCK 9#93 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36702:forward scatter|Experimental Factor: 60:side scatter|Experimental Factor: 1420:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_93_1.fq.gz LCK_9_93_2.fq.gz,fastq fastq,1015072000.0,4060288.0,E MTAB 46171473686057:LCK 9 93 ,0:125 1:125,A:314298041;C:203125138;G:177015908;T:319243223;N:1389690,125,125,,,314298041,203125138,177015908,319243223,1389690,ERX1690956,ERS1343644,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.80228,0.79924,0.32196,0.32224,0.98638,0.98652,0.50107,0.5056,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4165,ERR1620590,ERX1690955,ERS1343643,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#92,SAMEA4432194,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432194|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:10|Submitter Id:E MTAB 46171473686057:LCK 9#92|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30554|genotype:heterozygous Tglck:EGFP|gfp fluorescence:582|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#92|side scatter:42|single cell well quality:good quality|well:H8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#92 p,LCK 9#92 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30554:forward scatter|Experimental Factor: 42:side scatter|Experimental Factor: 582:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_92_1.fq LCK_9_92_2.fq,fastq fastq,438701250.0,1754805.0,E MTAB 46171473686057:LCK 9 92 ,0:125 1:125,A:132899983;C:89606484;G:80513081;T:135111829;N:569873,125,125,,,132899983,89606484,80513081,135111829,569873,ERX1690955,ERS1343643,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79916,0.7974,0.36491,0.36755,0.98547,0.98575,0.54153,0.52254,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4166,ERR1620589,ERX1690954,ERS1343642,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#91,SAMEA4432193,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432193|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:22|Submitter Id:E MTAB 46171473686057:LCK 9#91|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:43052|genotype:heterozygous Tglck:EGFP|gfp fluorescence:761|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#91|side scatter:71|single cell well quality:good quality|well:H7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#91 p,LCK 9#91 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 43052:forward scatter|Experimental Factor: 71:side scatter|Experimental Factor: 761:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_91_1.fq.gz LCK_9_91_2.fq.gz,fastq fastq,19000.0,76.0,E MTAB 46171473686057:LCK 9 91 ,0:125 1:125,A:4469;C:6507;G:4937;T:3087;N:0,125,125,,,4469,6507,4937,3087,0,ERX1690954,ERS1343642,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.7353,0.5,0.0147,0.5,0.99953,1.0,0.34693,,125,125,B,T,mate2 technical by mapping diff,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4167,ERR1620588,ERX1690953,ERS1343641,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#90,SAMEA4432192,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432192|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:21|Submitter Id:E MTAB 46171473686057:LCK 9#90|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39430|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1108|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#90|side scatter:44|single cell well quality:good quality|well:H6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#90 p,LCK 9#90 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39430:forward scatter|Experimental Factor: 44:side scatter|Experimental Factor: 1108:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_90_1.fq.gz LCK_9_90_2.fq.gz,fastq fastq,220510750.0,882043.0,E MTAB 46171473686057:LCK 9 90 ,0:125 1:125,A:63250451;C:48173039;G:44278169;T:64541378;N:267713,125,125,,,63250451,48173039,44278169,64541378,267713,ERX1690953,ERS1343641,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.74324,0.73809,0.23917,0.24021,0.98636,0.98742,0.59527,0.61371,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4168,ERR1620587,ERX1690952,ERS1343640,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#9,SAMEA4432191,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432191|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:30|Submitter Id:E MTAB 46171473686057:LCK 9#9|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40567|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1083|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#9|side scatter:48|single cell well quality:good quality|well:A9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#9 p,LCK 9#9 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40567:forward scatter|Experimental Factor: 48:side scatter|Experimental Factor: 1083:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_9_1.fq LCK_9_9_2.fq,fastq fastq,350162000.0,1400648.0,E MTAB 46171473686057:LCK 9 9 ,0:125 1:125,A:99955822;C:77407427;G:70474543;T:101918554;N:405654,125,125,,,99955822,77407427,70474543,101918554,405654,ERX1690952,ERS1343640,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.75741,0.75069,0.24338,0.24525,0.98474,0.98522,0.55927,0.44507,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4169,ERR1620586,ERX1690951,ERS1343639,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#89,SAMEA4432190,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432190|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:13|Submitter Id:E MTAB 46171473686057:LCK 9#89|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30767|genotype:heterozygous Tglck:EGFP|gfp fluorescence:898|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#89|side scatter:74|single cell well quality:good quality|well:H5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#89 p,LCK 9#89 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30767:forward scatter|Experimental Factor: 74:side scatter|Experimental Factor: 898:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_89_1.fq LCK_9_89_2.fq,fastq fastq,130313750.0,521255.0,E MTAB 46171473686057:LCK 9 89 ,0:125 1:125,A:36426425;C:29173883;G:27225328;T:37343854;N:144260,125,125,,,36426425,29173883,27225328,37343854,144260,ERX1690951,ERS1343639,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.75406,0.7501,0.23832,0.24,0.98488,0.98565,0.60407,0.61002,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4170,ERR1620585,ERX1690950,ERS1343638,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#88,SAMEA4432189,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432189|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:not available|Submitter Id:E MTAB 46171473686057:LCK 9#88|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:not available|genotype:heterozygous Tglck:EGFP|gfp fluorescence:not available|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#88|side scatter:not available|single cell well quality:good quality|well:H4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#88 p,LCK 9#88 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: not available:forward scatter|Experimental Factor: not available:side scatter|Experimental Factor: not available:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_88_1.fq LCK_9_88_2.fq,fastq fastq,157769000.0,631076.0,E MTAB 46171473686057:LCK 9 88 ,0:125 1:125,A:44320565;C:35472215;G:32345382;T:45452971;N:177867,125,125,,,44320565,35472215,32345382,45452971,177867,ERX1690950,ERS1343638,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.71628,0.71191,0.20717,0.20803,0.98792,0.98825,0.55812,0.55103,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4171,ERR1620584,ERX1690949,ERS1343637,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#87,SAMEA4432188,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432188|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:not available|Submitter Id:E MTAB 46171473686057:LCK 9#87|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:not available|genotype:heterozygous Tglck:EGFP|gfp fluorescence:not available|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#87|side scatter:not available|single cell well quality:good quality|well:H3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#87 p,LCK 9#87 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: not available:forward scatter|Experimental Factor: not available:side scatter|Experimental Factor: not available:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_87_1.fq.gz LCK_9_87_2.fq.gz,fastq fastq,197086000.0,788344.0,E MTAB 46171473686057:LCK 9 87 ,0:125 1:125,A:55271572;C:44060136;G:40899852;T:56618046;N:236394,125,125,,,55271572,44060136,40899852,56618046,236394,ERX1690949,ERS1343637,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78208,0.78182,0.21141,0.21368,0.98202,0.98265,0.5754,0.57068,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4172,ERR1620583,ERX1690948,ERS1343636,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#86,SAMEA4432187,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432187|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:not available|Submitter Id:E MTAB 46171473686057:LCK 9#86|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:not available|genotype:heterozygous Tglck:EGFP|gfp fluorescence:not available|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#86|side scatter:not available|single cell well quality:good quality|well:H2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#86 p,LCK 9#86 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: not available:forward scatter|Experimental Factor: not available:side scatter|Experimental Factor: not available:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_86_1.fq.gz LCK_9_86_2.fq.gz,fastq fastq,224629000.0,898516.0,E MTAB 46171473686057:LCK 9 86 ,0:125 1:125,A:61770403;C:51450915;G:47900404;T:63262980;N:244298,125,125,,,61770403,51450915,47900404,63262980,244298,ERX1690948,ERS1343636,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76028,0.75975,0.19225,0.19404,0.98668,0.98689,0.61927,0.61793,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4173,ERR1620582,ERX1690947,ERS1343635,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#85,SAMEA4432186,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432186|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:not available|Submitter Id:E MTAB 46171473686057:LCK 9#85|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:not available|genotype:heterozygous Tglck:EGFP|gfp fluorescence:not available|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#85|side scatter:not available|single cell well quality:good quality|well:H1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#85 p,LCK 9#85 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: not available:forward scatter|Experimental Factor: not available:side scatter|Experimental Factor: not available:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_85_1.fq.gz LCK_9_85_2.fq.gz,fastq fastq,199000500.0,796002.0,E MTAB 46171473686057:LCK 9 85 ,0:125 1:125,A:55193275;C:45423281;G:41496742;T:56668394;N:218808,125,125,,,55193275,45423281,41496742,56668394,218808,ERX1690947,ERS1343635,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.74084,0.73899,0.20224,0.20349,0.9867,0.98687,0.59679,0.59056,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4174,ERR1620581,ERX1690946,ERS1343634,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#84,SAMEA4432185,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432185|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:18|Submitter Id:E MTAB 46171473686057:LCK 9#84|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35715|genotype:heterozygous Tglck:EGFP|gfp fluorescence:873|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#84|side scatter:36|single cell well quality:good quality|well:G12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#84 p,LCK 9#84 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35715:forward scatter|Experimental Factor: 36:side scatter|Experimental Factor: 873:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_84_1.fq.gz LCK_9_84_2.fq.gz,fastq fastq,28062500.0,112250.0,E MTAB 46171473686057:LCK 9 84 ,0:125 1:125,A:7032031;C:7142576;G:6553430;T:7301171;N:33292,125,125,,,7032031,7142576,6553430,7301171,33292,ERX1690946,ERS1343634,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.00187,0.00012,0.00013,7e-05,0.99862,0.99993,0.63432,0.66666,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4175,ERR1620580,ERX1690945,ERS1343633,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#83,SAMEA4432184,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432184|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:37|Submitter Id:E MTAB 46171473686057:LCK 9#83|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40728|genotype:heterozygous Tglck:EGFP|gfp fluorescence:938|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#83|side scatter:44|single cell well quality:good quality|well:G11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#83 p,LCK 9#83 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40728:forward scatter|Experimental Factor: 44:side scatter|Experimental Factor: 938:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_83_1.fq.gz LCK_9_83_2.fq.gz,fastq fastq,52189500.0,208758.0,E MTAB 46171473686057:LCK 9 83 ,0:125 1:125,A:14138371;C:12080023;G:11427877;T:14490075;N:53154,125,125,,,14138371,12080023,11427877,14490075,53154,ERX1690945,ERS1343633,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.69436,0.6858,0.1889,0.18939,0.97973,0.98269,0.55341,0.54981,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4176,ERR1620579,ERX1690944,ERS1343632,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#82,SAMEA4432183,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432183|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:25|Submitter Id:E MTAB 46171473686057:LCK 9#82|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33459|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1082|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#82|side scatter:48|single cell well quality:good quality|well:G10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#82 p,LCK 9#82 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33459:forward scatter|Experimental Factor: 48:side scatter|Experimental Factor: 1082:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_82_1.fq LCK_9_82_2.fq,fastq fastq,58284250.0,233137.0,E MTAB 46171473686057:LCK 9 82 ,0:125 1:125,A:15859573;C:13476821;G:12691537;T:16188954;N:67365,125,125,,,15859573,13476821,12691537,16188954,67365,ERX1690944,ERS1343632,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.75001,0.74552,0.18627,0.18864,0.9822,0.98648,0.60937,0.60999,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4177,ERR1620578,ERX1690943,ERS1343631,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#81,SAMEA4432182,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432182|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:33|Submitter Id:E MTAB 46171473686057:LCK 9#81|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31707|genotype:heterozygous Tglck:EGFP|gfp fluorescence:810|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#81|side scatter:38|single cell well quality:good quality|well:G9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#81 p,LCK 9#81 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31707:forward scatter|Experimental Factor: 38:side scatter|Experimental Factor: 810:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_81_1.fq LCK_9_81_2.fq,fastq fastq,68489250.0,273957.0,E MTAB 46171473686057:LCK 9 81 ,0:125 1:125,A:19370861;C:15351988;G:14127103;T:19568110;N:71188,125,125,,,19370861,15351988,14127103,19568110,71188,ERX1690943,ERS1343631,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.69077,0.68342,0.23054,0.2327,0.98309,0.98662,0.52377,0.52621,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4178,ERR1620577,ERX1690942,ERS1343630,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#80,SAMEA4432181,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432181|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:67|Submitter Id:E MTAB 46171473686057:LCK 9#80|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:29352|genotype:heterozygous Tglck:EGFP|gfp fluorescence:830|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#80|side scatter:31|single cell well quality:good quality|well:G8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#80 p,LCK 9#80 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 29352:forward scatter|Experimental Factor: 31:side scatter|Experimental Factor: 830:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_80_1.fq LCK_9_80_2.fq,fastq fastq,86685500.0,346742.0,E MTAB 46171473686057:LCK 9 80 ,0:125 1:125,A:23598476;C:20045959;G:18812137;T:24137061;N:91867,125,125,,,23598476,20045959,18812137,24137061,91867,ERX1690942,ERS1343630,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.55748,0.55152,0.19719,0.19946,0.98634,0.98839,0.59414,0.599,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4179,ERR1620576,ERX1690941,ERS1343629,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#8,SAMEA4432180,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432180|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:19|Submitter Id:E MTAB 46171473686057:LCK 9#8|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35145|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1250|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#8|side scatter:42|single cell well quality:good quality|well:A8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#8 p,LCK 9#8 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35145:forward scatter|Experimental Factor: 42:side scatter|Experimental Factor: 1250:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_8_1.fq LCK_9_8_2.fq,fastq fastq,238347000.0,953388.0,E MTAB 46171473686057:LCK 9 8 ,0:125 1:125,A:65782361;C:54488168;G:50601970;T:67189207;N:285294,125,125,,,65782361,54488168,50601970,67189207,285294,ERX1690941,ERS1343629,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.65518,0.64464,0.18978,0.18905,0.98693,0.98748,0.52754,0.56709,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4180,ERR1620575,ERX1690940,ERS1343628,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#79,SAMEA4432179,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432179|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#79|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:41645|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1623|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#79|side scatter:61|single cell well quality:good quality|well:G7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#79 p,LCK 9#79 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 41645:forward scatter|Experimental Factor: 61:side scatter|Experimental Factor: 1623:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_79_1.fq.gz LCK_9_79_2.fq.gz,fastq fastq,23250.0,93.0,E MTAB 46171473686057:LCK 9 79 ,0:125 1:125,A:5549;C:8313;G:5681;T:3703;N:4,125,125,,,5549,8313,5681,3703,4,ERX1690940,ERS1343628,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76389,0.0,0.04166,0.0,0.99937,1.0,0.63461,,125,125,B,T,mate2 technical by mapping diff,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4181,ERR1620574,ERX1690939,ERS1343627,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#78,SAMEA4432178,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432178|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:18|Submitter Id:E MTAB 46171473686057:LCK 9#78|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31337|genotype:heterozygous Tglck:EGFP|gfp fluorescence:585|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#78|side scatter:31|single cell well quality:good quality|well:G6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#78 p,LCK 9#78 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31337:forward scatter|Experimental Factor: 31:side scatter|Experimental Factor: 585:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_78_1.fq LCK_9_78_2.fq,fastq fastq,68756500.0,275026.0,E MTAB 46171473686057:LCK 9 78 ,0:125 1:125,A:18812651;C:15763743;G:14907361;T:19199426;N:73319,125,125,,,18812651,15763743,14907361,19199426,73319,ERX1690939,ERS1343627,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76332,0.76198,0.15922,0.16204,0.9808,0.9833,0.47909,0.55176,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4182,ERR1620573,ERX1690938,ERS1343626,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#77,SAMEA4432177,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432177|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#77|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30123|genotype:heterozygous Tglck:EGFP|gfp fluorescence:603|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#77|side scatter:50|single cell well quality:good quality|well:G5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#77 p,LCK 9#77 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30123:forward scatter|Experimental Factor: 50:side scatter|Experimental Factor: 603:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_77_1.fq.gz LCK_9_77_2.fq.gz,fastq fastq,42395500.0,169582.0,E MTAB 46171473686057:LCK 9 77 ,0:125 1:125,A:11103947;C:10179905;G:9662627;T:11403946;N:45075,125,125,,,11103947,10179905,9662627,11403946,45075,ERX1690938,ERS1343626,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.38171,0.38131,0.16861,0.1712,0.98293,0.98498,0.57433,0.58312,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4183,ERR1620572,ERX1690937,ERS1343625,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#73,SAMEA4432176,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432176|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:27|Submitter Id:E MTAB 46171473686057:LCK 9#73|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:26913|genotype:heterozygous Tglck:EGFP|gfp fluorescence:986|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#73|side scatter:32|single cell well quality:good quality|well:G1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#73 p,LCK 9#73 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 26913:forward scatter|Experimental Factor: 32:side scatter|Experimental Factor: 986:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_73_1.fq LCK_9_73_2.fq,fastq fastq,37170250.0,148681.0,E MTAB 46171473686057:LCK 9 73 ,0:125 1:125,A:9388197;C:9542010;G:8403521;T:9795513;N:41009,125,125,,,9388197,9542010,8403521,9795513,41009,ERX1690937,ERS1343625,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.00216,0.00026,0.00031,0.00014,0.99793,0.99977,0.6,0.33333,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4184,ERR1620571,ERX1690936,ERS1343624,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#72,SAMEA4432175,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432175|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:28|Submitter Id:E MTAB 46171473686057:LCK 9#72|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34915|genotype:heterozygous Tglck:EGFP|gfp fluorescence:806|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#72|side scatter:28|single cell well quality:good quality|well:F12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#72 p,LCK 9#72 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34915:forward scatter|Experimental Factor: 28:side scatter|Experimental Factor: 806:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_72_1.fq LCK_9_72_2.fq,fastq fastq,253547500.0,1014190.0,E MTAB 46171473686057:LCK 9 72 ,0:125 1:125,A:68815104;C:58428601;G:55787415;T:70317269;N:199111,125,125,,,68815104,58428601,55787415,70317269,199111,ERX1690936,ERS1343624,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.53639,0.51058,0.20937,0.19956,0.98877,0.9891,0.60475,0.58998,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4185,ERR1620570,ERX1690935,ERS1343623,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#71,SAMEA4432174,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432174|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:14|Submitter Id:E MTAB 46171473686057:LCK 9#71|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37554|genotype:heterozygous Tglck:EGFP|gfp fluorescence:2246|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#71|side scatter:46|single cell well quality:good quality|well:F11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#71 p,LCK 9#71 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37554:forward scatter|Experimental Factor: 46:side scatter|Experimental Factor: 2246:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_71_1.fq LCK_9_71_2.fq,fastq fastq,920935750.0,3683743.0,E MTAB 46171473686057:LCK 9 71 ,0:125 1:125,A:279433924;C:182320675;G:173554894;T:284750509;N:875748,125,125,,,279433924,182320675,173554894,284750509,875748,ERX1690935,ERS1343623,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.83063,0.82446,0.35999,0.35776,0.98263,0.98291,0.56573,0.54032,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4186,ERR1620569,ERX1690934,ERS1343622,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#70,SAMEA4432173,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432173|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:8|Submitter Id:E MTAB 46171473686057:LCK 9#70|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:26499|genotype:heterozygous Tglck:EGFP|gfp fluorescence:277|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#70|side scatter:22|single cell well quality:good quality|well:F10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#70 p,LCK 9#70 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 26499:forward scatter|Experimental Factor: 22:side scatter|Experimental Factor: 277:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_70_1.fq LCK_9_70_2.fq,fastq fastq,1789625250.0,7158501.0,E MTAB 46171473686057:LCK 9 70 ,0:125 1:125,A:543842907;C:353622858;G:335898082;T:554482225;N:1779178,125,125,,,543842907,353622858,335898082,554482225,1779178,ERX1690934,ERS1343622,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.81639,0.80979,0.41926,0.41697,0.98839,0.98841,0.60185,0.59731,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4187,ERR1620568,ERX1690933,ERS1343621,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#7,SAMEA4432172,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432172|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:37|Submitter Id:E MTAB 46171473686057:LCK 9#7|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38988|genotype:heterozygous Tglck:EGFP|gfp fluorescence:709|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#7|side scatter:64|single cell well quality:good quality|well:A7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#7 p,LCK 9#7 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38988:forward scatter|Experimental Factor: 64:side scatter|Experimental Factor: 709:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_7_1.fq LCK_9_7_2.fq,fastq fastq,24250.0,97.0,E MTAB 46171473686057:LCK 9 7 ,0:125 1:125,A:5769;C:8295;G:6392;T:3794;N:0,125,125,,,5769,8295,6392,3794,0,ERX1690933,ERS1343621,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.56627,0.66667,0.02409,0.0,0.99953,0.99991,0.57142,0.25,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4188,ERR1620567,ERX1690932,ERS1343620,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#69,SAMEA4432171,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432171|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:38|Submitter Id:E MTAB 46171473686057:LCK 9#69|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34705|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1264|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#69|side scatter:31|single cell well quality:good quality|well:F9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#69 p,LCK 9#69 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34705:forward scatter|Experimental Factor: 31:side scatter|Experimental Factor: 1264:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_69_1.fq.gz LCK_9_69_2.fq.gz,fastq fastq,2813411000.0,11253644.0,E MTAB 46171473686057:LCK 9 69 ,0:125 1:125,A:849151900;C:573999347;G:527666010;T:859867519;N:2726224,125,125,,,849151900,573999347,527666010,859867519,2726224,ERX1690932,ERS1343620,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.77553,0.76235,0.32494,0.32029,0.98892,0.9893,0.50414,0.5235,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4189,ERR1620566,ERX1690931,ERS1343619,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#68,SAMEA4432170,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432170|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:28|Submitter Id:E MTAB 46171473686057:LCK 9#68|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39308|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1572|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#68|side scatter:45|single cell well quality:good quality|well:F8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#68 p,LCK 9#68 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39308:forward scatter|Experimental Factor: 45:side scatter|Experimental Factor: 1572:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_68_1.fq.gz LCK_9_68_2.fq.gz,fastq fastq,2216839000.0,8867356.0,E MTAB 46171473686057:LCK 9 68 ,0:125 1:125,A:668046554;C:444199358;G:424960844;T:677485270;N:2146974,125,125,,,668046554,444199358,424960844,677485270,2146974,ERX1690931,ERS1343619,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.89575,0.89254,0.38551,0.38478,0.98549,0.98567,0.71592,0.7066,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4190,ERR1620565,ERX1690930,ERS1343618,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#67,SAMEA4432169,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432169|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#67|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34235|genotype:heterozygous Tglck:EGFP|gfp fluorescence:349|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#67|side scatter:32|single cell well quality:good quality|well:F7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#67 p,LCK 9#67 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34235:forward scatter|Experimental Factor: 32:side scatter|Experimental Factor: 349:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_67_1.fq.gz LCK_9_67_2.fq.gz,fastq fastq,35750.0,143.0,E MTAB 46171473686057:LCK 9 67 ,0:125 1:125,A:8808;C:10966;G:8665;T:7301;N:10,125,125,,,8808,10966,8665,7301,10,ERX1690930,ERS1343618,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.69492,0.56,0.12711,0.28,0.99941,0.99989,0.64179,0.85714,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4191,ERR1620564,ERX1690929,ERS1343617,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#66,SAMEA4432168,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432168|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:18|Submitter Id:E MTAB 46171473686057:LCK 9#66|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33415|genotype:heterozygous Tglck:EGFP|gfp fluorescence:681|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#66|side scatter:38|single cell well quality:good quality|well:F6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#66 p,LCK 9#66 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33415:forward scatter|Experimental Factor: 38:side scatter|Experimental Factor: 681:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_66_1.fq LCK_9_66_2.fq,fastq fastq,706985000.0,2827940.0,E MTAB 46171473686057:LCK 9 66 ,0:125 1:125,A:214112483;C:140731528;G:135079288;T:216394040;N:667661,125,125,,,214112483,140731528,135079288,216394040,667661,ERX1690929,ERS1343617,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.85974,0.85858,0.29344,0.29204,0.98695,0.98719,0.5047,0.58447,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4192,ERR1620563,ERX1690928,ERS1343616,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#65,SAMEA4432167,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432167|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:29|Submitter Id:E MTAB 46171473686057:LCK 9#65|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36461|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1297|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#65|side scatter:37|single cell well quality:good quality|well:F5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#65 p,LCK 9#65 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36461:forward scatter|Experimental Factor: 37:side scatter|Experimental Factor: 1297:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_65_1.fq LCK_9_65_2.fq,fastq fastq,88420500.0,353682.0,E MTAB 46171473686057:LCK 9 65 ,0:125 1:125,A:23555099;C:20818010;G:20102375;T:23882180;N:62836,125,125,,,23555099,20818010,20102375,23882180,62836,ERX1690928,ERS1343616,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78208,0.77094,0.22912,0.22706,0.98739,0.98821,0.50449,0.50993,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4193,ERR1620562,ERX1690927,ERS1343615,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#64,SAMEA4432166,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432166|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:26|Submitter Id:E MTAB 46171473686057:LCK 9#64|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35174|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1140|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#64|side scatter:47|single cell well quality:good quality|well:F4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#64 p,LCK 9#64 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35174:forward scatter|Experimental Factor: 47:side scatter|Experimental Factor: 1140:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_64_1.fq.gz LCK_9_64_2.fq.gz,fastq fastq,345199750.0,1380799.0,E MTAB 46171473686057:LCK 9 64 ,0:125 1:125,A:102534015;C:70681864;G:67464984;T:104246516;N:272371,125,125,,,102534015,70681864,67464984,104246516,272371,ERX1690927,ERS1343615,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.83724,0.83578,0.27178,0.27661,0.98677,0.98689,0.61578,0.63698,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4194,ERR1620561,ERX1690926,ERS1343614,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#63,SAMEA4432165,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432165|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:17|Submitter Id:E MTAB 46171473686057:LCK 9#63|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30162|genotype:heterozygous Tglck:EGFP|gfp fluorescence:481|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#63|side scatter:58|single cell well quality:good quality|well:F3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#63 p,LCK 9#63 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30162:forward scatter|Experimental Factor: 58:side scatter|Experimental Factor: 481:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_63_1.fq LCK_9_63_2.fq,fastq fastq,937599500.0,3750398.0,E MTAB 46171473686057:LCK 9 63 ,0:125 1:125,A:285752424;C:184050097;G:173746752;T:293084604;N:965623,125,125,,,285752424,184050097,173746752,293084604,965623,ERX1690926,ERS1343614,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.87975,0.88057,0.33088,0.33334,0.98884,0.989,0.58797,0.62896,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4195,ERR1620560,ERX1690925,ERS1343613,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#62,SAMEA4432164,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432164|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:22|Submitter Id:E MTAB 46171473686057:LCK 9#62|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37186|genotype:heterozygous Tglck:EGFP|gfp fluorescence:812|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#62|side scatter:63|single cell well quality:good quality|well:F2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#62 p,LCK 9#62 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37186:forward scatter|Experimental Factor: 63:side scatter|Experimental Factor: 812:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_62_1.fq LCK_9_62_2.fq,fastq fastq,170587500.0,682350.0,E MTAB 46171473686057:LCK 9 62 ,0:125 1:125,A:48833185;C:36775374;G:35641739;T:49208992;N:128210,125,125,,,48833185,36775374,35641739,49208992,128210,ERX1690925,ERS1343613,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.77584,0.77392,0.23937,0.23925,0.98845,0.98879,0.48105,0.49164,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4196,ERR1620559,ERX1690924,ERS1343612,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#61,SAMEA4432163,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432163|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:11|Submitter Id:E MTAB 46171473686057:LCK 9#61|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31283|genotype:heterozygous Tglck:EGFP|gfp fluorescence:268|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#61|side scatter:58|single cell well quality:good quality|well:F1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#61 p,LCK 9#61 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31283:forward scatter|Experimental Factor: 58:side scatter|Experimental Factor: 268:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_61_1.fq LCK_9_61_2.fq,fastq fastq,70364000.0,281456.0,E MTAB 46171473686057:LCK 9 61 ,0:125 1:125,A:19661346;C:15846450;G:14730150;T:20070763;N:55291,125,125,,,19661346,15846450,14730150,20070763,55291,ERX1690924,ERS1343612,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.64891,0.64123,0.20112,0.19932,0.98906,0.98997,0.45416,0.46458,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4197,ERR1620558,ERX1690923,ERS1343611,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#60,SAMEA4432162,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432162|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:25|Submitter Id:E MTAB 46171473686057:LCK 9#60|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:29165|genotype:heterozygous Tglck:EGFP|gfp fluorescence:927|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#60|side scatter:22|single cell well quality:good quality|well:E12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#60 p,LCK 9#60 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 29165:forward scatter|Experimental Factor: 22:side scatter|Experimental Factor: 927:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_60_1.fq.gz LCK_9_60_2.fq.gz,fastq fastq,256373250.0,1025493.0,E MTAB 46171473686057:LCK 9 60 ,0:125 1:125,A:67888293;C:61202093;G:57308665;T:69714050;N:260149,125,125,,,67888293,61202093,57308665,69714050,260149,ERX1690923,ERS1343611,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.63022,0.62244,0.15653,0.15688,0.98496,0.98547,0.56542,0.56911,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4198,ERR1620557,ERX1690922,ERS1343610,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#6,SAMEA4432161,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432161|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:19|Submitter Id:E MTAB 46171473686057:LCK 9#6|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:32755|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1125|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#6|side scatter:38|single cell well quality:good quality|well:A6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#6 p,LCK 9#6 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 32755:forward scatter|Experimental Factor: 38:side scatter|Experimental Factor: 1125:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_6_1.fq.gz LCK_9_6_2.fq.gz,fastq fastq,134073750.0,536295.0,E MTAB 46171473686057:LCK 9 6 ,0:125 1:125,A:37489461;C:30174764;G:27861197;T:38396977;N:151351,125,125,,,37489461,30174764,27861197,38396977,151351,ERX1690922,ERS1343610,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.66609,0.65776,0.21861,0.21833,0.98445,0.98535,0.57405,0.56231,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4199,ERR1620556,ERX1690921,ERS1343609,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#59,SAMEA4432160,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432160|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#59|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38366|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1413|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#59|side scatter:39|single cell well quality:good quality|well:E11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#59 p,LCK 9#59 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38366:forward scatter|Experimental Factor: 39:side scatter|Experimental Factor: 1413:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_59_1.fq.gz LCK_9_59_2.fq.gz,fastq fastq,2399458500.0,9597834.0,E MTAB 46171473686057:LCK 9 59 ,0:125 1:125,A:758814965;C:454492444;G:403450698;T:779615964;N:3084429,125,125,,,758814965,454492444,403450698,779615964,3084429,ERX1690921,ERS1343609,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.81346,0.81387,0.35524,0.35617,0.98871,0.98894,0.52889,0.57752,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4200,ERR1620555,ERX1690920,ERS1343608,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#58,SAMEA4432159,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432159|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:25|Submitter Id:E MTAB 46171473686057:LCK 9#58|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37537|genotype:heterozygous Tglck:EGFP|gfp fluorescence:669|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#58|side scatter:44|single cell well quality:good quality|well:E10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#58 p,LCK 9#58 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37537:forward scatter|Experimental Factor: 44:side scatter|Experimental Factor: 669:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_58_1.fq LCK_9_58_2.fq,fastq fastq,3961744500.0,15846978.0,E MTAB 46171473686057:LCK 9 58 ,0:125 1:125,A:1228242214;C:782781362;G:685768880;T:1259800857;N:5151187,125,125,,,1228242214,782781362,685768880,1259800857,5151187,ERX1690920,ERS1343608,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.77803,0.78084,0.34288,0.34389,0.98557,0.98575,0.4839,0.48419,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4201,ERR1620554,ERX1690919,ERS1343607,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#56,SAMEA4432158,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432158|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:55Z|INSDC status:public|PI fluorescence:11|Submitter Id:E MTAB 46171473686057:LCK 9#56|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38611|genotype:heterozygous Tglck:EGFP|gfp fluorescence:862|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#56|side scatter:56|single cell well quality:good quality|well:E8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#56 p,LCK 9#56 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38611:forward scatter|Experimental Factor: 56:side scatter|Experimental Factor: 862:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_56_1.fq LCK_9_56_2.fq,fastq fastq,1424484500.0,5697938.0,E MTAB 46171473686057:LCK 9 56 ,0:125 1:125,A:452498287;C:270162607;G:238364446;T:461649169;N:1809991,125,125,,,452498287,270162607,238364446,461649169,1809991,ERX1690919,ERS1343607,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79823,0.79698,0.34328,0.34426,0.9867,0.98719,0.6392,0.62436,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4202,ERR1620553,ERX1690918,ERS1343606,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#55,SAMEA4432157,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432157|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:11|Submitter Id:E MTAB 46171473686057:LCK 9#55|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33661|genotype:heterozygous Tglck:EGFP|gfp fluorescence:645|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#55|side scatter:42|single cell well quality:good quality|well:E7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#55 p,LCK 9#55 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33661:forward scatter|Experimental Factor: 42:side scatter|Experimental Factor: 645:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_55_1.fq LCK_9_55_2.fq,fastq fastq,60000.0,240.0,E MTAB 46171473686057:LCK 9 55 ,0:125 1:125,A:15954;C:17694;G:13370;T:12978;N:4,125,125,,,15954,17694,13370,12978,4,ERX1690918,ERS1343606,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.60387,0.51021,0.1256,0.22448,0.9988,0.99973,0.52525,0.64285,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4203,ERR1620552,ERX1690917,ERS1343605,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#54,SAMEA4432156,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432156|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:21|Submitter Id:E MTAB 46171473686057:LCK 9#54|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36884|genotype:heterozygous Tglck:EGFP|gfp fluorescence:506|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#54|side scatter:40|single cell well quality:good quality|well:E6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#54 p,LCK 9#54 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36884:forward scatter|Experimental Factor: 40:side scatter|Experimental Factor: 506:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_54_1.fq LCK_9_54_2.fq,fastq fastq,983455000.0,3933820.0,E MTAB 46171473686057:LCK 9 54 ,0:125 1:125,A:307668147;C:189783625;G:169392422;T:315384487;N:1226319,125,125,,,307668147,189783625,169392422,315384487,1226319,ERX1690917,ERS1343605,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.84328,0.84671,0.38941,0.39293,0.98545,0.9861,0.58475,0.59234,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4204,ERR1620551,ERX1690916,ERS1343604,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#53,SAMEA4432155,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432155|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:12|Submitter Id:E MTAB 46171473686057:LCK 9#53|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39297|genotype:heterozygous Tglck:EGFP|gfp fluorescence:980|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#53|side scatter:48|single cell well quality:good quality|well:E5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#53 p,LCK 9#53 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39297:forward scatter|Experimental Factor: 48:side scatter|Experimental Factor: 980:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_53_1.fq LCK_9_53_2.fq,fastq fastq,423622250.0,1694489.0,E MTAB 46171473686057:LCK 9 53 ,0:125 1:125,A:123960715;C:89449390;G:82194349;T:127533595;N:484201,125,125,,,123960715,89449390,82194349,127533595,484201,ERX1690916,ERS1343604,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.81004,0.81047,0.25781,0.2593,0.98545,0.98569,0.55857,0.54272,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4205,ERR1620550,ERX1690915,ERS1343603,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#52,SAMEA4432154,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432154|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:21|Submitter Id:E MTAB 46171473686057:LCK 9#52|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36076|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1834|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#52|side scatter:35|single cell well quality:good quality|well:E4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#52 p,LCK 9#52 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36076:forward scatter|Experimental Factor: 35:side scatter|Experimental Factor: 1834:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_52_1.fq LCK_9_52_2.fq,fastq fastq,556625750.0,2226503.0,E MTAB 46171473686057:LCK 9 52 ,0:125 1:125,A:170233085;C:112086841;G:98890283;T:174754179;N:661362,125,125,,,170233085,112086841,98890283,174754179,661362,ERX1690915,ERS1343603,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79634,0.79843,0.30561,0.30767,0.98547,0.98543,0.54723,0.54948,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4206,ERR1620549,ERX1690914,ERS1343602,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#51,SAMEA4432153,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432153|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:13|Submitter Id:E MTAB 46171473686057:LCK 9#51|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36715|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1279|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#51|side scatter:48|single cell well quality:good quality|well:E3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#51 p,LCK 9#51 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36715:forward scatter|Experimental Factor: 48:side scatter|Experimental Factor: 1279:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_51_1.fq.gz LCK_9_51_2.fq.gz,fastq fastq,1409324250.0,5637297.0,E MTAB 46171473686057:LCK 9 51 ,0:125 1:125,A:453719761;C:261647794;G:223013782;T:469093978;N:1848935,125,125,,,453719761,261647794,223013782,469093978,1848935,ERX1690914,ERS1343602,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.8014,0.80261,0.35881,0.35948,0.98912,0.98924,0.56925,0.58077,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4207,ERR1620548,ERX1690913,ERS1343601,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#50,SAMEA4432152,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432152|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:29|Submitter Id:E MTAB 46171473686057:LCK 9#50|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31005|genotype:heterozygous Tglck:EGFP|gfp fluorescence:985|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#50|side scatter:67|single cell well quality:good quality|well:E2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#50 p,LCK 9#50 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31005:forward scatter|Experimental Factor: 67:side scatter|Experimental Factor: 985:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_50_1.fq LCK_9_50_2.fq,fastq fastq,278424000.0,1113696.0,E MTAB 46171473686057:LCK 9 50 ,0:125 1:125,A:83482909;C:57129466;G:51832506;T:85657242;N:321877,125,125,,,83482909,57129466,51832506,85657242,321877,ERX1690913,ERS1343601,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.7681,0.76765,0.26779,0.26956,0.98758,0.98798,0.5507,0.56164,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4208,ERR1620547,ERX1690912,ERS1343600,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#5,SAMEA4432151,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432151|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:22|Submitter Id:E MTAB 46171473686057:LCK 9#5|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38239|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1331|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#5|side scatter:40|single cell well quality:good quality|well:A5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#5 p,LCK 9#5 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38239:forward scatter|Experimental Factor: 40:side scatter|Experimental Factor: 1331:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_5_1.fq.gz LCK_9_5_2.fq.gz,fastq fastq,68965000.0,275860.0,E MTAB 46171473686057:LCK 9 5 ,0:125 1:125,A:18518737;C:16248138;G:15108765;T:19013012;N:76348,125,125,,,18518737,16248138,15108765,19013012,76348,ERX1690912,ERS1343600,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.6317,0.62761,0.16172,0.16296,0.98808,0.98861,0.60645,0.61138,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4209,ERR1620546,ERX1690911,ERS1343599,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#49,SAMEA4432150,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432150|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#49|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34890|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1206|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#49|side scatter:59|single cell well quality:good quality|well:E1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#49 p,LCK 9#49 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34890:forward scatter|Experimental Factor: 59:side scatter|Experimental Factor: 1206:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_49_1.fq.gz LCK_9_49_2.fq.gz,fastq fastq,136923000.0,547692.0,E MTAB 46171473686057:LCK 9 49 ,0:125 1:125,A:38500088;C:31023318;G:27760407;T:39504944;N:134243,125,125,,,38500088,31023318,27760407,39504944,134243,ERX1690911,ERS1343599,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.66203,0.66289,0.17977,0.18144,0.98908,0.99032,0.59894,0.59504,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4210,ERR1620545,ERX1690910,ERS1343598,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#48,SAMEA4432149,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432149|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:13|Submitter Id:E MTAB 46171473686057:LCK 9#48|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40953|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1994|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#48|side scatter:45|single cell well quality:good quality|well:D12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#48 p,LCK 9#48 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40953:forward scatter|Experimental Factor: 45:side scatter|Experimental Factor: 1994:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_48_1.fq.gz LCK_9_48_2.fq.gz,fastq fastq,294000.0,1176.0,E MTAB 46171473686057:LCK 9 48 ,0:125 1:125,A:77943;C:76156;G:65330;T:74347;N:224,125,125,,,77943,76156,65330,74347,224,ERX1690910,ERS1343598,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.60103,0.54121,0.09462,0.07349,0.99579,0.99732,0.52061,0.58737,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4211,ERR1620544,ERX1690909,ERS1343597,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#47,SAMEA4432148,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432148|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:18|Submitter Id:E MTAB 46171473686057:LCK 9#47|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30609|genotype:heterozygous Tglck:EGFP|gfp fluorescence:674|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#47|side scatter:46|single cell well quality:good quality|well:D11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#47 p,LCK 9#47 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30609:forward scatter|Experimental Factor: 46:side scatter|Experimental Factor: 674:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_47_1.fq LCK_9_47_2.fq,fastq fastq,530733500.0,2122934.0,E MTAB 46171473686057:LCK 9 47 ,0:125 1:125,A:157990327;C:109634142;G:98693284;T:163801102;N:614645,125,125,,,157990327,109634142,98693284,163801102,614645,ERX1690909,ERS1343597,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78508,0.78248,0.34694,0.35003,0.98604,0.98683,0.55859,0.5405,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4212,ERR1620543,ERX1690908,ERS1343596,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#46,SAMEA4432147,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432147|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:15|Submitter Id:E MTAB 46171473686057:LCK 9#46|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38185|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1638|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#46|side scatter:56|single cell well quality:good quality|well:D10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#46 p,LCK 9#46 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38185:forward scatter|Experimental Factor: 56:side scatter|Experimental Factor: 1638:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_46_1.fq LCK_9_46_2.fq,fastq fastq,1496341250.0,5985365.0,E MTAB 46171473686057:LCK 9 46 ,0:125 1:125,A:451412948;C:305739216;G:272791710;T:464537930;N:1859446,125,125,,,451412948,305739216,272791710,464537930,1859446,ERX1690908,ERS1343596,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.82158,0.82138,0.26396,0.26642,0.97922,0.97981,0.61964,0.63165,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4213,ERR1620542,ERX1690907,ERS1343595,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#45,SAMEA4432146,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432146|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:54|Submitter Id:E MTAB 46171473686057:LCK 9#45|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33093|genotype:heterozygous Tglck:EGFP|gfp fluorescence:778|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#45|side scatter:37|single cell well quality:good quality|well:D9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#45 p,LCK 9#45 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33093:forward scatter|Experimental Factor: 37:side scatter|Experimental Factor: 778:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_45_1.fq LCK_9_45_2.fq,fastq fastq,1397063500.0,5588254.0,E MTAB 46171473686057:LCK 9 45 ,0:125 1:125,A:430585720;C:284148017;G:237096827;T:443530657;N:1702279,125,125,,,430585720,284148017,237096827,443530657,1702279,ERX1690907,ERS1343595,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76709,0.76624,0.37672,0.38002,0.98701,0.9877,0.54309,0.54509,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4214,ERR1620541,ERX1690906,ERS1343594,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#44,SAMEA4432145,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432145|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:22|Submitter Id:E MTAB 46171473686057:LCK 9#44|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33049|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1185|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#44|side scatter:51|single cell well quality:good quality|well:D8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#44 p,LCK 9#44 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33049:forward scatter|Experimental Factor: 51:side scatter|Experimental Factor: 1185:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_44_1.fq LCK_9_44_2.fq,fastq fastq,739152000.0,2956608.0,E MTAB 46171473686057:LCK 9 44 ,0:125 1:125,A:224239217;C:149166771;G:133497123;T:231400509;N:848380,125,125,,,224239217,149166771,133497123,231400509,848380,ERX1690906,ERS1343594,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79454,0.79298,0.30467,0.3067,0.9866,0.98681,0.54854,0.55635,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4215,ERR1620540,ERX1690905,ERS1343593,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#43,SAMEA4432144,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432144|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:29|Submitter Id:E MTAB 46171473686057:LCK 9#43|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:26795|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1007|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#43|side scatter:32|single cell well quality:good quality|well:D7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#43 p,LCK 9#43 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 26795:forward scatter|Experimental Factor: 32:side scatter|Experimental Factor: 1007:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_43_1.fq LCK_9_43_2.fq,fastq fastq,33500.0,134.0,E MTAB 46171473686057:LCK 9 43 ,0:125 1:125,A:8829;C:9980;G:8064;T:6627;N:0,125,125,,,8829,9980,8064,6627,0,ERX1690905,ERS1343593,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.72381,0.69231,0.13333,0.30769,0.99949,0.99991,0.62711,0.75,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4216,ERR1620539,ERX1690904,ERS1343592,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#42,SAMEA4432143,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432143|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:9|Submitter Id:E MTAB 46171473686057:LCK 9#42|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:31575|genotype:heterozygous Tglck:EGFP|gfp fluorescence:783|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#42|side scatter:33|single cell well quality:good quality|well:D6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#42 p,LCK 9#42 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 31575:forward scatter|Experimental Factor: 33:side scatter|Experimental Factor: 783:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_42_1.fq LCK_9_42_2.fq,fastq fastq,360103000.0,1440412.0,E MTAB 46171473686057:LCK 9 42 ,0:125 1:125,A:105840816;C:75722986;G:69361332;T:108760079;N:417787,125,125,,,105840816,75722986,69361332,108760079,417787,ERX1690904,ERS1343592,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78404,0.78245,0.30299,0.30656,0.98415,0.98474,0.58043,0.57455,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4217,ERR1620538,ERX1690903,ERS1343591,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#41,SAMEA4432142,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432142|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:35|Submitter Id:E MTAB 46171473686057:LCK 9#41|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:29650|genotype:heterozygous Tglck:EGFP|gfp fluorescence:817|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#41|side scatter:47|single cell well quality:good quality|well:D5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#41 p,LCK 9#41 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 29650:forward scatter|Experimental Factor: 47:side scatter|Experimental Factor: 817:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_41_1.fq LCK_9_41_2.fq,fastq fastq,226287500.0,905150.0,E MTAB 46171473686057:LCK 9 41 ,0:125 1:125,A:64741328;C:48959781;G:45743423;T:66570263;N:272705,125,125,,,64741328,48959781,45743423,66570263,272705,ERX1690903,ERS1343591,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79685,0.79796,0.3246,0.32864,0.98348,0.98419,0.49579,0.49399,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4218,ERR1620537,ERX1690902,ERS1343590,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#40,SAMEA4432141,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432141|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:17|Submitter Id:E MTAB 46171473686057:LCK 9#40|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:26984|genotype:heterozygous Tglck:EGFP|gfp fluorescence:445|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#40|side scatter:43|single cell well quality:good quality|well:D4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#40 p,LCK 9#40 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 26984:forward scatter|Experimental Factor: 43:side scatter|Experimental Factor: 445:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_40_1.fq LCK_9_40_2.fq,fastq fastq,699132250.0,2796529.0,E MTAB 46171473686057:LCK 9 40 ,0:125 1:125,A:211289204;C:142897782;G:127054905;T:217073635;N:816724,125,125,,,211289204,142897782,127054905,217073635,816724,ERX1690902,ERS1343590,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76106,0.76174,0.32385,0.32782,0.98829,0.98849,0.57698,0.56874,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4219,ERR1620536,ERX1690901,ERS1343589,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#4,SAMEA4432140,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432140|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:25|Submitter Id:E MTAB 46171473686057:LCK 9#4|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36207|genotype:heterozygous Tglck:EGFP|gfp fluorescence:769|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#4|side scatter:46|single cell well quality:good quality|well:A4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#4 p,LCK 9#4 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36207:forward scatter|Experimental Factor: 46:side scatter|Experimental Factor: 769:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_4_1.fq LCK_9_4_2.fq,fastq fastq,84267500.0,337070.0,E MTAB 46171473686057:LCK 9 4 ,0:125 1:125,A:23156008;C:19615254;G:17731083;T:23674447;N:90708,125,125,,,23156008,19615254,17731083,23674447,90708,ERX1690901,ERS1343589,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.71683,0.70933,0.187,0.18755,0.98827,0.98853,0.58422,0.42234,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4220,ERR1620535,ERX1690900,ERS1343588,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#39,SAMEA4432139,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432139|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:12|Submitter Id:E MTAB 46171473686057:LCK 9#39|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38628|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1428|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#39|side scatter:47|single cell well quality:good quality|well:D3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#39 p,LCK 9#39 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38628:forward scatter|Experimental Factor: 47:side scatter|Experimental Factor: 1428:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_39_1.fq LCK_9_39_2.fq,fastq fastq,460656750.0,1842627.0,E MTAB 46171473686057:LCK 9 39 ,0:125 1:125,A:137606590;C:95351735;G:83324811;T:143873722;N:499892,125,125,,,137606590,95351735,83324811,143873722,499892,ERX1690900,ERS1343588,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.80021,0.79987,0.29451,0.29836,0.98662,0.98711,0.5754,0.55996,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4221,ERR1620534,ERX1690899,ERS1343587,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#38,SAMEA4432138,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432138|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:10|Submitter Id:E MTAB 46171473686057:LCK 9#38|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35394|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1703|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#38|side scatter:51|single cell well quality:good quality|well:D2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#38 p,LCK 9#38 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35394:forward scatter|Experimental Factor: 51:side scatter|Experimental Factor: 1703:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_38_1.fq LCK_9_38_2.fq,fastq fastq,168297750.0,673191.0,E MTAB 46171473686057:LCK 9 38 ,0:125 1:125,A:47533610;C:37705646;G:33476452;T:49399324;N:182718,125,125,,,47533610,37705646,33476452,49399324,182718,ERX1690899,ERS1343587,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.75279,0.74883,0.21822,0.22019,0.98656,0.98725,0.56848,0.54329,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4222,ERR1620533,ERX1690898,ERS1343586,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#37,SAMEA4432137,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432137|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:24|Submitter Id:E MTAB 46171473686057:LCK 9#37|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33788|genotype:heterozygous Tglck:EGFP|gfp fluorescence:549|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#37|side scatter:47|single cell well quality:good quality|well:D1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#37 p,LCK 9#37 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33788:forward scatter|Experimental Factor: 47:side scatter|Experimental Factor: 549:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_37_1.fq LCK_9_37_2.fq,fastq fastq,177275750.0,709103.0,E MTAB 46171473686057:LCK 9 37 ,0:125 1:125,A:47179098;C:42509315;G:38373205;T:49031571;N:182561,125,125,,,47179098,42509315,38373205,49031571,182561,ERX1690898,ERS1343586,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.52619,0.51927,0.1435,0.14327,0.98758,0.98819,0.56862,0.39286,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4223,ERR1620532,ERX1690897,ERS1343585,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#36,SAMEA4432136,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432136|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:28|Submitter Id:E MTAB 46171473686057:LCK 9#36|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35833|genotype:heterozygous Tglck:EGFP|gfp fluorescence:2444|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#36|side scatter:52|single cell well quality:good quality|well:C12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#36 p,LCK 9#36 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35833:forward scatter|Experimental Factor: 52:side scatter|Experimental Factor: 2444:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_36_1.fq LCK_9_36_2.fq,fastq fastq,270627500.0,1082510.0,E MTAB 46171473686057:LCK 9 36 ,0:125 1:125,A:73705184;C:62455677;G:58486650;T:75670336;N:309653,125,125,,,73705184,62455677,58486650,75670336,309653,ERX1690897,ERS1343585,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.71531,0.70368,0.17547,0.17418,0.98496,0.98545,0.5259,0.53914,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4224,ERR1620531,ERX1690896,ERS1343584,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#35,SAMEA4432135,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432135|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:11|Submitter Id:E MTAB 46171473686057:LCK 9#35|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35022|genotype:heterozygous Tglck:EGFP|gfp fluorescence:630|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#35|side scatter:33|single cell well quality:good quality|well:C11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#35 p,LCK 9#35 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35022:forward scatter|Experimental Factor: 33:side scatter|Experimental Factor: 630:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_35_2.fq.gz LCK_9_35_1.fq.gz,fastq fastq,658569000.0,2634276.0,E MTAB 46171473686057:LCK 9 35 ,0:125 1:125,A:198911153;C:134001581;G:120480503;T:204336959;N:838804,125,125,,,198911153,134001581,120480503,204336959,838804,ERX1690896,ERS1343584,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.80156,0.7968,0.29153,0.29278,0.98638,0.98707,0.57116,0.57873,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4225,ERR1620530,ERX1690895,ERS1343583,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#34,SAMEA4432134,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432134|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:27|Submitter Id:E MTAB 46171473686057:LCK 9#34|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36048|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1911|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#34|side scatter:50|single cell well quality:good quality|well:C10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#34 p,LCK 9#34 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36048:forward scatter|Experimental Factor: 50:side scatter|Experimental Factor: 1911:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_34_1.fq.gz LCK_9_34_2.fq.gz,fastq fastq,2513867500.0,10055470.0,E MTAB 46171473686057:LCK 9 34 ,0:125 1:125,A:762559346;C:511666619;G:454748139;T:781404243;N:3489153,125,125,,,762559346,511666619,454748139,781404243,3489153,ERX1690895,ERS1343583,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.82318,0.82292,0.36763,0.3688,0.98468,0.9849,0.53575,0.54395,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4226,ERR1620529,ERX1690894,ERS1343582,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#33,SAMEA4432133,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432133|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:28|Submitter Id:E MTAB 46171473686057:LCK 9#33|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35549|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1499|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#33|side scatter:55|single cell well quality:good quality|well:C9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#33 p,LCK 9#33 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35549:forward scatter|Experimental Factor: 55:side scatter|Experimental Factor: 1499:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_33_1.fq.gz LCK_9_33_2.fq.gz,fastq fastq,2211875250.0,8847501.0,E MTAB 46171473686057:LCK 9 33 ,0:125 1:125,A:679550710;C:451865508;G:389649655;T:687918190;N:2891187,125,125,,,679550710,451865508,389649655,687918190,2891187,ERX1690894,ERS1343582,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78428,0.77784,0.33713,0.33624,0.98914,0.98948,0.58772,0.59724,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4227,ERR1620528,ERX1690893,ERS1343581,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#32,SAMEA4432132,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432132|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:29|Submitter Id:E MTAB 46171473686057:LCK 9#32|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37324|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1017|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#32|side scatter:39|single cell well quality:good quality|well:C8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#32 p,LCK 9#32 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37324:forward scatter|Experimental Factor: 39:side scatter|Experimental Factor: 1017:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_32_1.fq.gz LCK_9_32_2.fq.gz,fastq fastq,1915874000.0,7663496.0,E MTAB 46171473686057:LCK 9 32 ,0:125 1:125,A:588937193;C:380844622;G:341308331;T:602169121;N:2614733,125,125,,,588937193,380844622,341308331,602169121,2614733,ERX1690893,ERS1343581,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.83864,0.837,0.33835,0.3381,0.98699,0.98729,0.60989,0.61408,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4228,ERR1620527,ERX1690892,ERS1343580,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#31,SAMEA4432131,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432131|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#31|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38254|genotype:heterozygous Tglck:EGFP|gfp fluorescence:958|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#31|side scatter:38|single cell well quality:good quality|well:C7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#31 p,LCK 9#31 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38254:forward scatter|Experimental Factor: 38:side scatter|Experimental Factor: 958:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_31_1.fq LCK_9_31_2.fq,fastq fastq,60500.0,242.0,E MTAB 46171473686057:LCK 9 31 ,0:125 1:125,A:14707;C:19967;G:15042;T:10784;N:0,125,125,,,14707,19967,15042,10784,0,ERX1690892,ERS1343580,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.51942,0.55556,0.0631,0.22222,0.99914,0.99981,0.60215,0.55555,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4229,ERR1620526,ERX1690891,ERS1343579,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#30,SAMEA4432130,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432130|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:30|Submitter Id:E MTAB 46171473686057:LCK 9#30|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:41607|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1591|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#30|side scatter:39|single cell well quality:good quality|well:C6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#30 p,LCK 9#30 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 41607:forward scatter|Experimental Factor: 39:side scatter|Experimental Factor: 1591:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_30_1.fq LCK_9_30_2.fq,fastq fastq,431943750.0,1727775.0,E MTAB 46171473686057:LCK 9 30 ,0:125 1:125,A:126269151;C:91668422;G:84244852;T:129225487;N:535838,125,125,,,126269151,91668422,84244852,129225487,535838,ERX1690891,ERS1343579,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.77735,0.77601,0.25855,0.26143,0.98212,0.98273,0.62475,0.63644,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4230,ERR1620525,ERX1690890,ERS1343578,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#3,SAMEA4432129,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432129|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:14|Submitter Id:E MTAB 46171473686057:LCK 9#3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35173|genotype:heterozygous Tglck:EGFP|gfp fluorescence:997|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#3|side scatter:52|single cell well quality:good quality|well:A3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#3 p,LCK 9#3 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35173:forward scatter|Experimental Factor: 52:side scatter|Experimental Factor: 997:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_3_1.fq LCK_9_3_2.fq,fastq fastq,53417500.0,213670.0,E MTAB 46171473686057:LCK 9 3 ,0:125 1:125,A:15170830;C:12021822;G:10576604;T:15585539;N:62705,125,125,,,15170830,12021822,10576604,15585539,62705,ERX1690890,ERS1343578,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.67102,0.66189,0.18604,0.18613,0.98784,0.98867,0.56931,0.55859,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4231,ERR1620524,ERX1690889,ERS1343577,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#29,SAMEA4432128,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432128|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:69|Submitter Id:E MTAB 46171473686057:LCK 9#29|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33928|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1010|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#29|side scatter:103|single cell well quality:good quality|well:C5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#29 p,LCK 9#29 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33928:forward scatter|Experimental Factor: 103:side scatter|Experimental Factor: 1010:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_29_1.fq LCK_9_29_2.fq,fastq fastq,400731000.0,1602924.0,E MTAB 46171473686057:LCK 9 29 ,0:125 1:125,A:116671373;C:84818936;G:79728402;T:119000154;N:512135,125,125,,,116671373,84818936,79728402,119000154,512135,ERX1690889,ERS1343577,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.817,0.81956,0.33674,0.33915,0.98401,0.98439,0.60776,0.61518,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4232,ERR1620523,ERX1690888,ERS1343576,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#28,SAMEA4432127,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432127|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#28|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37784|genotype:heterozygous Tglck:EGFP|gfp fluorescence:613|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#28|side scatter:98|single cell well quality:good quality|well:C4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#28 p,LCK 9#28 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37784:forward scatter|Experimental Factor: 98:side scatter|Experimental Factor: 613:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_28_1.fq LCK_9_28_2.fq,fastq fastq,445330500.0,1781322.0,E MTAB 46171473686057:LCK 9 28 ,0:125 1:125,A:131995962;C:92552781;G:85567682;T:134671551;N:542524,125,125,,,131995962,92552781,85567682,134671551,542524,ERX1690888,ERS1343576,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.84012,0.83909,0.25757,0.26024,0.97944,0.98011,0.5814,0.58785,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4233,ERR1620522,ERX1690887,ERS1343575,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#27,SAMEA4432126,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432126|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:26|Submitter Id:E MTAB 46171473686057:LCK 9#27|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:32075|genotype:heterozygous Tglck:EGFP|gfp fluorescence:787|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#27|side scatter:30|single cell well quality:good quality|well:C3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#27 p,LCK 9#27 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 32075:forward scatter|Experimental Factor: 30:side scatter|Experimental Factor: 787:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_27_1.fq LCK_9_27_2.fq,fastq fastq,702894500.0,2811578.0,E MTAB 46171473686057:LCK 9 27 ,0:125 1:125,A:214185302;C:141638244;G:125423883;T:220699482;N:947589,125,125,,,214185302,141638244,125423883,220699482,947589,ERX1690887,ERS1343575,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.77633,0.77484,0.46607,0.46856,0.97948,0.98068,0.52536,0.50049,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4234,ERR1620521,ERX1690886,ERS1343574,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#26,SAMEA4432125,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432125|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:26|Submitter Id:E MTAB 46171473686057:LCK 9#26|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34180|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1344|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#26|side scatter:49|single cell well quality:good quality|well:C2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#26 p,LCK 9#26 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34180:forward scatter|Experimental Factor: 49:side scatter|Experimental Factor: 1344:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_26_1.fq LCK_9_26_2.fq,fastq fastq,264248500.0,1056994.0,E MTAB 46171473686057:LCK 9 26 ,0:125 1:125,A:76906878;C:56288108;G:52128806;T:78594639;N:330069,125,125,,,76906878,56288108,52128806,78594639,330069,ERX1690886,ERS1343574,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76358,0.75974,0.29593,0.29677,0.9853,0.98583,0.59667,0.59946,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4235,ERR1620520,ERX1690885,ERS1343573,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#25,SAMEA4432124,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432124|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:18|Submitter Id:E MTAB 46171473686057:LCK 9#25|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30506|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1058|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#25|side scatter:24|single cell well quality:good quality|well:C1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#25 p,LCK 9#25 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30506:forward scatter|Experimental Factor: 24:side scatter|Experimental Factor: 1058:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_25_1.fq LCK_9_25_2.fq,fastq fastq,194061500.0,776246.0,E MTAB 46171473686057:LCK 9 25 ,0:125 1:125,A:53076597;C:45095249;G:41253858;T:54422186;N:213610,125,125,,,53076597,45095249,41253858,54422186,213610,ERX1690885,ERS1343573,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.65517,0.65108,0.1946,0.19681,0.98413,0.98472,0.595,0.59544,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4236,ERR1620519,ERX1690884,ERS1343572,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#24,SAMEA4432123,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432123|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:9|Submitter Id:E MTAB 46171473686057:LCK 9#24|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38631|genotype:heterozygous Tglck:EGFP|gfp fluorescence:2299|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#24|side scatter:67|single cell well quality:good quality|well:B12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#24 p,LCK 9#24 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38631:forward scatter|Experimental Factor: 67:side scatter|Experimental Factor: 2299:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_24_1.fq LCK_9_24_2.fq,fastq fastq,317841250.0,1271365.0,E MTAB 46171473686057:LCK 9 24 ,0:125 1:125,A:87443769;C:72350386;G:68356562;T:89269081;N:421452,125,125,,,87443769,72350386,68356562,89269081,421452,ERX1690884,ERS1343572,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.765,0.7614,0.22441,0.22455,0.98405,0.98457,0.54945,0.54908,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4237,ERR1620518,ERX1690883,ERS1343571,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#23,SAMEA4432122,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432122|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:31|Submitter Id:E MTAB 46171473686057:LCK 9#23|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34281|genotype:heterozygous Tglck:EGFP|gfp fluorescence:848|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#23|side scatter:31|single cell well quality:good quality|well:B11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#23 p,LCK 9#23 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34281:forward scatter|Experimental Factor: 31:side scatter|Experimental Factor: 848:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_23_1.fq LCK_9_23_2.fq,fastq fastq,350435500.0,1401742.0,E MTAB 46171473686057:LCK 9 23 ,0:125 1:125,A:99821826;C:76988893;G:71482078;T:101680832;N:461871,125,125,,,99821826,76988893,71482078,101680832,461871,ERX1690883,ERS1343571,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.67348,0.66912,0.24318,0.24341,0.99032,0.99064,0.56673,0.54529,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4238,ERR1620517,ERX1690882,ERS1343570,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#22,SAMEA4432121,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432121|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:21|Submitter Id:E MTAB 46171473686057:LCK 9#22|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39716|genotype:heterozygous Tglck:EGFP|gfp fluorescence:3498|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#22|side scatter:68|single cell well quality:good quality|well:B10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#22 p,LCK 9#22 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39716:forward scatter|Experimental Factor: 68:side scatter|Experimental Factor: 3498:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_22_1.fq.gz LCK_9_22_2.fq.gz,fastq fastq,610625250.0,2442501.0,E MTAB 46171473686057:LCK 9 22 ,0:125 1:125,A:185949779;C:123158840;G:111788337;T:188835997;N:892297,125,125,,,185949779,123158840,111788337,188835997,892297,ERX1690882,ERS1343570,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.79181,0.79289,0.38976,0.39368,0.98267,0.98317,0.53398,0.54343,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4239,ERR1620516,ERX1690881,ERS1343569,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#21,SAMEA4432120,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432120|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:10|Submitter Id:E MTAB 46171473686057:LCK 9#21|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:29223|genotype:heterozygous Tglck:EGFP|gfp fluorescence:820|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#21|side scatter:46|single cell well quality:good quality|well:B9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#21 p,LCK 9#21 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 29223:forward scatter|Experimental Factor: 46:side scatter|Experimental Factor: 820:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_21_1.fq.gz LCK_9_21_2.fq.gz,fastq fastq,1486186750.0,5944747.0,E MTAB 46171473686057:LCK 9 21 ,0:125 1:125,A:463125146;C:294854645;G:259484614;T:466566596;N:2155749,125,125,,,463125146,294854645,259484614,466566596,2155749,ERX1690881,ERS1343569,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.81356,0.81367,0.37507,0.37673,0.98561,0.98543,0.40477,0.56369,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4240,ERR1620515,ERX1690880,ERS1343568,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#20,SAMEA4432119,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432119|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:17|Submitter Id:E MTAB 46171473686057:LCK 9#20|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37877|genotype:heterozygous Tglck:EGFP|gfp fluorescence:719|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#20|side scatter:39|single cell well quality:good quality|well:B8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#20 p,LCK 9#20 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37877:forward scatter|Experimental Factor: 39:side scatter|Experimental Factor: 719:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_20_1.fq LCK_9_20_2.fq,fastq fastq,721498750.0,2885995.0,E MTAB 46171473686057:LCK 9 20 ,0:125 1:125,A:218528953;C:146945928;G:133607460;T:221382175;N:1034234,125,125,,,218528953,146945928,133607460,221382175,1034234,ERX1690880,ERS1343568,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78193,0.78415,0.33638,0.33943,0.98762,0.98804,0.60407,0.59556,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4241,ERR1620514,ERX1690879,ERS1343567,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#2,SAMEA4432118,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432118|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:10|Submitter Id:E MTAB 46171473686057:LCK 9#2|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40605|genotype:heterozygous Tglck:EGFP|gfp fluorescence:769|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#2|side scatter:55|single cell well quality:good quality|well:A2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#2 p,LCK 9#2 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40605:forward scatter|Experimental Factor: 55:side scatter|Experimental Factor: 769:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_2_1.fq LCK_9_2_2.fq,fastq fastq,130088500.0,520354.0,E MTAB 46171473686057:LCK 9 2 ,0:125 1:125,A:35951139;C:29494894;G:27668066;T:36829765;N:144636,125,125,,,35951139,29494894,27668066,36829765,144636,ERX1690879,ERS1343567,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.78789,0.7845,0.27179,0.27377,0.9825,0.98234,0.56228,0.57076,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4242,ERR1620513,ERX1690878,ERS1343566,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#19,SAMEA4432117,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432117|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:16|Submitter Id:E MTAB 46171473686057:LCK 9#19|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37031|genotype:heterozygous Tglck:EGFP|gfp fluorescence:893|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#19|side scatter:43|single cell well quality:good quality|well:B7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#19 p,LCK 9#19 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37031:forward scatter|Experimental Factor: 43:side scatter|Experimental Factor: 893:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_19_1.fq LCK_9_19_2.fq,fastq fastq,54250.0,217.0,E MTAB 46171473686057:LCK 9 19 ,0:125 1:125,A:12756;C:18509;G:13357;T:9595;N:33,125,125,,,12756,18509,13357,9595,33,ERX1690878,ERS1343566,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.64172,0.5,0.04278,0.07142,0.99912,0.99989,0.77777,0.83333,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4243,ERR1620512,ERX1690877,ERS1343565,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#18,SAMEA4432116,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432116|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#18|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34240|genotype:heterozygous Tglck:EGFP|gfp fluorescence:734|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#18|side scatter:41|single cell well quality:good quality|well:B6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#18 p,LCK 9#18 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34240:forward scatter|Experimental Factor: 41:side scatter|Experimental Factor: 734:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_18_1.fq LCK_9_18_2.fq,fastq fastq,375759000.0,1503036.0,E MTAB 46171473686057:LCK 9 18 ,0:125 1:125,A:107293403;C:82189292;G:76920626;T:108868180;N:487499,125,125,,,107293403,82189292,76920626,108868180,487499,ERX1690877,ERS1343565,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.695,0.69382,0.23471,0.2368,0.98567,0.98664,0.56936,0.56874,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4244,ERR1620511,ERX1690876,ERS1343564,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#17,SAMEA4432115,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432115|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:54Z|INSDC status:public|PI fluorescence:15|Submitter Id:E MTAB 46171473686057:LCK 9#17|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:36004|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1038|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#17|side scatter:50|single cell well quality:good quality|well:B5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#17 p,LCK 9#17 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 36004:forward scatter|Experimental Factor: 50:side scatter|Experimental Factor: 1038:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_17_1.fq LCK_9_17_2.fq,fastq fastq,230247250.0,920989.0,E MTAB 46171473686057:LCK 9 17 ,0:125 1:125,A:65688064;C:50045475;G:47193424;T:67001456;N:318831,125,125,,,65688064,50045475,47193424,67001456,318831,ERX1690876,ERS1343564,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.80376,0.80305,0.28121,0.28381,0.98658,0.98715,0.58975,0.58174,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4245,ERR1620510,ERX1690875,ERS1343563,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#16,SAMEA4432114,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432114|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:24|Submitter Id:E MTAB 46171473686057:LCK 9#16|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:37585|genotype:heterozygous Tglck:EGFP|gfp fluorescence:663|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#16|side scatter:60|single cell well quality:good quality|well:B4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#16 p,LCK 9#16 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 37585:forward scatter|Experimental Factor: 60:side scatter|Experimental Factor: 663:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_16_1.fq LCK_9_16_2.fq,fastq fastq,152102250.0,608409.0,E MTAB 46171473686057:LCK 9 16 ,0:125 1:125,A:44312603;C:33141661;G:29639107;T:44812943;N:195936,125,125,,,44312603,33141661,29639107,44812943,195936,ERX1690875,ERS1343563,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.68299,0.68319,0.22787,0.23043,0.98788,0.98845,0.61495,0.61758,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4246,ERR1620509,ERX1690874,ERS1343562,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#15,SAMEA4432113,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432113|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:64|Submitter Id:E MTAB 46171473686057:LCK 9#15|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39656|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1505|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#15|side scatter:98|single cell well quality:good quality|well:B3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#15 p,LCK 9#15 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39656:forward scatter|Experimental Factor: 98:side scatter|Experimental Factor: 1505:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_15_1.fq LCK_9_15_2.fq,fastq fastq,266111000.0,1064444.0,E MTAB 46171473686057:LCK 9 15 ,0:125 1:125,A:77813259;C:56572621;G:52255374;T:79107116;N:362630,125,125,,,77813259,56572621,52255374,79107116,362630,ERX1690874,ERS1343562,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.7857,0.78669,0.2791,0.28238,0.98305,0.98356,0.55716,0.54631,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4247,ERR1620508,ERX1690873,ERS1343561,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#14,SAMEA4432112,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432112|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:22|Submitter Id:E MTAB 46171473686057:LCK 9#14|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35756|genotype:heterozygous Tglck:EGFP|gfp fluorescence:910|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#14|side scatter:29|single cell well quality:good quality|well:B2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#14 p,LCK 9#14 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35756:forward scatter|Experimental Factor: 29:side scatter|Experimental Factor: 910:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_14_1.fq LCK_9_14_2.fq,fastq fastq,183685500.0,734742.0,E MTAB 46171473686057:LCK 9 14 ,0:125 1:125,A:52448302;C:40324561;G:37699565;T:52983394;N:229678,125,125,,,52448302,40324561,37699565,52983394,229678,ERX1690873,ERS1343561,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.72936,0.72964,0.22377,0.22687,0.98419,0.98466,0.58412,0.59481,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4248,ERR1620507,ERX1690872,ERS1343560,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#13,SAMEA4432111,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432111|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:35|Submitter Id:E MTAB 46171473686057:LCK 9#13|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40047|genotype:heterozygous Tglck:EGFP|gfp fluorescence:552|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#13|side scatter:62|single cell well quality:good quality|well:B1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#13 p,LCK 9#13 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40047:forward scatter|Experimental Factor: 62:side scatter|Experimental Factor: 552:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_13_1.fq LCK_9_13_2.fq,fastq fastq,184971750.0,739887.0,E MTAB 46171473686057:LCK 9 13 ,0:125 1:125,A:51592242;C:42149603;G:38441744;T:52559034;N:229127,125,125,,,51592242,42149603,38441744,52559034,229127,ERX1690872,ERS1343560,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.58753,0.58435,0.21447,0.21393,0.98587,0.9866,0.51901,0.52694,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4249,ERR1620506,ERX1690871,ERS1343559,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#12,SAMEA4432110,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432110|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:17|Submitter Id:E MTAB 46171473686057:LCK 9#12|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34674|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1171|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#12|side scatter:40|single cell well quality:good quality|well:A12|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#12 p,LCK 9#12 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34674:forward scatter|Experimental Factor: 40:side scatter|Experimental Factor: 1171:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_12_1.fq LCK_9_12_2.fq,fastq fastq,68500.0,274.0,E MTAB 46171473686057:LCK 9 12 ,0:125 1:125,A:18435;C:20110;G:15142;T:14808;N:5,125,125,,,18435,20110,15142,14808,5,ERX1690871,ERS1343559,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.53659,0.54167,0.03658,0.04166,0.9992,0.99975,0.5679,0.33333,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4250,ERR1620505,ERX1690870,ERS1343558,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#11,SAMEA4432109,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432109|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:11|Submitter Id:E MTAB 46171473686057:LCK 9#11|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39468|genotype:heterozygous Tglck:EGFP|gfp fluorescence:598|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#11|side scatter:59|single cell well quality:good quality|well:A11|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#11 p,LCK 9#11 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39468:forward scatter|Experimental Factor: 59:side scatter|Experimental Factor: 598:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_11_1.fq.gz LCK_9_11_2.fq.gz,fastq fastq,262326250.0,1049305.0,E MTAB 46171473686057:LCK 9 11 ,0:125 1:125,A:71255079;C:60824638;G:56934624;T:73000150;N:311759,125,125,,,71255079,60824638,56934624,73000150,311759,ERX1690870,ERS1343558,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.66736,0.65347,0.18944,0.18657,0.98673,0.9867,0.52041,0.52245,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4251,ERR1620504,ERX1690869,ERS1343557,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#10,SAMEA4432108,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432108|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:30|Submitter Id:E MTAB 46171473686057:LCK 9#10|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:40922|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1191|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#10|side scatter:47|single cell well quality:good quality|well:A10|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#10 p,LCK 9#10 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 40922:forward scatter|Experimental Factor: 47:side scatter|Experimental Factor: 1191:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_9_10_1.fq.gz LCK_9_10_2.fq.gz,fastq fastq,385292750.0,1541171.0,E MTAB 46171473686057:LCK 9 10 ,0:125 1:125,A:106339101;C:87781231;G:81794837;T:108890761;N:486820,125,125,,,106339101,87781231,81794837,108890761,486820,ERX1690869,ERS1343557,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.72987,0.71664,0.19705,0.19603,0.98689,0.98727,0.58065,0.58479,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4252,ERR1620503,ERX1690868,ERS1343556,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 9#1,SAMEA4432107,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432107|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:20|Submitter Id:E MTAB 46171473686057:LCK 9#1|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38064|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1408|individual:2|organism part:spleen|plate:9|sample name:E MTAB 46171473686057:LCK 9#1|side scatter:49|single cell well quality:good quality|well:A1|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 9#1 p,LCK 9#1 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38064:forward scatter|Experimental Factor: 49:side scatter|Experimental Factor: 1408:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_9_1_1.fq LCK_9_1_2.fq,fastq fastq,162490000.0,649960.0,E MTAB 46171473686057:LCK 9 1 ,0:125 1:125,A:45331628;C:36735182;G:33728117;T:46509543;N:185530,125,125,,,45331628,36735182,33728117,46509543,185530,ERX1690868,ERS1343556,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.74727,0.74298,0.24396,0.24573,0.98161,0.98141,0.49079,0.48358,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4253,ERR1620502,ERX1690867,ERS1343555,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#9,SAMEA4432106,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432106|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:13|Submitter Id:E MTAB 46171473686057:LCK 8#9|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39150|genotype:heterozygous Tglck:EGFP|gfp fluorescence:480|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#9|side scatter:68|single cell well quality:good quality|well:A9|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#9 p,LCK 8#9 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39150:forward scatter|Experimental Factor: 68:side scatter|Experimental Factor: 480:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_9_1.fq.gz LCK_8_9_2.fq.gz,fastq fastq,321790750.0,1287163.0,E MTAB 46171473686057:LCK 8 9 ,0:125 1:125,A:92303566;C:70926100;G:65388744;T:92407267;N:765073,125,125,,,92303566,70926100,65388744,92407267,765073,ERX1690867,ERS1343555,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76909,0.77068,0.20517,0.20995,0.97761,0.97822,0.57192,0.56239,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4254,ERR1620501,ERX1690866,ERS1343554,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#8,SAMEA4432105,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432105|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:9|Submitter Id:E MTAB 46171473686057:LCK 8#8|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38690|genotype:heterozygous Tglck:EGFP|gfp fluorescence:719|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#8|side scatter:35|single cell well quality:good quality|well:A8|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#8 p,LCK 8#8 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38690:forward scatter|Experimental Factor: 35:side scatter|Experimental Factor: 719:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_8_1.fq.gz LCK_8_8_2.fq.gz,fastq fastq,264057500.0,1056230.0,E MTAB 46171473686057:LCK 8 8 ,0:125 1:125,A:74266704;C:58957248;G:55164989;T:75024394;N:644165,125,125,,,74266704,58957248,55164989,75024394,644165,ERX1690866,ERS1343554,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.68044,0.68052,0.1982,0.20001,0.98453,0.98551,0.488,0.58804,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4255,ERR1620500,ERX1690865,ERS1343553,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#7,SAMEA4432104,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432104|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:44|Submitter Id:E MTAB 46171473686057:LCK 8#7|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30221|genotype:heterozygous Tglck:EGFP|gfp fluorescence:845|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#7|side scatter:29|single cell well quality:good quality|well:A7|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#7 p,LCK 8#7 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30221:forward scatter|Experimental Factor: 29:side scatter|Experimental Factor: 845:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_7_1.fq LCK_8_7_2.fq,fastq fastq,72607000.0,290428.0,E MTAB 46171473686057:LCK 8 7 ,0:125 1:125,A:20962383;C:16075445;G:14106982;T:21286579;N:175611,125,125,,,20962383,16075445,14106982,21286579,175611,ERX1690865,ERS1343553,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.56374,0.55869,0.15373,0.15614,0.98573,0.98748,0.61041,0.61515,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4256,ERR1620499,ERX1690864,ERS1343552,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#6,SAMEA4432103,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432103|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:46|Submitter Id:E MTAB 46171473686057:LCK 8#6|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:33571|genotype:heterozygous Tglck:EGFP|gfp fluorescence:661|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#6|side scatter:54|single cell well quality:good quality|well:A6|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#6 p,LCK 8#6 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 33571:forward scatter|Experimental Factor: 54:side scatter|Experimental Factor: 661:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_8_6_1.fq LCK_8_6_2.fq,fastq fastq,132079500.0,528318.0,E MTAB 46171473686057:LCK 8 6 ,0:125 1:125,A:37881943;C:29097279;G:26662941;T:38123649;N:313688,125,125,,,37881943,29097279,26662941,38123649,313688,ERX1690864,ERS1343552,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.63313,0.62967,0.22695,0.22942,0.98638,0.98774,0.55539,0.55001,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4257,ERR1620498,ERX1690863,ERS1343551,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#5,SAMEA4432102,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432102|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:55|Submitter Id:E MTAB 46171473686057:LCK 8#5|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:38889|genotype:heterozygous Tglck:EGFP|gfp fluorescence:2449|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#5|side scatter:43|single cell well quality:good quality|well:A5|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#5 p,LCK 8#5 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 38889:forward scatter|Experimental Factor: 43:side scatter|Experimental Factor: 2449:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_8_5_1.fq LCK_8_5_2.fq,fastq fastq,259622250.0,1038489.0,E MTAB 46171473686057:LCK 8 5 ,0:125 1:125,A:70294454;C:60562889;G:55907864;T:72261072;N:595971,125,125,,,70294454,60562889,55907864,72261072,595971,ERX1690863,ERS1343551,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.50845,0.50406,0.15833,0.16088,0.97804,0.97944,0.5751,0.57925,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4258,ERR1620497,ERX1690862,ERS1343550,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#4,SAMEA4432101,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432101|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:44|Submitter Id:E MTAB 46171473686057:LCK 8#4|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:34206|genotype:heterozygous Tglck:EGFP|gfp fluorescence:609|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#4|side scatter:29|single cell well quality:good quality|well:A4|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#4 p,LCK 8#4 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 34206:forward scatter|Experimental Factor: 29:side scatter|Experimental Factor: 609:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2019 01 23,LCK_8_4_1.fq LCK_8_4_2.fq,fastq fastq,223037500.0,892150.0,E MTAB 46171473686057:LCK 8 4 ,0:125 1:125,A:64103523;C:48835067;G:44820926;T:64749033;N:528951,125,125,,,64103523,48835067,44820926,64749033,528951,ERX1690862,ERS1343550,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.66738,0.66751,0.26433,0.26787,0.98691,0.9879,0.59795,0.6032,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4259,ERR1620496,ERX1690861,ERS1343549,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#3,SAMEA4432100,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432100|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:15|Submitter Id:E MTAB 46171473686057:LCK 8#3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:39434|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1769|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#3|side scatter:35|single cell well quality:good quality|well:A3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#3 p,LCK 8#3 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 39434:forward scatter|Experimental Factor: 35:side scatter|Experimental Factor: 1769:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_3_1.fq LCK_8_3_2.fq,fastq fastq,80979500.0,323918.0,E MTAB 46171473686057:LCK 8 3 ,0:125 1:125,A:24733446;C:16721540;G:14416910;T:24901839;N:205765,125,125,,,24733446,16721540,14416910,24901839,205765,ERX1690861,ERS1343549,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.65177,0.64614,0.16794,0.16959,0.98336,0.98549,0.55341,0.55637,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4260,ERR1620495,ERX1690860,ERS1343548,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#27,SAMEA4432099,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432099|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:14|Submitter Id:E MTAB 46171473686057:LCK 8#27|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:30818|genotype:heterozygous Tglck:EGFP|gfp fluorescence:692|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#27|side scatter:40|single cell well quality:good quality|well:C3|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#27 p,LCK 8#27 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 30818:forward scatter|Experimental Factor: 40:side scatter|Experimental Factor: 692:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_27_1.fq LCK_8_27_2.fq,fastq fastq,1152812500.0,4611250.0,E MTAB 46171473686057:LCK 8 27 ,0:125 1:125,A:340109783;C:242696953;G:211779212;T:355709569;N:2516983,125,125,,,340109783,242696953,211779212,355709569,2516983,ERX1690860,ERS1343548,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.8102,0.81382,0.26627,0.27235,0.9861,0.98656,0.5797,0.5765,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System
4261,ERR1620494,ERX1690859,ERS1343547,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 8#26,SAMEA4432098,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 09 12|External Id:SAMEA4432098|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:25Z|INSDC last update:2016 09 12T14:14:53Z|INSDC status:public|PI fluorescence:28|Submitter Id:E MTAB 46171473686057:LCK 8#26|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|forward scatter:35854|genotype:heterozygous Tglck:EGFP|gfp fluorescence:1048|individual:2|organism part:spleen|plate:8|sample name:E MTAB 46171473686057:LCK 8#26|side scatter:64|single cell well quality:good quality|well:C2|well information:single cell,,,,,,,,,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,E MTAB 46171473686057:LCK 8#26 p,LCK 8#26 p,Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,Spleens from two heterozygous Tglck:EGFP fish were dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: spleen:organism part|Experimental Factor: 35854:forward scatter|Experimental Factor: 64:side scatter|Experimental Factor: 1048:GFP fluorescence,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2000 paired end sequencing; Single cell RNA sequencing of spleen derived LCK expressing cells from adult zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_8_26_1.fq LCK_8_26_2.fq,fastq fastq,410481250.0,1641925.0,E MTAB 46171473686057:LCK 8 26 ,0:125 1:125,A:115373409;C:91610126;G:82943446;T:119775715;N:778554,125,125,,,115373409,91610126,82943446,119775715,778554,ERX1690859,ERS1343547,ERA701304,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.76258,0.76471,0.24418,0.24963,0.98557,0.98616,0.50436,0.51005,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Spleen,Hematopoietic System