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
41564,SRR5044691,SRX2367699,SRS1813797,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 4,GSM2399713,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 4,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399713,GSM2399713: ZMEL1 METASTATIC REP 4; Danio rerio; RNA Seq,GSM2399713,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399713,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-A1-ISK-GFP-pos_CTTGTA_AHBENJADXX_L001_001.R1.fastq,fastq,1021688450.0,20433769.0,GSM2399713 r1,0:50,A:263964434;C:226020906;G:246160135;T:285440788;N:102187,50,,,,263964434,226020906,246160135,285440788,102187,SRX2367699,SRS1813797,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.86173,,0.35054,,0.78305,,0.63081,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41565,SRR5044692,SRX2367699,SRS1813797,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 4,GSM2399713,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 4,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399713,GSM2399713: ZMEL1 METASTATIC REP 4; Danio rerio; RNA Seq,GSM2399713,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399713,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-A1-ISK-GFP-pos_CTTGTA_AHBENJADXX_L002_001.R1.fastq,fastq,948274550.0,18965491.0,GSM2399713 r2,0:50,A:244756056;C:209496504;G:228095978;T:264427260;N:1498752,50,,,,244756056,209496504,228095978,264427260,1498752,SRX2367699,SRS1813797,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.86249,,0.35012,,0.78147,,0.61412,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41566,SRR5044689,SRX2367698,SRS1813796,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 3,GSM2399712,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 3,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399712,GSM2399712: ZMEL1 METASTATIC REP 3; Danio rerio; RNA Seq,GSM2399712,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399712,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-4-GFP-POS_AGTTCC_AHBENJADXX_L001_001.R1.fastq,fastq,547347950.0,10946959.0,GSM2399712 r1,0:50,A:142532772;C:118021475;G:130457816;T:156280877;N:55010,50,,,,142532772,118021475,130457816,156280877,55010,SRX2367698,SRS1813796,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.82238,,0.37848,,0.81511,,0.68704,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41567,SRR5044690,SRX2367698,SRS1813796,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 3,GSM2399712,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 3,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399712,GSM2399712: ZMEL1 METASTATIC REP 3; Danio rerio; RNA Seq,GSM2399712,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399712,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-4-GFP-POS_AGTTCC_AHBENJADXX_L002_001.R1.fastq,fastq,507753450.0,10155069.0,GSM2399712 r2,0:50,A:132079203;C:109301536;G:120877231;T:144665731;N:829749,50,,,,132079203,109301536,120877231,144665731,829749,SRX2367698,SRS1813796,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.8144,,0.37493,,0.81682,,0.68224,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41568,SRR5044687,SRX2367697,SRS1813798,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 2,GSM2399711,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 2,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399711,GSM2399711: ZMEL1 METASTATIC REP 2; Danio rerio; RNA Seq,GSM2399711,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399711,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-3-GFP-POS_AGTCAA_AHBENJADXX_L001_001.R1.fastq,fastq,487099600.0,9741992.0,GSM2399711 r1,0:50,A:128774562;C:103935704;G:114312614;T:140027704;N:49016,50,,,,128774562,103935704,114312614,140027704,49016,SRX2367697,SRS1813798,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.83241,,0.38945,,0.77759,,0.63782,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41569,SRR5044688,SRX2367697,SRS1813798,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 METASTATIC REP 2,GSM2399711,,tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma,ZMEL1 METASTATIC REP 2,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vivo,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399711,GSM2399711: ZMEL1 METASTATIC REP 2; Danio rerio; RNA Seq,GSM2399711,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399711,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,DISSEMINATED-3-GFP-POS_AGTCAA_AHBENJADXX_L002_001.R1.fastq,fastq,452003900.0,9040078.0,GSM2399711 r2,0:50,A:119365829;C:96270497;G:105927958;T:129699772;N:739844,50,,,,119365829,96270497,105927958,129699772,739844,SRX2367697,SRS1813798,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.8334,,0.39284,,0.78033,,0.63687,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41571,SRR5044684,SRX2367695,SRS1813794,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 IN VITRO REP 2,GSM2399709,,tissue:ZMEL1 cells in vitro|cell type:ZMEL1|tissue type:melanoma,ZMEL1 IN VITRO REP 2,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vitro,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399709,GSM2399709: ZMEL1 IN VITRO REP 2; Danio rerio; RNA Seq,GSM2399709,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399709,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,ZMEL3-ISK_CGATGT_AHBENJADXX_L001_001.R1.fastq,fastq,769908950.0,15398179.0,GSM2399709 r1,0:50,A:182817342;C:191713397;G:197387080;T:197914424;N:76707,50,,,,182817342,191713397,197387080,197914424,76707,SRX2367695,SRS1813794,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.90333,,0.27932,,0.80894,,0.6691,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41572,SRR5044685,SRX2367695,SRS1813794,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 IN VITRO REP 2,GSM2399709,,tissue:ZMEL1 cells in vitro|cell type:ZMEL1|tissue type:melanoma,ZMEL1 IN VITRO REP 2,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vitro,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399709,GSM2399709: ZMEL1 IN VITRO REP 2; Danio rerio; RNA Seq,GSM2399709,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399709,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,ZMEL3-ISK_CGATGT_AHBENJADXX_L002_001.R1.fastq,fastq,713052900.0,14261058.0,GSM2399709 r2,0:50,A:169193359;C:177235371;G:182562897;T:182889589;N:1171684,50,,,,169193359,177235371,182562897,182889589,1171684,SRX2367695,SRS1813794,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.90483,,0.2787,,0.80892,,0.66955,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41573,SRR5044682,SRX2367694,SRS1813793,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 IN VITRO REP 1,GSM2399708,,tissue:ZMEL1 cells in vitro|cell type:ZMEL1|tissue type:melanoma,ZMEL1 IN VITRO REP 1,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vitro,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399708,GSM2399708: ZMEL1 IN VITRO REP 1; Danio rerio; RNA Seq,GSM2399708,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399708,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,ZMEL1_ATCACG_AHBENJADXX_L001_001.R1.fastq,fastq,480071700.0,9601434.0,GSM2399708 r1,0:50,A:126381285;C:102596587;G:111718527;T:139327539;N:47762,50,,,,126381285,102596587,111718527,139327539,47762,SRX2367694,SRS1813793,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.86224,,0.32994,,0.78106,,0.62148,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41574,SRR5044683,SRX2367694,SRS1813793,SRP093723,PRJNA354577,RNA seq of zebrafish melanoma cells post metastatic dissemination,GSE90143,Transcriptome Analysis,We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos  as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish,,pubmed:28181494,,ZMEL1 IN VITRO REP 1,GSM2399708,,tissue:ZMEL1 cells in vitro|cell type:ZMEL1|tissue type:melanoma,ZMEL1 IN VITRO REP 1,GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq,ZMEL1 cells in vitro,n/a,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,in vitro: DMEM/10% FCS/1X glutamax/28.5C     in vivo: growth in the zebrafish from 2 21dpf,cell type:ZMEL1|tissue type:melanoma,GSM2399708,GSM2399708: ZMEL1 IN VITRO REP 1; Danio rerio; RNA Seq,GSM2399708,,1,Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq,GEO Accession:GSM2399708,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093723,,,ZMEL1_ATCACG_AHBENJADXX_L002_001.R1.fastq,fastq,444225800.0,8884516.0,GSM2399708 r2,0:50,A:116866564;C:94744486;G:103253213;T:128645533;N:716004,50,,,,116866564,94744486,103253213,128645533,716004,SRX2367694,SRS1813793,SRA497524,GEO,"White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center",1,0.86139,,0.32876,,0.78259,,0.62694,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Cancer or Tumor,Cancer or Tumor
41616,SRR5099113,SRX2415891,SRS1853479,SRP094947,PRJNA357051,Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods,GSE92260,Transcriptome Analysis,we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes  rb1  induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry  we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB like PNETs Overall design: QuantSeq three prime mRNA sequencing with whole brain tissue wild type WT zebrafish and tumors induced by rb1 TALENs injected zebrafish at xxx mpf,,pubmed:28903419,,FFPE 2,GSM2424730,,source name:tumor 2 induced by rb1 TALENs|strain:p53M214K|tissue:tumor tissues 2 induced by rb1 TALENs|developmental stage:5 mpf,FFPE 2,Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequenceusing fastx trimmer  then mapped to danRer10 whole genome using Bowtie2 Read count extraction and nomalization were performed using edgeR. Genome build: danRer10 Supplementary files format and content: FFPE 1.txt and FFPE 2.txt report quantile normalized abundance measurements. Supplementary files format and content: WT.txt report quantile normalized abundance measurements.  Column WT1 reports quantile normalized abundance measurements post quantile   normalization had done between WT and FFPE 1.  Column WT2 reports quantile normalized abundance measurements post quantile   normalization had done between WT and FFPE 2.,tumor 2 induced by rb1 TALENs,,RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.,,strain:p53M214K|tissue:tumor tissues 2 induced by rb1 TALENs|developmental stage:5 mpf,GSM2424730,GSM2424730: FFPE 2; Danio rerio; RNA Seq,GSM2424730,,1,RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.,GEO Accession:GSM2424730,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP094947,,,FFPE-2_fastq.gz,fastq,900420050.0,8915050.0,GSM2424730 r1,0:101,A:404381931;C:201118712;G:149335807;T:145550067;N:33533,101,,,,404381931,201118712,149335807,145550067,33533,SRX2415891,SRS1853479,SRA502460,GEO,"Research Institute, National Cancer Center",1,0.03639,,0.02825,,0.9978,,0.55688,,101,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Unknown,2016-12-12,Adult,Adult,Cancer or Tumor,Cancer or Tumor
41617,SRR5099112,SRX2415890,SRS1853478,SRP094947,PRJNA357051,Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods,GSE92260,Transcriptome Analysis,we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes  rb1  induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry  we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB like PNETs Overall design: QuantSeq three prime mRNA sequencing with whole brain tissue wild type WT zebrafish and tumors induced by rb1 TALENs injected zebrafish at xxx mpf,,pubmed:28903419,,FFPE 1,GSM2424729,,source name:tumor 1 induced by rb1 TALENs|strain:p53M214K|tissue:tumor tissues 1 induced by rb1 TALENs|developmental stage:5 mpf,FFPE 1,Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequenceusing fastx trimmer  then mapped to danRer10 whole genome using Bowtie2 Read count extraction and nomalization were performed using edgeR. Genome build: danRer10 Supplementary files format and content: FFPE 1.txt and FFPE 2.txt report quantile normalized abundance measurements. Supplementary files format and content: WT.txt report quantile normalized abundance measurements.  Column WT1 reports quantile normalized abundance measurements post quantile   normalization had done between WT and FFPE 1.  Column WT2 reports quantile normalized abundance measurements post quantile   normalization had done between WT and FFPE 2.,tumor 1 induced by rb1 TALENs,,RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.,,strain:p53M214K|tissue:tumor tissues 1 induced by rb1 TALENs|developmental stage:5 mpf,GSM2424729,GSM2424729: FFPE 1; Danio rerio; RNA Seq,GSM2424729,,1,RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.,GEO Accession:GSM2424729,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP094947,,,FFPE-1_fastq.gz,fastq,985654556.0,9758956.0,GSM2424729 r1,0:101,A:642158389;C:109642019;G:103170689;T:130633868;N:49591,101,,,,642158389,109642019,103170689,130633868,49591,SRX2415890,SRS1853478,SRA502460,GEO,"Research Institute, National Cancer Center",1,0.71847,,0.59813,,0.9376,,0.57167,,101,,B,,usable mapping rate,illumina,nextseq,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Unknown,2016-12-12,Adult,Adult,Cancer or Tumor,Cancer or Tumor
41811,SRR5196075,SRX2511746,SRS1935439,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably  complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma  livers of  transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,CarcinomaM,GSM2465779,,source name:Hepatocellular carcinoma of transgenic fishes post mifeprist1 withdrawal|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,CarcinomaM,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Hepatocellular carcinoma of transgenic fishes post mifepristone withdrawal,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465779,GSM2465779: CarcinomaM; Danio rerio; RNA Seq,GSM2465779,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465779,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE_6T2_F3.csfasta.gz solid_SAGE_6T2_F3_QV.qual.gz,SOLiD_native SOLiD_native,818910190.0,23397434.0,GSM2465779 r1,0:35,0:347259734;1:164743259;2:162029194;3:130508344;.:14369659,35,,,,,,,,,SRX2511746,SRS1935439,SRA530985,GEO,The Biomedical Center,1,0.03756,,0.00615,,0.99928,,0.91338,,35,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
41812,SRR5196074,SRX2511745,SRS1935438,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably  complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma  livers of  transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,Carcinoma,GSM2465778,,source name:Hepatocellular carcinoma of transgenic fishes|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,Carcinoma,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Hepatocellular carcinoma of  transgenic fishes,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465778,GSM2465778: Carcinoma; Danio rerio; RNA Seq,GSM2465778,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465778,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE_6T1_F3.csfasta.gz solid_SAGE_6T1_F3_QV.qual.gz,SOLiD_native SOLiD_native,761241005.0,21749743.0,GSM2465778 r1,0:35,0:306840116;1:164725874;2:160786359;3:126370697;.:2517959,35,,,,,,,,,SRX2511745,SRS1935438,SRA530985,GEO,The Biomedical Center,1,0.0543,,0.00668,,0.9988,,0.95092,,35,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
50848,SRR8312803,SRX5126180,SRS4139302,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1314,GSM3509262,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1314,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509262,GSM3509262: nonSP 1314; Danio rerio; RNA Seq,GSM3509262,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509262,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,1102240750.0,22044815.0,GSM3509262 r1,0:50 1:0,A:238366338;C:290902481;G:270336209;T:302466123;N:169599,50,0,,,238366338,290902481,270336209,302466123,169599,SRX5126180,SRS4139302,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.95733,,0.05326,,0.82195,,0.45391,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50849,SRR8312804,SRX5126180,SRS4139302,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1314,GSM3509262,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1314,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509262,GSM3509262: nonSP 1314; Danio rerio; RNA Seq,GSM3509262,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509262,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,2100323600.0,42006472.0,GSM3509262 r2,0:50 1:0,A:454665602;C:553824333;G:514968464;T:576182722;N:682479,50,0,,,454665602,553824333,514968464,576182722,682479,SRX5126180,SRS4139302,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.95581,,0.05304,,0.82246,,0.44598,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50850,SRR8312801,SRX5126179,SRS4139301,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1314,GSM3509261,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1314,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509261,GSM3509261: SP 1314; Danio rerio; RNA Seq,GSM3509261,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509261,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,1795016300.0,35900326.0,GSM3509261 r1,0:50 1:0,A:414364764;C:453952517;G:425127792;T:501295946;N:275281,50,0,,,414364764,453952517,425127792,501295946,275281,SRX5126179,SRS4139301,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.94054,,0.1034,,0.77199,,0.50665,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50851,SRR8312802,SRX5126179,SRS4139301,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1314,GSM3509261,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1314,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509261,GSM3509261: SP 1314; Danio rerio; RNA Seq,GSM3509261,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509261,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,1643807200.0,32876144.0,GSM3509261 r2,0:50 1:0,A:379875320;C:415331594;G:389155351;T:458912143;N:532792,50,0,,,379875320,415331594,389155351,458912143,532792,SRX5126179,SRS4139301,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.93812,,0.1016,,0.77281,,0.50853,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50852,SRR8312799,SRX5126178,SRS4139300,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1279,GSM3509260,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1279,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509260,GSM3509260: nonSP 1279; Danio rerio; RNA Seq,GSM3509260,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509260,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,971515350.0,19430307.0,GSM3509260 r1,0:50 1:0,A:209882045;C:255304153;G:238689373;T:267489989;N:149790,50,0,,,209882045,255304153,238689373,267489989,149790,SRX5126178,SRS4139300,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.96223,,0.08865,,0.85437,,0.45664,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50853,SRR8312800,SRX5126178,SRS4139300,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1279,GSM3509260,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1279,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509260,GSM3509260: nonSP 1279; Danio rerio; RNA Seq,GSM3509260,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509260,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,859048800.0,17180976.0,GSM3509260 r2,0:50 1:0,A:185797914;C:225529235;G:211061558;T:236378727;N:281366,50,0,,,185797914,225529235,211061558,236378727,281366,SRX5126178,SRS4139300,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.96055,,0.08804,,0.85283,,0.48896,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50854,SRR8312797,SRX5126177,SRS4139299,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1279,GSM3509259,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1279,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509259,GSM3509259: SP 1279; Danio rerio; RNA Seq,GSM3509259,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509259,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,843819050.0,16876381.0,GSM3509259 r1,0:50 1:0,A:199287616;C:210295815;G:195583208;T:238522867;N:129544,50,0,,,199287616,210295815,195583208,238522867,129544,SRX5126177,SRS4139299,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.9391,,0.1451,,0.79683,,0.50281,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50855,SRR8312798,SRX5126177,SRS4139299,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1279,GSM3509259,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1279,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509259,GSM3509259: SP 1279; Danio rerio; RNA Seq,GSM3509259,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509259,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,2285635100.0,45712702.0,GSM3509259 r2,0:50 1:0,A:540527368;C:568996224;G:529423615;T:645948448;N:739445,50,0,,,540527368,568996224,529423615,645948448,739445,SRX5126177,SRS4139299,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.93725,,0.14453,,0.79746,,0.4961,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50856,SRR8312795,SRX5126176,SRS4139298,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1404,GSM3509258,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1404,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509258,GSM3509258: nonSP 1404; Danio rerio; RNA Seq,GSM3509258,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509258,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,2069543600.0,41390872.0,GSM3509258 r1,0:50 1:0,A:459382162;C:532071054;G:508544948;T:569228380;N:317056,50,0,,,459382162,532071054,508544948,569228380,317056,SRX5126176,SRS4139298,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.96095,,0.06905,,0.83412,,0.4818,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50857,SRR8312796,SRX5126176,SRS4139298,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,nonSP 1404,GSM3509258,,source name:ALL tumor|strain:CG2|tissue:ALL,nonSP 1404,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509258,GSM3509258: nonSP 1404; Danio rerio; RNA Seq,GSM3509258,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509258,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,1547447200.0,30948944.0,GSM3509258 r2,0:50 1:0,A:343821341;C:397523901;G:380174292;T:425426296;N:501370,50,0,,,343821341,397523901,380174292,425426296,501370,SRX5126176,SRS4139298,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.95838,,0.06884,,0.83414,,0.48727,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50858,SRR8312793,SRX5126175,SRS4139297,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1404,GSM3509257,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1404,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509257,GSM3509257: SP 1404; Danio rerio; RNA Seq,GSM3509257,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509257,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,2020346850.0,40406937.0,GSM3509257 r1,0:50 1:0,A:476259938;C:502400578;G:476364320;T:565010528;N:311486,50,0,,,476259938,502400578,476364320,565010528,311486,SRX5126175,SRS4139297,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.94163,,0.11567,,0.79287,,0.52008,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
50859,SRR8312794,SRX5126175,SRS4139297,SRP173302,PRJNA509471,The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia.,GSE123665,Transcriptome Analysis,Cancer stem cells have been strongly linked to resistance and relapse in many malignancies. However  purifying them from within the bulk tumor has been challenging  so their precise genetic and functional characteristics are not well defined. The side population assay exploits the ability of some cells to efflux Hoechst dye via ABC transporters. Stem cells have increased expression of these transporters and this assay has been shown to enrich for stem cells in various tissues and cancers. This study identifies the side population within a zebrafish model of acute lymphoblastic leukemia and correlates the frequency of side population cells with the frequency of leukemia stem cells more precisely referred to as leukemia propagating cells within our transplantation model. In addition  the side population within the leukemia evolves with serial transplantation  increasing in tandem with leukemia propagating cell frequency over subsequent generations. Sorted side population cells from these tumors are enriched for leukemia propagating cells and have enhanced engraftment compared to sorted non side population cells when transplanted into syngeneic recipients. RNA sequencing analysis of sorted side population cells compared to non side population cells identified a shared expression profile within the side population and pathway analysis yielded Wnt signaling as the most overrepresented. Gene set enrichment analysis showed that stem cell differentiation and canonical Wnt signaling were significantly upregulated in the side population. Overall  these results demonstrate that the side population in zebrafish acute lymphoblastic leukemia significantly enriches for leukemia propagating cells and identifies the Wnt pathway as a likely genetic driver of leukemia stem cell fate. Overall design: mRNA expression comparison between sorted side population and non side population in 3 zebrafish ALL tumors,,pubmed:30630989,,SP 1404,GSM3509257,,source name:ALL tumor|strain:CG2|tissue:ALL,SP 1404,Illumina Casava1.7 software used for basecalling. All RNA seq reads were used to align to the genome assembly GRCz10 using STAR v2.5.1b with default configurations. Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM Fragments Per Kilobase Million tables. Using 4 as the fold change cutoff  DEGs Differentially expressed genes were detected using both Tuxedo suite FPKM based method and featureCounts DESeq v1.30.0  edgeR v3.20.7 read count based method with default configurations. Genes detected by at least more than one method were collected to create a high confidence DEG lists. Genome build: GRCz10 Supplementary files format and content: Count tables were generated using featureCount v1.28.1 based on Ensembl annotation GRCz10.,ALL tumor,None,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,None,strain:CG2|tissue:ALL,GSM3509257,GSM3509257: SP 1404; Danio rerio; RNA Seq,GSM3509257,,1,Tumors were removed  sorted by FACS and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3509257,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP173302,,,,,1560387300.0,31207746.0,GSM3509257 r2,0:50 1:0,A:368229806;C:387650010;G:367757630;T:436243680;N:506174,50,0,,,368229806,387650010,367757630,436243680,506174,SRX5126175,SRS4139297,SRA822847,GEO,"Bioinformatics Core, Biological Sciences Division, The University of Chicago",1,0.93995,,0.11774,,0.79444,,0.49697,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-12-11,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59561,SRR11926643,SRX8472289,SRS6772890,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T2,GSM4591324,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,T2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591324,GSM4591324: T2; Danio rerio; RNA Seq,GSM4591324,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591324,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_24.fastq.gz,fastq,3352396700.0,44370046.0,GSM4591324 r1,0:75.56 1:0,A:755348675;C:859386520;G:800067906;T:937329969;N:263630,75,0,,,755348675,859386520,800067906,937329969,263630,SRX8472289,SRS6772890,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96963,,0.06719,,0.81755,,0.50255,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59562,SRR11926642,SRX8472288,SRS6772889,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T2 2,GSM4591323,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T2 2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591323,GSM4591323: T2 2; Danio rerio; RNA Seq,GSM4591323,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591323,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_23.fastq.gz,fastq,3718498010.0,49228779.0,GSM4591323 r1,0:75.54 1:0,A:848213188;C:950067431;G:877745427;T:1042167763;N:304201,75,0,,,848213188,950067431,877745427,1042167763,304201,SRX8472288,SRS6772889,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96846,,0.08566,,0.80708,,0.51642,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59563,SRR11926641,SRX8472287,SRS6772888,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T2 2 3,GSM4591322,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T2 2 3,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591322,GSM4591322: T2 2 3; Danio rerio; RNA Seq,GSM4591322,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591322,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_22.fastq.gz,fastq,3433698150.0,45471576.0,GSM4591322 r1,0:75.51 1:0,A:791522856;C:866434769;G:797134042;T:978335562;N:270921,75,0,,,791522856,866434769,797134042,978335562,270921,SRX8472287,SRS6772888,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96727,,0.13235,,0.80375,,0.51948,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59564,SRR11926640,SRX8472286,SRS6772887,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T2 2 1,GSM4591321,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T2 2 1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591321,GSM4591321: T2 2 1; Danio rerio; RNA Seq,GSM4591321,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591321,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_21.fastq.gz,fastq,3340319927.0,44222057.0,GSM4591321 r1,0:75.54 1:0,A:783394487;C:834577900;G:758192327;T:963889109;N:266104,75,0,,,783394487,834577900,758192327,963889109,266104,SRX8472286,SRS6772887,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.95862,,0.19113,,0.80117,,0.51412,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59565,SRR11926639,SRX8472285,SRS6772885,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T2 1,GSM4591320,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T2 1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591320,GSM4591320: T2 1; Danio rerio; RNA Seq,GSM4591320,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591320,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_20.fastq.gz,fastq,3407895222.0,45108733.0,GSM4591320 r1,0:75.55 1:0,A:772284922;C:869002714;G:804588273;T:961751439;N:267874,75,0,,,772284922,869002714,804588273,961751439,267874,SRX8472285,SRS6772885,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96729,,0.10404,,0.80819,,0.50282,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59566,SRR11926638,SRX8472284,SRS6772886,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T1,GSM4591319,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,T1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591319,GSM4591319: T1; Danio rerio; RNA Seq,GSM4591319,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591319,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_19.fastq.gz,fastq,3399960459.0,45000945.0,GSM4591319 r1,0:75.55 1:0,A:757716117;C:885849357;G:808221386;T:947866574;N:307025,75,0,,,757716117,885849357,808221386,947866574,307025,SRX8472284,SRS6772886,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96322,,0.0579,,0.80509,,0.51314,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59567,SRR11926637,SRX8472283,SRS6772884,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T1 2,GSM4591318,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T1 2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591318,GSM4591318: T1 2; Danio rerio; RNA Seq,GSM4591318,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591318,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_18.fastq.gz,fastq,3375335979.0,44692348.0,GSM4591318 r1,0:75.52 1:0,A:752811966;C:868444009;G:810580314;T:943232624;N:267066,75,0,,,752811966,868444009,810580314,943232624,267066,SRX8472283,SRS6772884,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96578,,0.07571,,0.82558,,0.50359,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59568,SRR11926636,SRX8472282,SRS6772883,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,T1 1,GSM4591317,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,T1 1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591317,GSM4591317: T1 1; Danio rerio; RNA Seq,GSM4591317,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591317,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_17.fastq.gz,fastq,3010940849.0,39848118.0,GSM4591317 r1,0:75.56 1:0,A:668391154;C:785449019;G:724383036;T:832480672;N:236968,75,0,,,668391154,785449019,724383036,832480672,236968,SRX8472282,SRS6772883,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96967,,0.04925,,0.84764,,0.52577,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59569,SRR11926635,SRX8472281,SRS6772882,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT4,GSM4591316,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,PT4,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591316,GSM4591316: PT4; Danio rerio; RNA Seq,GSM4591316,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591316,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_16.fastq.gz,fastq,2704327748.0,35795276.0,GSM4591316 r1,0:75.55 1:0,A:606123714;C:696847421;G:651551202;T:749582467;N:222944,75,0,,,606123714,696847421,651551202,749582467,222944,SRX8472281,SRS6772882,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.97216,,0.06109,,0.81832,,0.49375,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59570,SRR11926634,SRX8472280,SRS6772881,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT3,GSM4591315,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,PT3,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591315,GSM4591315: PT3; Danio rerio; RNA Seq,GSM4591315,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591315,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_15.fastq.gz,fastq,2516254096.0,33304042.0,GSM4591315 r1,0:75.55 1:0,A:572120254;C:639148525;G:596715581;T:708079869;N:189867,75,0,,,572120254,639148525,596715581,708079869,189867,SRX8472280,SRS6772881,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.96526,,0.07769,,0.80758,,0.53064,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59571,SRR11926633,SRX8472279,SRS6772880,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT2,GSM4591314,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,PT2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591314,GSM4591314: PT2; Danio rerio; RNA Seq,GSM4591314,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591314,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_14.fastq.gz,fastq,2805545977.0,37135357.0,GSM4591314 r1,0:75.55 1:0,A:632305395;C:719045953;G:676770065;T:777205477;N:219087,75,0,,,632305395,719045953,676770065,777205477,219087,SRX8472279,SRS6772880,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.97087,,0.01807,,0.83364,,0.54322,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59572,SRR11926632,SRX8472278,SRS6772879,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT2 3,GSM4591313,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT2 3,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591313,GSM4591313: PT2 3; Danio rerio; RNA Seq,GSM4591313,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591313,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_13.fastq.gz,fastq,3227070397.0,42713584.0,GSM4591313 r1,0:75.55 1:0,A:717490964;C:839799892;G:773804253;T:895714100;N:261188,75,0,,,717490964,839799892,773804253,895714100,261188,SRX8472278,SRS6772879,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.97134,,0.05713,,0.81099,,0.49228,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59573,SRR11926631,SRX8472277,SRS6772878,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT2 2,GSM4591312,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT2 2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591312,GSM4591312: PT2 2; Danio rerio; RNA Seq,GSM4591312,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591312,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_12.fastq.gz,fastq,3212726304.0,42523190.0,GSM4591312 r1,0:75.55 1:0,A:719132496;C:829799997;G:771562071;T:891973714;N:258026,75,0,,,719132496,829799997,771562071,891973714,258026,SRX8472277,SRS6772878,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.9721,,0.04902,,0.80902,,0.52414,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59574,SRR11926630,SRX8472276,SRS6772877,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT2 1,GSM4591311,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT2 1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591311,GSM4591311: PT2 1; Danio rerio; RNA Seq,GSM4591311,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591311,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_11.fastq.gz,fastq,3021393530.0,39988248.0,GSM4591311 r1,0:75.56 1:0,A:672620933;C:786720838;G:726121643;T:835686624;N:243492,75,0,,,672620933,786720838,726121643,835686624,243492,SRX8472276,SRS6772877,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.97407,,0.03891,,0.81716,,0.49217,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59575,SRR11926629,SRX8472275,SRS6772876,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT1,GSM4591310,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,PT1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Primary T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591310,GSM4591310: PT1; Danio rerio; RNA Seq,GSM4591310,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591310,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_10.fastq.gz,fastq,3216194683.0,42575567.0,GSM4591310 r1,0:75.54 1:0,A:754906399;C:800124470;G:747953707;T:912956321;N:253786,75,0,,,754906399,800124470,747953707,912956321,253786,SRX8472275,SRS6772876,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.95808,,0.13813,,0.79782,,0.5126,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59576,SRR11926628,SRX8472274,SRS6772875,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT1 3,GSM4591309,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT1 3,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591309,GSM4591309: PT1 3; Danio rerio; RNA Seq,GSM4591309,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591309,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_9.fastq.gz,fastq,3632705131.0,48084818.0,GSM4591309 r1,0:75.55 1:0,A:864204924;C:896630766;G:806140808;T:1065445772;N:282861,75,0,,,864204924,896630766,806140808,1065445772,282861,SRX8472274,SRS6772875,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.94792,,0.24728,,0.78882,,0.49754,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59577,SRR11926627,SRX8472273,SRS6772874,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT1 2,GSM4591308,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT1 2,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591308,GSM4591308: PT1 2; Danio rerio; RNA Seq,GSM4591308,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591308,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_8.fastq.gz,fastq,2694796792.0,35662689.0,GSM4591308 r1,0:75.56 1:0,A:647242858;C:662131043;G:597596390;T:787640018;N:186483,75,0,,,647242858,662131043,597596390,787640018,186483,SRX8472273,SRS6772874,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.94581,,0.21549,,0.79064,,0.50568,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
59578,SRR11926626,SRX8472272,SRS6772873,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,PT1 1,GSM4591307,,tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,PT1 1,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab,GSM4591307,GSM4591307: PT1 1; Danio rerio; RNA Seq,GSM4591307,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591307,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP265974,,,sample_7.fastq.gz,fastq,3283930508.0,43472772.0,GSM4591307 r1,0:75.54 1:0,A:777409453;C:814864928;G:740583382;T:950812702;N:260043,75,0,,,777409453,814864928,740583382,950812702,260043,SRX8472272,SRS6772873,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",1,0.94952,,0.17765,,0.78108,,0.50322,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor
65013,SRR14902693,SRX11217415,SRS9271514,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma  understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes  pathways  and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MA3C RNAseq,GSM5397960,,source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma,MA3C RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells  as well as,Sorted melanoma tumor,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1,GSM5397960,GSM5397960: MA3C RNAseq; Danio rerio; RNA Seq,GSM5397960,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397960,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MA3C.fq.gz,fastq,1678480250.0,33569605.0,GSM5397960 r1,0:50 1:0,A:463941895;C:370163467;G:364477555;T:478705617;N:1191716,50,0,,,463941895,370163467,364477555,478705617,1191716,SRX11217415,SRS9271514,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.90303,,0.16625,,0.74696,,0.55133,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
65014,SRR14902692,SRX11217414,SRS9271513,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma  understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes  pathways  and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MA3B RNAseq,GSM5397959,,source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma,MA3B RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells  as well as,Sorted melanoma tumor,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1,GSM5397959,GSM5397959: MA3B RNAseq; Danio rerio; RNA Seq,GSM5397959,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397959,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MA3B.fq.gz,fastq,1437189100.0,28743782.0,GSM5397959 r1,0:50 1:0,A:398259972;C:317724608;G:311519412;T:408662664;N:1022444,50,0,,,398259972,317724608,311519412,408662664,1022444,SRX11217414,SRS9271513,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.89689,,0.14892,,0.73959,,0.52927,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
65015,SRR14902691,SRX11217413,SRS9271512,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma  understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes  pathways  and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MA3A RNAseq,GSM5397958,,source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma,MA3A RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells  as well as,Sorted melanoma tumor,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1,GSM5397958,GSM5397958: MA3A RNAseq; Danio rerio; RNA Seq,GSM5397958,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397958,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MA3A.fq.gz,fastq,1442377200.0,28847544.0,GSM5397958 r1,0:50 1:0,A:405524842;C:314014451;G:304964281;T:416845768;N:1027858,50,0,,,405524842,314014451,304964281,416845768,1027858,SRX11217413,SRS9271512,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.88956,,0.1683,,0.74018,,0.52927,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
65016,SRR14902690,SRX11217412,SRS9271511,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma  understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes  pathways  and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MA2 RNAseq,GSM5397957,,source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma,MA2 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells  as well as,Sorted melanoma tumor,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1,GSM5397957,GSM5397957: MA2 RNAseq; Danio rerio; RNA Seq,GSM5397957,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397957,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MA2.fq.gz,fastq,1402279300.0,28045586.0,GSM5397957 r1,0:50 1:0,A:389166788;C:306462364;G:298729361;T:406923403;N:997384,50,0,,,389166788,306462364,298729361,406923403,997384,SRX11217412,SRS9271511,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.88844,,0.14383,,0.74923,,0.53282,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
65017,SRR14902689,SRX11217411,SRS9271510,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma  understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes  pathways  and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MA1 RNAseq,GSM5397956,,source name:Sorted melanoma tumor|genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma,MA1 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells  as well as,Sorted melanoma tumor,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/p53lf/lf/crestin:EGFP|tissue:Melanoma|run #:1,GSM5397956,GSM5397956: MA1 RNAseq; Danio rerio; RNA Seq,GSM5397956,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA  then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397956,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MA1.fq.gz,fastq,1456780700.0,29135614.0,GSM5397956 r1,0:50 1:0,A:403913103;C:308144749;G:305293739;T:438394612;N:1034497,50,0,,,403913103,308144749,305293739,438394612,1034497,SRX11217411,SRS9271510,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.85833,,0.16781,,0.73407,,0.52469,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Cancer or Tumor,Cancer or Tumor
67037,SRR17007607,SRX13197809,SRS11124869,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 6 S6: EVs3,GSM5699732,,tissue:EVs3|cell type:extracellular vesicles|strain:kita:RAS,VA 6 S6: EVs3,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,EVs3,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:extracellular vesicles|strain:kita:RAS,GSM5699732,GSM5699732: VA 6 S6: EVs3; Danio rerio; ncRNA Seq,GSM5699732 r1,GSM5699732,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_6_S6.fastq,fastq,1252482921.0,12400821.0,GSM5699732 r1,0:101,A:419008099;C:291188018;G:325856780;T:216362198;N:67826,101,,,,419008099,291188018,325856780,216362198,67826,SRX13197809,SRS11124869,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.39065,,0.05651,,0.9752,,0.82248,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor
67038,SRR17007608,SRX13197808,SRS11124868,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 5 S5: EVs2,GSM5699731,,tissue:EVs2|cell type:extracellular vesicles|strain:kita:RAS,VA 5 S5: EVs2,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,EVs2,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:extracellular vesicles|strain:kita:RAS,GSM5699731,GSM5699731: VA 5 S5: EVs2; Danio rerio; ncRNA Seq,GSM5699731 r1,GSM5699731,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_5_S5.fastq,fastq,1338062039.0,13248139.0,GSM5699731 r1,0:101,A:479478471;C:303639439;G:333339820;T:221533029;N:71280,101,,,,479478471,303639439,333339820,221533029,71280,SRX13197808,SRS11124868,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.20158,,0.0338,,0.98979,,0.73724,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor
67039,SRR17007609,SRX13197807,SRS11124867,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 4 S4: EVs1,GSM5699730,,tissue:EVs1|cell type:extracellular vesicles|strain:kita:RAS,VA 4 S4: EVs1,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,EVs1,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:extracellular vesicles|strain:kita:RAS,GSM5699730,GSM5699730: VA 4 S4: EVs1; Danio rerio; ncRNA Seq,GSM5699730 r1,GSM5699730,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_4_S4.fastq,fastq,1355391215.0,13419715.0,GSM5699730 r1,0:101,A:480538643;C:302531816;G:333018117;T:239227931;N:74708,101,,,,480538643,302531816,333018117,239227931,74708,SRX13197807,SRS11124867,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.15363,,0.03047,,0.98563,,0.85818,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor
67040,SRR17007610,SRX13197806,SRS11124866,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 24 S14: Melanoma3,GSM5699729,,tissue:Melanoma3|cell type:Melanocytes|strain:kita:RAS,VA 24 S14: Melanoma3,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,Melanoma3,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:Melanocytes|strain:kita:RAS,GSM5699729,GSM5699729: VA 24 S14: Melanoma3; Danio rerio; ncRNA Seq,GSM5699729 r1,GSM5699729,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_24_S14.fastq,fastq,1029043954.0,10188554.0,GSM5699729 r1,0:101,A:385266918;C:235984418;G:223100119;T:184638731;N:53768,101,,,,385266918,235984418,223100119,184638731,53768,SRX13197806,SRS11124866,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.31444,,0.04431,,0.97477,,0.79077,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor
67041,SRR17007611,SRX13197805,SRS11124865,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 23 S13: Melanoma2,GSM5699728,,tissue:Melanoma2|cell type:Melanocytes|strain:kita:RAS,VA 23 S13: Melanoma2,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,Melanoma2,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:Melanocytes|strain:kita:RAS,GSM5699728,GSM5699728: VA 23 S13: Melanoma2; Danio rerio; ncRNA Seq,GSM5699728 r1,GSM5699728,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_23_S13.fastq,fastq,1191776669.0,11799769.0,GSM5699728 r1,0:101,A:445740725;C:275311735;G:268819689;T:201841457;N:63063,101,,,,445740725,275311735,268819689,201841457,63063,SRX13197805,SRS11124865,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.3168,,0.04419,,0.96978,,0.837,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor
67042,SRR17007612,SRX13197804,SRS11124864,SRP347244,PRJNA782626,Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content,GSE189352,Transcriptome Analysis,Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs  iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of  140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion  but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene  GFP HRASV12G within their vesicular membrane.  Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs  with only 18 of them be ing selectively enriched in iEVs. Among these  the RNA components of RNAses MRP and P  which process ribosomal RNA precursors  mitochondrial RNAs and some mRNAs  were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma   we performed RNA sequencing analysis RNA Seq  of small RNAs isolated from EVs and melanoma samples.,,pubmed:35628321,,VA 22 S12: Melanoma1,GSM5699727,,tissue:Melanoma1|cell type:Melanocytes|strain:Kita:RAS,VA 22 S12: Melanoma1,Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing  the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample,Melanoma1,,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,Melanomas were induced in developing zebrafish through the Gal4/UAS system  using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid,cell type:Melanocytes|strain:Kita:RAS,GSM5699727,GSM5699727: VA 22 S12: Melanoma1; Danio rerio; ncRNA Seq,GSM5699727 r1,GSM5699727,1,RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions  subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP347244,,loader:fastq load.py,VA_22_S12.fastq,fastq,849183861.0,8407761.0,GSM5699727 r1,0:101,A:315648935;C:198401378;G:181384813;T:153698818;N:49917,101,,,,315648935,198401378,181384813,153698818,49917,SRX13197804,SRS11124864,SRA1429699,"Experimental Cancer Biology, CIBIO, University of Trento","Experimental Cancer Biology, CIBIO, University of Trento",1,0.37018,,0.04901,,0.96209,,0.55085,,101,,B,,usable mapping rate,illumina,hiseq_era,full_length,size_fractionation,smarter,bulk,unknown,unknown,,Italy,2021-11-22,Adult,Adult,Cancer or Tumor,Cancer or Tumor