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run_metadata

11 rows where devstage_curation_coarse = "Larval" and tissue_curation_coarse = "Cancer or Tumor"

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experiment.library_layout 2

tissue_curation_coarse 1

  • Cancer or Tumor · 11 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation_coarse 1

  • Larval · 11 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
41564 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 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 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 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 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 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
41570 41570 SRR5044686 SRX2367696 SRS1813795 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 1 GSM2399710   tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma ZMEL1 METASTATIC 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 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 GSM2399710 GSM2399710: ZMEL1 METASTATIC REP 1; Danio rerio; RNA Seq GSM2399710   1 Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq GEO Accession:GSM2399710 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP093723     DISSEMINATED-1-GFP-POS_GGCTAC_AC62F2ANXX_L006_001.R1.fastq DISSEMINATED-1-GFP-POS_GGCTAC_AC62F2ANXX_L006_001.R2.fastq fastq fastq 1056705000.0 10567050.0 GSM2399710 r1 0:50 1:50 A:276214070;C:230055594;G:254656322;T:295743831;N:35183 50 50     276214070 230055594 254656322 295743831 35183 SRX2367696 SRS1813795 SRA497524 GEO White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center 2 0.87206 0.87707 0.36 0.36551 0.80661 0.81442 0.67855 0.54025 50 50 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2016-11-22 Larval Larval Cancer or Tumor Cancer or Tumor
41571 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 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 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 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

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