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 50529,SRR8129708,SRX4950830,SRS3993021,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2 replicate b,GSM3449969,,tissue:Fli:GFP sorted 3 days RNeasy sample 2 replicate b|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2 replicate b,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP sorted 3 days RNeasy sample 2 replicate b,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449969,GSM3449969: RNeasy sorted 2 replicate b; Danio rerio; RNA Seq,GSM3449969,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449969,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,Q_2b_R1.fastq.gz Q_2b_R2.fastq.gz,fastq fastq,3579768697.0,23697156.0,GSM3449969 r1,0:75.53 1:75.53,A:917613628;C:877326634;G:877017498;T:907801181;N:9756,75,75,,,917613628,877326634,877017498,907801181,9756,SRX4950830,SRS3993021,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93264,0.93171,0.08657,0.08851,0.73878,0.74383,0.48764,0.4769,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined 50530,SRR8129707,SRX4950829,SRS3993019,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2 replicate a,GSM3449968,,tissue:Fli:GFP sorted 3 days RNeasy sample 2 replicate a|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2 replicate a,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP sorted 3 days RNeasy sample 2 replicate a,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449968,GSM3449968: RNeasy sorted 2 replicate a; Danio rerio; RNA Seq,GSM3449968,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449968,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,Q_2a_R1.fastq.gz Q_2a_R2.fastq.gz,fastq fastq,3145186655.0,20819322.0,GSM3449968 r1,0:75.54 1:75.54,A:794507127;C:779916130;G:782068102;T:788686496;N:8800,75,75,,,794507127,779916130,782068102,788686496,8800,SRX4950829,SRS3993019,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93181,0.93429,0.07677,0.08034,0.73703,0.74736,0.49133,0.47929,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined 50531,SRR8129706,SRX4950828,SRS3993020,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 2 replicate b,GSM3449967,,tissue:Fli:GFP sorted 3 days RNAqueous sample 2 replicate b|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 2 replicate b,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP sorted 3 days RNAqueous sample 2 replicate b,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449967,GSM3449967: RNAqueous sorted 2 replicate b; Danio rerio; RNA Seq,GSM3449967,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449967,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,A_2b_R2.fastq.gz A_2b_R1.fastq.gz,fastq fastq,2391676247.0,15831796.0,GSM3449967 r1,0:75.53 1:75.53,A:602794312;C:593325110;G:594803186;T:600747475;N:6164,75,75,,,602794312,593325110,594803186,600747475,6164,SRX4950828,SRS3993020,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.9382,0.93646,0.08421,0.08835,0.73919,0.7502,0.48177,0.485,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined 50532,SRR8129705,SRX4950827,SRS3993018,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 2 replicate a,GSM3449966,,tissue:Fli:GFP sorted 3 days RNAqueous sample 2 replicate a|cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 2 replicate a,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP sorted 3 days RNAqueous sample 2 replicate a,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449966,GSM3449966: RNAqueous sorted 2 replicate a; Danio rerio; RNA Seq,GSM3449966,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449966,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,A_2a_R1.fastq.gz A_2a_R2.fastq.gz,fastq fastq,3489621694.0,23100721.0,GSM3449966 r1,0:75.53 1:75.53,A:884597345;C:865637159;G:859062299;T:880315566;N:9325,75,75,,,884597345,865637159,859062299,880315566,9325,SRX4950827,SRS3993018,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93703,0.93839,0.09176,0.09203,0.73381,0.73206,0.46533,0.47636,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined 51961,SRR8928878,SRX5709835,SRS4649006,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 TCCTGAGC TCGACTAG control psbulk,GSM3730589,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 TCCTGAGC TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730589,GSM3730589: GC056865 TCCTGAGC TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730589,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730589,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_TCCTGAGC-TCGACTAG.R1.fastq.gz GC056865_TCCTGAGC-TCGACTAG.R2.fastq.gz,fastq fastq,444398220.0,1763485.0,GSM3730589 r1,0:126 1:126,A:119701118;C:101307242;G:100291786;T:123064017;N:34057,126,126,,,119701118,101307242,100291786,123064017,34057,SRX5709835,SRS4649006,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.89209,0.88921,0.1536,0.15422,0.79894,0.79738,0.53717,0.54281,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51962,SRR8928877,SRX5709834,SRS4649005,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 TAAGGCGA TCGACTAG control psbulk,GSM3730588,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 TAAGGCGA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730588,GSM3730588: GC056865 TAAGGCGA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730588,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730588,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_TAAGGCGA-TCGACTAG.R1.fastq.gz GC056865_TAAGGCGA-TCGACTAG.R2.fastq.gz,fastq fastq,528144372.0,2095811.0,GSM3730588 r1,0:126 1:126,A:138899905;C:124559386;G:123781108;T:140862443;N:41530,126,126,,,138899905,124559386,123781108,140862443,41530,SRX5709834,SRS4649005,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91379,0.91147,0.16599,0.16703,0.7763,0.77621,0.57465,0.57604,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51963,SRR8928876,SRX5709833,SRS4649004,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 GGAGCTAC TCGACTAG control psbulk,GSM3730587,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 GGAGCTAC TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730587,GSM3730587: GC056865 GGAGCTAC TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730587,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_GGAGCTAC-TCGACTAG.R1.fastq.gz GC056865_GGAGCTAC-TCGACTAG.R2.fastq.gz,fastq fastq,349714260.0,1387755.0,GSM3730587 r1,0:126 1:126,A:95856833;C:77706299;G:77143719;T:98982484;N:24925,126,126,,,95856833,77706299,77143719,98982484,24925,SRX5709833,SRS4649004,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91376,0.91378,0.11578,0.11732,0.82546,0.82446,0.61066,0.61085,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51964,SRR8928875,SRX5709832,SRS4649003,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 GCGTAGTA TCGACTAG control psbulk,GSM3730586,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 GCGTAGTA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730586,GSM3730586: GC056865 GCGTAGTA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730586,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730586,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_GCGTAGTA-TCGACTAG.R1.fastq.gz GC056865_GCGTAGTA-TCGACTAG.R2.fastq.gz,fastq fastq,397190556.0,1576153.0,GSM3730586 r1,0:126 1:126,A:108614389;C:88489174;G:87744396;T:112305346;N:37251,126,126,,,108614389,88489174,87744396,112305346,37251,SRX5709832,SRS4649003,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91036,0.90994,0.14864,0.15033,0.82856,0.82775,0.55841,0.55225,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51966,SRR8928873,SRX5709830,SRS4649001,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 CGTACTAG TCGACTAG control psbulk,GSM3730584,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 CGTACTAG TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730584,GSM3730584: GC056865 CGTACTAG TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730584,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730584,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_CGTACTAG-TCGACTAG.R1.fastq.gz GC056865_CGTACTAG-TCGACTAG.R2.fastq.gz,fastq fastq,357178500.0,1417375.0,GSM3730584 r1,0:126 1:126,A:95513887;C:82092508;G:81942895;T:97595862;N:33348,126,126,,,95513887,82092508,81942895,97595862,33348,SRX5709830,SRS4649001,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91549,0.91361,0.16607,0.16725,0.79149,0.79348,0.59191,0.59784,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51967,SRR8928872,SRX5709829,SRS4649000,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 CGGAGCCT TCGACTAG control psbulk,GSM3730583,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 CGGAGCCT TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730583,GSM3730583: GC056865 CGGAGCCT TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730583,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730583,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_CGGAGCCT-TCGACTAG.R1.fastq.gz GC056865_CGGAGCCT-TCGACTAG.R2.fastq.gz,fastq fastq,382960620.0,1519685.0,GSM3730583 r1,0:126 1:126,A:103791762;C:86709889;G:85905860;T:106521094;N:32015,126,126,,,103791762,86709889,85905860,106521094,32015,SRX5709829,SRS4649000,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.92265,0.92161,0.10837,0.10936,0.81619,0.81653,0.55235,0.53794,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51969,SRR8928870,SRX5709827,SRS4648998,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 AGGCAGAA TCGACTAG control psbulk,GSM3730581,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 AGGCAGAA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730581,GSM3730581: GC056865 AGGCAGAA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730581,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730581,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_AGGCAGAA-TCGACTAG.R1.fastq.gz GC056865_AGGCAGAA-TCGACTAG.R2.fastq.gz,fastq fastq,552338892.0,2191821.0,GSM3730581 r1,0:126 1:126,A:147583784;C:127503198;G:126780271;T:150428519;N:43120,126,126,,,147583784,127503198,126780271,150428519,43120,SRX5709827,SRS4648998,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.92013,0.91808,0.11656,0.11807,0.82148,0.82181,0.55295,0.5503,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51971,SRR8928868,SRX5709825,SRS4648996,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 ACTCGCTA TCGACTAG control psbulk,GSM3730579,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 ACTCGCTA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730579,GSM3730579: GC056865 ACTCGCTA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730579,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730579,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_ACTCGCTA-TCGACTAG.R1.fastq.gz GC056865_ACTCGCTA-TCGACTAG.R2.fastq.gz,fastq fastq,349502076.0,1386913.0,GSM3730579 r1,0:126 1:126,A:95872070;C:77657456;G:76918048;T:99026360;N:28142,126,126,,,95872070,77657456,76918048,99026360,28142,SRX5709825,SRS4648996,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.90596,0.90497,0.17112,0.17311,0.80275,0.80273,0.61121,0.6138,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51974,SRR8928865,SRX5709822,SRS4648993,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056829 TAAGGCGA CTCTCTAT control psbulk,GSM3730576,,source name:mitfa:GFP cells from control|tissue:GFP+ cells from control,GC056829 TAAGGCGA CTCTCTAT control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,tissue:GFP+ cells from control,GSM3730576,GSM3730576: GC056829 TAAGGCGA CTCTCTAT control psbulk; Danio rerio; RNA Seq,GSM3730576,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730576,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056829_TAAGGCGA-CTCTCTAT.R1.fastq.gz GC056829_TAAGGCGA-CTCTCTAT.R2.fastq.gz,fastq fastq,99705564.0,395657.0,GSM3730576 r1,0:126 1:126,A:26405998;C:23306835;G:22991686;T:26965397;N:35648,126,126,,,26405998,23306835,22991686,26965397,35648,SRX5709822,SRS4648993,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.88077,0.88005,0.07214,0.07291,0.82885,0.8283,0.55221,0.55358,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined 51977,SRR8928862,SRX5709819,SRS4648990,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056829 CGTACTAG CTCTCTAT control psbulk,GSM3730573,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056829 CGTACTAG CTCTCTAT control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730573,GSM3730573: GC056829 CGTACTAG CTCTCTAT control psbulk; Danio rerio; RNA Seq,GSM3730573,,1,FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads,GEO Accession:GSM3730573,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056829_CGTACTAG-CTCTCTAT.R1.fastq.gz GC056829_CGTACTAG-CTCTCTAT.R2.fastq.gz,fastq fastq,160942320.0,638660.0,GSM3730573 r1,0:126 1:126,A:41566703;C:39183347;G:38725528;T:41411306;N:55436,126,126,,,41566703,39183347,38725528,41411306,55436,SRX5709819,SRS4648990,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.94263,0.9412,0.04967,0.04955,0.823,0.82242,0.5265,0.53254,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined