Series Summary for DCD000207SR

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish ChIP-seq, ATAC-seq, RNA-seq]

Survey

10.1126/science.aad2197

GSE75356

We report 1) the distribution of H3K27Ac histone marks in a zebrafish melanoma cell line and a zebrafish primary melanoma tumor with the aim of identifying super-enhancer regions and regions of interest. We also report sox10 ChIP-Seq on the same zebrafish melanoma cell line (GSE75353), 2) gene expression data for FACS sorted zebrafish crestin_1kb:EGFP + cells collected at 15 somite stage (SS) (GSE75355), and 3) the locations of accessible/open chromatin as assayed by ATAC-Seq on two zebrafish melanoma cell lines, zcrest 1 and zcrest 2 (GSE75351)

True

syang

June 2, 2016, 3:02 p.m.

Feb. 28, 2019, 1:38 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By anatomical_term Treatment Hours Post Fertilization Mutation Description
DCD006548BS DCD000207SR whole organism Zon Lab, Boston Children's Hospital AB 14-19 somites 16 crestin_1kb:EGFP
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001241AA DCD012671BR RNA-seq_Zon_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD001007SQ DCD001262TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 unstranded 100 06/02/2015
DCD000709DT: FASTQ
DCD004184DT: LOG GRCz10/danRer10
DCD004185DT: TSV GRCz10/danRer10
DCD004186DT: BEDGRAPH GRCz10/danRer10
DCD004187DT: BEDGRAPH GRCz10/danRer10
DCD004188DT: BEDGRAPH GRCz10/danRer10
DCD004190DT: BEDGRAPH GRCz10/danRer10
DCD004191DT: PDF GRCz10/danRer10
DCD004192DT: LOG GRCz10/danRer10
DCD004193DT: PDF GRCz10/danRer10
DCD004195DT: LOG GRCz10/danRer10
DCD004196DT: BEDGRAPH GRCz10/danRer10
DCD004202DT: BAM GRCz10/danRer10
DCD008671DT: BIGWIG GRCz10/danRer10
DCD014314DT: LOG GRCz11/danRer11
DCD014315DT: TSV GRCz11/danRer11
DCD014316DT: TSV GRCz11/danRer11
DCD014317DT: BEDGRAPH GRCz11/danRer11
DCD014318DT: BEDGRAPH GRCz11/danRer11
DCD014319DT: BAM GRCz11/danRer11
DCD014320DT: LOG GRCz11/danRer11
DCD014321DT: LOG GRCz11/danRer11
DCD014322DT: PDF GRCz11/danRer11
DCD014323DT: PDF GRCz11/danRer11
DCD014324DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006550BS DCD000207SR cell line Zon Lab, Boston Children's Hospital WT
Applied Assay ID Biosample Replicate Assay
DCD001243AA DCD012682BR ChIP-seq_Zon_Lab_Input_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD001014SQ DCD001236TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 11/17/2014
DCD000716DT: FASTQ
DCD006597DT: LOG GRCz10/danRer10
DCD006600DT: BAM GRCz10/danRer10
DCD006601DT: LOG GRCz10/danRer10
DCD006602DT: LOG GRCz10/danRer10
DCD006603DT: LOG GRCz10/danRer10
DCD006605DT: PDF GRCz10/danRer10
DCD006606DT: LOG GRCz10/danRer10
DCD006609DT: BAM GRCz10/danRer10
DCD006612DT: BAM GRCz10/danRer10
DCD006615DT: BAM GRCz10/danRer10
DCD006620DT: BAM GRCz10/danRer10
DCD017037DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001246AA DCD012682BR ChIP-seq_Zon_Lab_H3K27Ac_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD001027SQ DCD001243TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 11/17/2014
DCD000719DT: FASTQ
DCD006607DT: LOG GRCz10/danRer10
DCD006610DT: LOG GRCz10/danRer10
DCD006611DT: BAM GRCz10/danRer10
DCD006613DT: LOG GRCz10/danRer10
DCD006614DT: LOG GRCz10/danRer10
DCD006616DT: PDF GRCz10/danRer10
DCD006617DT: LOG GRCz10/danRer10
DCD006619DT: BAM GRCz10/danRer10
DCD006623DT: BAM GRCz10/danRer10
DCD006626DT: BAM GRCz10/danRer10
DCD006630DT: BAM GRCz10/danRer10
DCD008998DT: BIGNARROWPEAK GRCz10/danRer10
DCD009109DT: BIGWIG GRCz10/danRer10
DCD016350DT: BAM GRCz11/danRer11
DCD016351DT: BED GRCz11/danRer11
DCD016352DT: BIGNARROWPEAK GRCz11/danRer11
DCD016353DT: BIGNARROWPEAK GRCz11/danRer11
DCD016354DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006551BS DCD000207SR whole organism Zon Lab, Boston Children's Hospital AB
Applied Assay ID Biosample Replicate Assay
DCD001244AA DCD012672BR RNA-seq_Zon_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Paired End Strand Maximum Read Length Sequencing Date
DCD001016SQ DCD001256TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 unstranded 100 06/02/2015
DCD000712DT: FASTQ
DCD004172DT: LOG GRCz10/danRer10
DCD004173DT: TSV GRCz10/danRer10
DCD004174DT: BEDGRAPH GRCz10/danRer10
DCD004175DT: BEDGRAPH GRCz10/danRer10
DCD004176DT: BEDGRAPH GRCz10/danRer10
DCD004177DT: BEDGRAPH GRCz10/danRer10
DCD004178DT: BEDGRAPH GRCz10/danRer10
DCD004179DT: PDF GRCz10/danRer10
DCD004180DT: LOG GRCz10/danRer10
DCD004181DT: PDF GRCz10/danRer10
DCD004182DT: LOG GRCz10/danRer10
DCD004189DT: BAM GRCz10/danRer10
DCD008670DT: BIGWIG GRCz10/danRer10
DCD014325DT: LOG GRCz11/danRer11
DCD014326DT: TSV GRCz11/danRer11
DCD014327DT: TSV GRCz11/danRer11
DCD014328DT: BEDGRAPH GRCz11/danRer11
DCD014329DT: BEDGRAPH GRCz11/danRer11
DCD014330DT: LOG GRCz11/danRer11
DCD014331DT: PDF GRCz11/danRer11
DCD014332DT: LOG GRCz11/danRer11
DCD014333DT: PDF GRCz11/danRer11
DCD014334DT: BIGWIG GRCz11/danRer11
DCD014335DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization Mutation Description
DCD006552BS DCD000207SR cell line Zon Lab, Boston Children's Hospital WT
Applied Assay ID Biosample Replicate Assay
DCD001249AA DCD012677BR ATAC-seq_Zon_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Paired End Strand Maximum Read Length Sequencing Date
DCD001006SQ DCD001231TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 unstranded 100 12/31/2014
DCD000740DT: FASTQ
DCD007674DT: BED GRCz10/danRer10
DCD007675DT: BED GRCz10/danRer10
DCD007676DT: BIGWIG GRCz10/danRer10
DCD007677DT: BIGWIG GRCz10/danRer10
DCD007678DT: BED GRCz10/danRer10
DCD007679DT: BIGWIG GRCz10/danRer10
DCD007680DT: BIGWIG GRCz10/danRer10
DCD007681DT: LOG GRCz10/danRer10
DCD007682DT: LOG GRCz10/danRer10
DCD007683DT: LOG GRCz10/danRer10
DCD007684DT: LOG GRCz10/danRer10
DCD007685DT: LOG GRCz10/danRer10
DCD007686DT: LOG GRCz10/danRer10
DCD007687DT: LOG GRCz10/danRer10
DCD007688DT: LOG GRCz10/danRer10
DCD007689DT: LOG GRCz10/danRer10
DCD007690DT: BED GRCz10/danRer10
DCD007691DT: BIGWIG GRCz10/danRer10
DCD007692DT: BED GRCz10/danRer10
DCD007693DT: BED GRCz10/danRer10
DCD007694DT: BED GRCz10/danRer10
DCD007695DT: BED GRCz10/danRer10
DCD007696DT: BED GRCz10/danRer10
DCD007697DT: BED GRCz10/danRer10
DCD007698DT: BED GRCz10/danRer10
DCD007707DT: BAM GRCz10/danRer10
DCD007775DT: BAM GRCz10/danRer10
DCD008902DT: BIGNARROWPEAK GRCz10/danRer10
DCD008906DT: BIGNARROWPEAK GRCz10/danRer10
DCD018966DT: BED GRCz10/danRer10
DCD018967DT: BIGNARROWPEAK GRCz10/danRer10
DCD018968DT: BAM GRCz10/danRer10
DCD018969DT: BIGNARROWPEAK GRCz10/danRer10
DCD018970DT: BIGWIG GRCz10/danRer10
DCD019276DT: BAM GRCz11/danRer11
DCD019277DT: BIGNARROWPEAK GRCz11/danRer11
DCD019278DT: BIGNARROWPEAK GRCz11/danRer11
DCD019279DT: BED GRCz11/danRer11
DCD019280DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006553BS DCD000207SR cell line Zon Lab, Boston Children's Hospital WT
Applied Assay ID Biosample Replicate Assay
DCD001245AA DCD012684BR ChIP-seq_Zon_Lab_Input_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD001013SQ DCD001240TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 12/05/2014
DCD000722DT: FASTQ
DCD006618DT: LOG GRCz10/danRer10
DCD006621DT: LOG GRCz10/danRer10
DCD006622DT: BAM GRCz10/danRer10
DCD006624DT: LOG GRCz10/danRer10
DCD006625DT: LOG GRCz10/danRer10
DCD006627DT: PDF GRCz10/danRer10
DCD006628DT: LOG GRCz10/danRer10
DCD006631DT: BAM GRCz10/danRer10
DCD006634DT: BAM GRCz10/danRer10
DCD006637DT: BAM GRCz10/danRer10
DCD006640DT: BAM GRCz10/danRer10
DCD017002DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001247AA DCD012684BR ChIP-seq_Zon_Lab_Input_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD001024SQ DCD001238TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 12/05/2014
DCD000729DT: FASTQ
DCD006641DT: LOG GRCz10/danRer10
DCD006643DT: LOG GRCz10/danRer10
DCD006644DT: BAM GRCz10/danRer10
DCD006647DT: LOG GRCz10/danRer10
DCD006648DT: LOG GRCz10/danRer10
DCD006649DT: PDF GRCz10/danRer10
DCD006650DT: LOG GRCz10/danRer10
DCD006653DT: BAM GRCz10/danRer10
DCD006656DT: BAM GRCz10/danRer10
DCD006659DT: BAM GRCz10/danRer10
DCD006663DT: BAM GRCz10/danRer10
DCD017036DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001248AA DCD012684BR ChIP-seq_Zon_Lab_sox10_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Maximum Read Length Sequencing Date
DCD001029SQ DCD001239TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 12/05/2014
DCD000726DT: FASTQ
DCD006629DT: LOG GRCz10/danRer10
DCD006632DT: LOG GRCz10/danRer10
DCD006633DT: BAM GRCz10/danRer10
DCD006635DT: LOG GRCz10/danRer10
DCD006636DT: LOG GRCz10/danRer10
DCD006638DT: PDF GRCz10/danRer10
DCD006639DT: LOG GRCz10/danRer10
DCD006642DT: BAM GRCz10/danRer10
DCD006645DT: BAM GRCz10/danRer10
DCD006646DT: BAM GRCz10/danRer10
DCD006652DT: BAM GRCz10/danRer10
DCD009003DT: BIGNARROWPEAK GRCz10/danRer10
DCD009120DT: BIGWIG GRCz10/danRer10
DCD016484DT: BIGNARROWPEAK GRCz11/danRer11
DCD016485DT: BIGNARROWPEAK GRCz11/danRer11
DCD016486DT: BED GRCz11/danRer11
DCD016488DT: BAM GRCz11/danRer11
DCD016490DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001250AA DCD012684BR ChIP-seq_Zon_Lab_H3K27Ac_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Paired End Strand Maximum Read Length Sequencing Date
DCD001020SQ DCD001233TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 50 12/05/2014
DCD000732DT: FASTQ
DCD006651DT: LOG GRCz10/danRer10
DCD006654DT: LOG GRCz10/danRer10
DCD006655DT: BAM GRCz10/danRer10
DCD006657DT: LOG GRCz10/danRer10
DCD006658DT: LOG GRCz10/danRer10
DCD006660DT: PDF GRCz10/danRer10
DCD006661DT: LOG GRCz10/danRer10
DCD006664DT: BAM GRCz10/danRer10
DCD006667DT: BAM GRCz10/danRer10
DCD006670DT: BAM GRCz10/danRer10
DCD006674DT: BAM GRCz10/danRer10
DCD008999DT: BIGNARROWPEAK GRCz10/danRer10
DCD009112DT: BIGWIG GRCz10/danRer10
DCD016473DT: BAM GRCz11/danRer11
DCD016474DT: BIGNARROWPEAK GRCz11/danRer11
DCD016475DT: BIGNARROWPEAK GRCz11/danRer11
DCD016476DT: BED GRCz11/danRer11
DCD016477DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background
DCD006554BS DCD000207SR cell line Zon Lab, Boston Children's Hospital WT
Applied Assay ID Biosample Replicate Assay
DCD001251AA DCD012674BR ATAC-seq_Zon_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Paired End Strand Maximum Read Length Sequencing Date
DCD001019SQ DCD001241TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 unstranded 100 12/31/2014
DCD000743DT: FASTQ
DCD007649DT: BIGWIG GRCz10/danRer10
DCD007650DT: BIGWIG GRCz10/danRer10
DCD007651DT: BIGWIG GRCz10/danRer10
DCD007652DT: BED GRCz10/danRer10
DCD007653DT: BED GRCz10/danRer10
DCD007654DT: LOG GRCz10/danRer10
DCD007655DT: BED GRCz10/danRer10
DCD007656DT: LOG GRCz10/danRer10
DCD007657DT: LOG GRCz10/danRer10
DCD007658DT: LOG GRCz10/danRer10
DCD007659DT: LOG GRCz10/danRer10
DCD007660DT: LOG GRCz10/danRer10
DCD007661DT: LOG GRCz10/danRer10
DCD007662DT: LOG GRCz10/danRer10
DCD007663DT: LOG GRCz10/danRer10
DCD007664DT: BED GRCz10/danRer10
DCD007665DT: BED GRCz10/danRer10
DCD007666DT: BED GRCz10/danRer10
DCD007667DT: BED GRCz10/danRer10
DCD007668DT: BED GRCz10/danRer10
DCD007669DT: BED GRCz10/danRer10
DCD007670DT: BED GRCz10/danRer10
DCD007671DT: BED GRCz10/danRer10
DCD007672DT: BIGWIG GRCz10/danRer10
DCD007673DT: BIGWIG GRCz10/danRer10
DCD007699DT: BAM GRCz10/danRer10
DCD007753DT: BAM GRCz10/danRer10
DCD008910DT: BIGNARROWPEAK GRCz10/danRer10
DCD018971DT: BIGNARROWPEAK GRCz10/danRer10
DCD018972DT: BIGNARROWPEAK GRCz10/danRer10
DCD018973DT: BED GRCz10/danRer10
DCD018974DT: BIGWIG GRCz10/danRer10
DCD018975DT: BAM GRCz10/danRer10
DCD019281DT: BED GRCz11/danRer11
DCD019282DT: BIGNARROWPEAK GRCz11/danRer11
DCD019283DT: BIGNARROWPEAK GRCz11/danRer11
DCD019284DT: BIGWIG GRCz11/danRer11
DCD019285DT: BAM GRCz11/danRer11