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.

Nov. 7, 2018, 2:58 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006548BS DCD000207SR whole organism Zon Lab, Boston Children's Hospital AB 14-19 somites 16
Applied Assay ID Biosample Replicate Assay
DCD001241AA DCD012671BR RNA-seq_Zon_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001007SQ DCD001262TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001014SQ DCD001236TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001027SQ DCD001243TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001016SQ DCD001256TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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
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 Sequencing Date
DCD001006SQ DCD001231TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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
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 Sequencing Date
DCD001013SQ DCD001240TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001024SQ DCD001238TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001029SQ DCD001239TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001020SQ DCD001233TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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 Sequencing Date
DCD001019SQ DCD001241TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2500 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