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 | anatomical_term | 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 | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD001007SQ | DCD001262TR | Zon Lab, Boston Children's Hospital | Illumina | HiSeq 2500 | — | ✔ | unstranded | 06/02/2015 |
| 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 |
| 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 |
| 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 | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD001016SQ | DCD001256TR | Zon Lab, Boston Children's Hospital | Illumina | HiSeq 2500 | ✔ | unstranded | 06/02/2015 |
| 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 | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD001006SQ | DCD001231TR | Zon Lab, Boston Children's Hospital | Illumina | HiSeq 2500 | ✔ | unstranded | 12/31/2014 |
| 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 |
| 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 |
| 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 |
| 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 | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD001020SQ | DCD001233TR | Zon Lab, Boston Children's Hospital | Illumina | HiSeq 2500 | ✘ | — | 12/05/2014 |
| 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 | Sequencing Date |
|---|---|---|---|---|---|---|---|
| DCD001019SQ | DCD001241TR | Zon Lab, Boston Children's Hospital | Illumina | HiSeq 2500 | ✔ | unstranded | 12/31/2014 |