|
| Status |
Public on Feb 01, 2016 |
| Title |
Zcrest H3K27Ac |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish melanoma tumor cell line zcrest 1
|
| Organism |
Danio rerio |
| Characteristics |
cell type: zebrafish melanoma tumor cell line
passages: > 20 passages
chip antibody: H3K27Ac (ab4729) (Abcam)
genotype of founder fish: p53/BRAF/Na; crestin:EGFP, MiniCoopR alone
|
| Growth protocol |
Zebrafish melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 3-5X10^7 cells were formaldehyde crosslinked and collected. The primary melanoma was generated in a p53/BRAF/Na zebrafish injected with MiniCoopR;mitf:EGFP control Tol2 plasmid as in Ceol, Houvras, et al, Nature, 2011. The bulk tumor was carefully dissected and manually dissociated with a razor blade and trypsinized prior to formaldehyde crosslinking.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the methods of T. I. Lee, S. E. Johnstone, R. A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc. 1, 729–748 (2006).
Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP'ed genomic DNA
|
| Data processing |
ChIP-Seq aligned to zebrafish Zv9 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: Zv9
Supplementary_files_format_and_content: called peaked in narrowPeak bed file
|
| |
|
| Submission date |
Nov 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE75353 |
A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish ChIP-seq] |
| GSE75356 |
A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation |
|
| Relations |
| BioSample |
SAMN04292917 |
| SRA |
SRX1451237 |
