|
| Status |
Public on Feb 08, 2021 |
| Title |
MCR:SATB2-Input |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish primary melanoma tumor
|
| Organism |
Danio rerio |
| Characteristics |
tissue: primary melanoma tumor
antibody: none
genotype: Tg(mitfa:BRAFV600E); p53-/-; mitfa-/-
|
| Growth protocol |
Zebrafish Tg(mitfa:BRAFV600E); p53-/-; mitfa-/- one cell stage embryos were injected with a MiniCoopR (MCR) expression vector to induce melanocyte-specific overexpression of either EGFP (control) or human SATB2, raised to adulthood and monitored for melanoma formation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Zebrafish melanomas were excised, finely minced using a scalpel blade and cross linked using 1.1% formaldehyde. The tumor suspension was mechanically homogenized on ice, and passed through a 100 μm filter. Whole cell extracts were sonicated to solubilize the chromatin, and target bound fragments (average size of 300 bp) were isolated with antibodies as indicated.
Purified immunoprecipitated DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end-repaired and libraries were prepared using the NEBNext Multiplex Oligos Kit (18-cycle PCR enrichment step). Amplified fragments between 150 and 350bp were isolated by agarose gel electrophoresis, and run on an Illumina Hi-Seq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| 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: danRer7
Supplementary_files_format_and_content: called peaked in bed file
|
| |
|
| Submission date |
Feb 15, 2016 |
| Last update date |
Feb 08, 2021 |
| 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 |
GPL9319 |
| Series (2) |
| GSE77921 |
SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [ChIP-Seq] |
| GSE77923 |
SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior |
|
| Relations |
| SRA |
SRX1584891 |
| BioSample |
SAMN04504665 |
