|
| Status |
Public on Apr 16, 2019 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
Input DNA from melanoma tumors
|
| Organism |
Mus musculus |
| Characteristics |
strain: C56BL/6J
genotype: BrafV600E Pten-/-
tissue: Melanoma
chip antibody: none (input)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Epigenetic profiling experiments were performed on native Mnase-digested chromatin isolated from BrafV600E Pten-/- mouse melanoma tumors. PolII occupancy profiling was performed on 0,4% PFA-fixed chromatin (Input data) isolated from BrafV600E Pten-/- mouse melanoma tumors according to standard protocols as previously described (Laurette et al., 2014). Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody.
The libraries were sequenced on the Illumina Hiseq 4000 as single-end 50 base reads following Illumina’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).
|
| |
|
| Submission date |
Jul 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Irwin Davidson |
| E-mail(s) |
irwin67000@gmail.com
|
| Organization name |
IGBMC
|
| Street address |
1 Rue Laurent Fries
|
| City |
Strasbourg |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE100998 |
Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma [ChIP-seq] |
| GSE129621 |
Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma |
|
| Relations |
| BioSample |
SAMN07337728 |
| SRA |
SRX2992458 |
