|
| Status |
Public on Mar 05, 2015 |
| Title |
MM074_FAIRE |
| Sample type |
SRA |
| |
|
| Source name |
low passage primary melanoma cultures
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: low passage primary melanoma cultures
|
| Growth protocol |
cells were grown at 37°C to 85% confluency before harvest. Medium used was Ham's F-10 nutrient mix supplemented with FBS and l-alanyl-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted using the Magna ChIP kit; cells were sonicated for 12 cycles with 30sec pulses using the biorupter; phenol/chlorophorm extraction was performed using the Maxtract tubes (qiagen)
Illumina Truseq
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were mapped to the genome using Bowtie2 2.1.0.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pair for each read
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools 2.17.0 and the scores represent the coverage
|
| |
|
| Submission date |
Aug 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Zeynep Kalender Atak |
| Organization name |
KULeuven
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE60665 |
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. |
| GSE60666 |
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. |
|
| Relations |
| BioSample |
SAMN03002750 |
| SRA |
SRX685296 |
