|
| Status |
Public on Apr 15, 2021 |
| Title |
3xKO dox melanocytes_IgG_rep_3 |
| Sample type |
SRA |
| |
|
| Source name |
melanocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hPSC-derived melanocytes
cut&run antibody: IgG (Abcam, ab6709)
treatment: doxycycline
|
| Treatment protocol |
72h doxycycline treatment
|
| Growth protocol |
hPSC-derived melanoblasts were replated at Day 11 of differentiation, after FACS sorting. At day 40, melanocytes were infected with either lenti-ATAD2 or lenti-Tomato and selected for 1 week with blastocidin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were treated as recommended in Skene et al., 2018
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: Cut&Run
Sequencing reads were trimmed and filtered using version 0.4.5 of TrimGalore
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2
Normalized read density profiles were made using BEDTools
Global peak atlas was made using version 1.6.1 of featureCounts
DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts
Genome_build: hg38
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
Apr 15, 2021 |
| Contact name |
Richard Mark White |
| E-mail(s) |
whiter@mskcc.org
|
| Phone |
646-888-3415
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Cancer Biology & Genetics
|
| Lab |
White Lab
|
| Street address |
1275 York Avenue MB 424
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE172066 |
Developmental chromatin programs determine oncogenic competence in melanoma [Cut&Run] |
| GSE172069 |
Developmental chromatin programs determine oncogenic competence in melanoma |
|
| Relations |
| BioSample |
SAMN18741521 |
| SRA |
SRX10601265 |
