|
| Status |
Public on May 08, 2024 |
| Title |
WM1552_H3K27Ac |
| Sample type |
SRA |
| |
|
| Source name |
Primary melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary melanoma cells
chip antibody: H3K27Ac (EpiCypher 13-0045)
|
| Growth protocol |
Primary melanocytes were grown in melanocyte growth media. WM35, 983, 902, and 1552 cell lines were grown in 2% tumor media. YUPEET and YUCHIME cell lines were grown in basic FGF media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27Ac antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S). Libraries were sequenced on Illumina's NextSeq500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the human reference genome hg19 using Bowtie v1.1.2 (Langmead et al., 2009) with parameters –l 40 –n 2 –best –k 1 –m 1, and read quality was assessed using fastQC (Simon Andrews, 2019).
Duplicate reads were removed with PICARD v2.2.4 (Broad Institute)
Binary alignment maps (BAM) files were generated with samtools v1.9 (Li et al., 2009) which were used in downstream analysis. MACS2 v2.1.0 (Zhang et al., 2008) was used to call significant peaks (For H3K27ac: q < 1e-11).
Peaks within ENCODE blacklisted regions were removed. Coverage tracks were generated from BAM files using deepTools 3.2.1 (Ramírez et al., 2016) bamCoverage with parameters –scaleFactor X and –binsize 10.
The normalization scale factor was calculated for each sample based on the Drosophila de-duplicated uniquely aligned reads as previously described (Egan et al., 2016).
Genome_build: Human genome hg10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Feb 22, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
[email protected]
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE197235 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas [ChIP-seq] |
| GSE198432 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas. |
|
| Relations |
| BioSample |
SAMN26177712 |
| SRA |
SRX14255591 |
