|
| Status |
Public on Nov 16, 2021 |
| Title |
H3K27ac_ChIPSeq_SCC_3_3 |
| Sample type |
SRA |
| |
|
| Source name |
OSCC cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SCC-25
|
| Treatment protocol |
SCC cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation.
|
| Growth protocol |
SCC-25 (ATCCR CRL-168TM) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were obtained, nuclei sonicated and histone-DNA complexes isolated with antibody according to the ChIP-IT High Sensitivity kit® from Active Motif (ref. 53040).
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep kit (Ref.:#7370).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H3K27ac_ChIPSeq
post-PA 4D
|
| Data processing |
Trimmomatic (v0.36) software (Bolger et al., 2014) was used to remove possible contaminations
Reads were aligned to the human genome build hg19 using BWA (v0.7.12) software (Li H. and Durbin R., 2009)
Aligned bam files were coordinate sorted and duplicates were removed with samtools (v1.3.1) software (Li, Handsaker et al. 2009)
Peaks were called using GeneRich (version 0.6) and an FDR < 0.05. GeneRich was also used to remove duplicate reads. Differential peaks were determined using the DiffBind package (version 2.4.8) in R (version 3.5.2) and an FDR < 0.05. The distribution of the differential regions within genomic features was conducted with HOMER (version 2015-03-22).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: Browser peak files. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Antoni Berenguer-LLergo |
| E-mail(s) |
aberenguerl@tauli.cat
|
| Organization name |
Parc Taulí Research and Innovation Institute (I3PT)
|
| Department |
A8G2 Group - Rheumatology Service
|
| Street address |
Parc del Taulí, 1
|
| City |
Sabadell |
| State/province |
Barcelona |
| ZIP/Postal code |
08208 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE148321 |
Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation |
| GSE169419 |
H3K27ac in vitro ChIP-Sequencing data [SCC-25] |
|
| Relations |
| BioSample |
SAMN18437860 |
| SRA |
SRX10418073 |
