|
| Status |
Public on Jul 01, 2024 |
| Title |
NGKO-H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
SCC23
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SCC23
cell type: HNSCC cells
genotype: KMT2D Knock out
treatment: Anti H3K27ac
treatment: Low Glucose condition
|
| Treatment protocol |
To generate KMT2D knockout cell lines, SCC23 and SCC1 cells were transfected with pSpCas9(BB)-2A-GFP plasmid (Addgene, Cat#48138) containing sgRNA targeting either LacZ or KMT2D for 24 hours.
|
| Growth protocol |
Human HNSCC cell line SCC23 was obtained from the University of Michigan, SCC46 and SCC74A cells were from Dr. Zhong Chen’s lab (National Institutes of Health) with permission from Dr. Thomas E. Carey (University of Michigan). These cell lines were maintained in high glucose DMEM (Thermo Fisher Scientific, Cat#11995065) containing 10% FBS and 1% antibiotics at 37°C in a 5% CO2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, cells were incubated in 1% formaldehyde for 10 minutes at RT for cross-linking. A final concentration of 1×glycine solution was added to the medium to stop cross-linking. The crosslinked cells were rinsed with ice-cold PBS and lysed with membrane extraction buffer containing protease/phosphatase inhibitors. Nuclei were extracted and sonicated to generate 200-500 bp chromatin fragments.
ChIP assays were performed using Pierce™ Magnetic ChIP Kit (Thermo Fisher Scientific, Cat#26157) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
ChIP-Seq reads were mapped to human genome hg19(GRCh37) by bowtie2
MACS2 was used for calling KMT2D peak with P value less than 0.01
Deeptools were used to generating bigwig file for each sample
Supplementary files format and content: Bigwig for genome covering reads
Supplementary files format and content: Peak files generated by MACS2
|
| |
|
| Submission date |
Jun 09, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Cunyu Wang |
| E-mail(s) |
cwang@dentistry.ucla.edu
|
| Phone |
3108256317
|
| Organization name |
UCLA
|
| Department |
School of Dentistry
|
| Lab |
CHS 56-200
|
| Street address |
10833 Le Conte Ave
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE234640 |
KMT2D regulates Fanconi anemia pathway genes through regulating promoters/enhances upon glucose deprivation (CHIPseq) |
| GSE234716 |
KMT2D regulates gene expression through regulating promoters/enhances upon glucose deprivation. |
|
| Relations |
| BioSample |
SAMN35688572 |
| SRA |
SRX20650000 |
