|
| Status |
Public on Apr 29, 2024 |
| Title |
H3K27Ac_D4 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
cell line: mT4
cell type: Murine PDAC cells
genotype: KPC
chip antibody: H3K27Ac
treatment: GEM 4 days
|
| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Tag Operate through cell permiabilization with 0.05% Digitonin. Tn5 Transposase cleaves DNA and addition of 6.67 µL 0.5M EDTA, 2 µL 10% SDS and 1.67 µL 20 mg/mL Proteinase K, Incubation at 50C for 1hr and 37C overnight to extract DNA
NEB High Fidelity PCR MasterMix
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read trimming: CutAdapt
Read Alignment: Bowtie2
Read filter: Samtools, MarkDuplicates
Assembly: mm10
Supplementary files format and content: BigWig: Normalized aligned read counts
Library strategy: Cut&Tag
|
| |
|
| Submission date |
Mar 10, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Chan Dinh Khac Nguyen |
| E-mail(s) |
cdn14@georgetown.edu
|
| Phone |
2028204474
|
| Organization name |
Lombardi Comprehensive Cancer Center
|
| Department |
Oncology
|
| Lab |
E301
|
| Street address |
3970 Reservoir Rd
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20057 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE227129 |
PRMT1 Promotes Epigenetic Reprogramming Associated with Acquired Chemoresistance in Pancreatic Cancer |
|
| Relations |
| BioSample |
SAMN33716679 |
| SRA |
SRX19636167 |
