|
| Status |
Public on May 24, 2024 |
| Title |
Metastatic mouse UPS cell, IgG, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse UPS cell
|
| Organism |
Mus musculus |
| Characteristics |
cell line: mouse UPS cell
cell type: sarcoma
chip antibody: IgG
|
| Growth protocol |
DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the SimpleChIP Plus Sonication Chromatin IP kit (CST). 10 ug of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit and 2% Agarose gel
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq reads were trimmed using TrimGalore (v 0.6.6) and then aligned to GRCm38/mm10 reference genome by bwa (v 0.7.17-r1188).
Unmapped reads reads aligned to multiple locations were removed using samtools (v 1.11).
Duplicated reads were marked by picard (v 2.26.0).
The genomic coverage was saved in bigwig format and normalized by CPM method by bedTools (v 2.29.2) and UCSC Utilities bedGraphToBigWig (v 377).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig normalized by total reads
|
| |
|
| Submission date |
Jul 18, 2022 |
| Last update date |
May 24, 2024 |
| Contact name |
jianhong ou |
| E-mail(s) |
jianhong.ou@duke.edu
|
| Phone |
5084102796
|
| Organization name |
Duke University
|
| Department |
Cell Biology
|
| Lab |
Regeneromics
|
| Street address |
465 Nanaline Duke Building, Duke University Medical Center
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE208365 |
Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells |
| GSE208367 |
COMPASS complex inhibition targets the metastasis initiating cell in undifferentiated pleomorphic sarcoma |
|
| Relations |
| BioSample |
SAMN29794401 |
| SRA |
SRX16314660 |
