|
| Status |
Public on Jul 28, 2023 |
| Title |
Trim33KO_HA_E2f4-dC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell line: Trim33KO_HA_E2f4-dC
cell type: HCC
genotype: sgTrim33_pRRL_HA_E2f4-dC
treatment: Recql antibody
|
| Treatment protocol |
none
|
| Growth protocol |
p19Nras cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Pen-Strep in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 0.2% formaldehyde and Cut&Run assay was performed using the anti-HA tag antibody (Cell Signaling #2367S) or anti-Recql antibody (Abcam ab151501) and the NEB CUT&RUN kit (#86652P).
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Trim33KO_HA_E2f4-dC
|
| Data processing |
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to mouse genome (mm9) with STAR (version 2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Jul 28, 2023 |
| Contact name |
Nikita Popov |
| E-mail(s) |
[email protected]
|
| Phone |
49 7071 29 84399
|
| Organization name |
University Hospital Tübingen
|
| Department |
Clinical Tumor Biology
|
| Street address |
Otfried-Müller-Str 14
|
| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE217524 |
The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication |
| GSE235671 |
The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [Cut&Run II] |
|
| Relations |
| BioSample |
SAMN35879546 |
| SRA |
SRX20761828 |
