|
| Status |
Public on Jun 01, 2024 |
| Title |
ChIPseq_A375_RUVBL1_Control |
| Sample type |
SRA |
| |
|
| Source name |
NA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: NA
cell line: KPC
cell type: pancreatic ductal adenocarcinoma
genotype: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1
treatment: Control
|
| Treatment protocol |
KPC-AID-Ruvbl1 cells were treated with 1 µM 5-Ph-IAA for 15 h. A375-MYC-AID cells were treated with 1 µM 5-Ph-IAA for 3 h
|
| Growth protocol |
KPC-AID-Ruvbl1 cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin. A375-MYC-AID cells were grown in RPMI-1640 supllemented with 10 % FCS and 1 % Penicillin/Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. Formaldehyde was quenching with glycine, cells were lysed and chromatin was sonicated.
NEBNext Ultra II DNA Library Prep Kit for Illumina, libraries were amplified for 13 cycles and concentration and size distribution were evaluated using an Agilent Fragment Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Illumina NextSeq500/2000
Base calling was performed using bcl2fastq (version 3.7.4)
KPC-AID-RUVBL1: Alignment against mouse (mm10) and human (hg19, spike-in) genome with Bowtie2 (version 2.3.4.1), A375-MYC-AID: Alignment against human (hg19) and mouse (mm10, spike-in) genome with Bowtie2 (version 2.3.4.1)
Normalization according to spike-in
Conversion to bedgraphs with bedtools genomecov (version 2.26.0)
Peak calling with MACS2 (version 2.2.7.1) and p-value cutoffs 0.01 (MYC) and 0.001 (RUVBL1)
Assembly: mm10/hg19
Supplementary files format and content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary files format and content: narrowPeak files contain MYC and RUVBL1 peak locations
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Elmar Wolf |
| E-mail(s) |
elmar.wolf@biozentrum.uni-wuerzburg.de
|
| Organization name |
Biocenter of the University of Würzburg
|
| Department |
Department of Molecular Biology and Biochemistry
|
| Lab |
Cancer Systems Biology Lab
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| State/province |
Bavaria |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE216090 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 (ChIP-Seq) |
| GSE216095 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 |
|
| Relations |
| BioSample |
SAMN37129262 |
| SRA |
SRX21472473 |
