|
| Status |
Public on Jun 01, 2024 |
| Title |
KPC_allograft_screen_Ctrl_R3 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: KPC
cell type: pancreatic ductal adenocarcinoma
genotype: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre
treatment: Control (standard chow)
|
| Treatment protocol |
Cells were treated with 1 µg/ml doxycycline. Control cells were treated with ethanol. Mice were treated with doxycycline by feeding them with chow containing 625 mg/kg doxycycline (ssniff) ad libitum. Control mice received control chow.
|
| Growth protocol |
KPC cells were grown in DMEM supplemented with 10 % FCS and 1% Penicillin/Streptomycin. 100,000 KPC cells were orthotopically transplanted into the pancreata of C57BL/6J mice in 50 µl PBS/Matrigel (1:1)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells/Tumors were lysed in lysis buffer (10 mM TRIS/HCl, pH 8, 100 mM NaCl, 10 mM EDTA, 0.5 % SDS, 400 µg/ml proteinase K) at 56 °C overnight. gDNA was isolated by phenol/chloroform/isoamylalcohol extraction and isopropanol precipitation.
PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
OTHER: PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PCR amplified gDNA
|
| Data processing |
Fastq files were generated on Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
Bowtie1 (version 1.2.2) alignment (option -v 0) to the shRNA oligonucleotide reference
Counting of alignment per shRNA (bash script)
Differential enrichment (DESeq2)
Assembly: NA, fastq files were aligned to a custom reference containing the shRNA oligonucleotide sequences
Supplementary files format and content: .csv file containing raw read counts per shRNA sequence
|
| |
|
| Submission date |
Oct 19, 2022 |
| 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 |
GPL19057 |
| Series (2) |
| GSE216091 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 (Screen) |
| GSE216095 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 |
|
| Relations |
| BioSample |
SAMN31367017 |
| SRA |
SRX17955571 |
